Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Jul 20 10:20:25 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/07_2023/6v3e_21034_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/07_2023/6v3e_21034.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/07_2023/6v3e_21034_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/07_2023/6v3e_21034_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/07_2023/6v3e_21034_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/07_2023/6v3e_21034.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/07_2023/6v3e_21034.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/07_2023/6v3e_21034_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3e_21034/07_2023/6v3e_21034_updated.pdb"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
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=   0.002 sd=   0.033
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    1527      5.49       5
     S      61      5.16       5
     C   25917      2.51       5
     N    9466      2.21       5
     O   13879      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "b TYR    4": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "b ARG    9": "NH1" <-> "NH2"
    Residue "b ASP   10": "OD1" <-> "OD2"
    Residue "b ARG   30": "NH1" <-> "NH2"
    Residue "b ARG   37": "NH1" <-> "NH2"
    Residue "b ARG   76": "NH1" <-> "NH2"
    Residue "b ARG   83": "NH1" <-> "NH2"
    Residue "b GLU   84": "OE1" <-> "OE2"
    Residue "b ARG   88": "NH1" <-> "NH2"
    Residue "b TYR   93": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "b ARG  110": "NH1" <-> "NH2"
    Residue "b ARG  134": "NH1" <-> "NH2"
    Residue "b ARG  141": "NH1" <-> "NH2"
    Residue "b GLU  142": "OE1" <-> "OE2"
    Residue "b ARG  148": "NH1" <-> "NH2"
    Residue "b GLU  171": "OE1" <-> "OE2"
    Residue "b ASP  190": "OD1" <-> "OD2"
    Residue "b ASP  196": "OD1" <-> "OD2"
    Residue "b ASP  199": "OD1" <-> "OD2"
    Residue "b ARG  210": "NH1" <-> "NH2"
    Residue "b TYR  215": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "c ARG   11": "NH1" <-> "NH2"
    Residue "c GLU   31": "OE1" <-> "OE2"
    Residue "c ARG  108": "NH1" <-> "NH2"
    Residue "c ARG  114": "NH1" <-> "NH2"
    Residue "c GLU  118": "OE1" <-> "OE2"
    Residue "c PHE  130": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "c ARG  131": "NH1" <-> "NH2"
    Residue "c ARG  132": "NH1" <-> "NH2"
    Residue "c ARG  136": "NH1" <-> "NH2"
    Residue "c ARG  143": "NH1" <-> "NH2"
    Residue "c ARG  156": "NH1" <-> "NH2"
    Residue "c GLU  166": "OE1" <-> "OE2"
    Residue "c ARG  169": "NH1" <-> "NH2"
    Residue "c GLU  170": "OE1" <-> "OE2"
    Residue "c ARG  188": "NH1" <-> "NH2"
    Residue "c ARG  204": "NH1" <-> "NH2"
    Residue "d ARG   14": "NH1" <-> "NH2"
    Residue "d GLU   15": "OE1" <-> "OE2"
    Residue "d ARG   46": "NH1" <-> "NH2"
    Residue "d ARG   58": "NH1" <-> "NH2"
    Residue "d ARG   64": "NH1" <-> "NH2"
    Residue "d GLU   80": "OE1" <-> "OE2"
    Residue "d GLU   97": "OE1" <-> "OE2"
    Residue "d ARG  106": "NH1" <-> "NH2"
    Residue "d ARG  113": "NH1" <-> "NH2"
    Residue "d ARG  123": "NH1" <-> "NH2"
    Residue "d ARG  130": "NH1" <-> "NH2"
    Residue "d GLU  204": "OE1" <-> "OE2"
    Residue "e PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "e ARG   49": "NH1" <-> "NH2"
    Residue "e ARG   53": "NH1" <-> "NH2"
    Residue "e ARG   92": "NH1" <-> "NH2"
    Residue "e ARG  111": "NH1" <-> "NH2"
    Residue "e GLU  115": "OE1" <-> "OE2"
    Residue "e ARG  144": "NH1" <-> "NH2"
    Residue "f GLU   40": "OE1" <-> "OE2"
    Residue "f ASP   41": "OD1" <-> "OD2"
    Residue "f ASP   72": "OD1" <-> "OD2"
    Residue "f GLU   73": "OE1" <-> "OE2"
    Residue "f GLU   76": "OE1" <-> "OE2"
    Residue "f PHE   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "f ARG   79": "NH1" <-> "NH2"
    Residue "f ARG   91": "NH1" <-> "NH2"
    Residue "f ARG   92": "NH1" <-> "NH2"
    Residue "g ARG   10": "NH1" <-> "NH2"
    Residue "g GLU   60": "OE1" <-> "OE2"
    Residue "g GLU   63": "OE1" <-> "OE2"
    Residue "g GLU   90": "OE1" <-> "OE2"
    Residue "g ARG   95": "NH1" <-> "NH2"
    Residue "g ARG  102": "NH1" <-> "NH2"
    Residue "g ASP  106": "OD1" <-> "OD2"
    Residue "g GLU  113": "OE1" <-> "OE2"
    Residue "g ARG  119": "NH1" <-> "NH2"
    Residue "g ARG  138": "NH1" <-> "NH2"
    Residue "h ARG   13": "NH1" <-> "NH2"
    Residue "h TYR   45": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "h GLU   68": "OE1" <-> "OE2"
    Residue "h ARG   88": "NH1" <-> "NH2"
    Residue "h ARG  115": "NH1" <-> "NH2"
    Residue "h ARG  118": "NH1" <-> "NH2"
    Residue "i ARG    9": "NH1" <-> "NH2"
    Residue "i TYR   36": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "i GLU   51": "OE1" <-> "OE2"
    Residue "i GLU   57": "OE1" <-> "OE2"
    Residue "i GLU  108": "OE1" <-> "OE2"
    Residue "i ARG  122": "NH1" <-> "NH2"
    Residue "j ARG    5": "NH1" <-> "NH2"
    Residue "j ARG    7": "NH1" <-> "NH2"
    Residue "j ARG   16": "NH1" <-> "NH2"
    Residue "j ARG   45": "NH1" <-> "NH2"
    Residue "j GLU   47": "OE1" <-> "OE2"
    Residue "j TYR   70": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "j ARG   72": "NH1" <-> "NH2"
    Residue "k ARG   13": "NH1" <-> "NH2"
    Residue "k GLU   17": "OE1" <-> "OE2"
    Residue "k ARG   36": "NH1" <-> "NH2"
    Residue "k PHE   51": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "k ASP   82": "OD1" <-> "OD2"
    Residue "k GLU   93": "OE1" <-> "OE2"
    Residue "k ARG   97": "NH1" <-> "NH2"
    Residue "k ASP  111": "OD1" <-> "OD2"
    Residue "l GLU   17": "OE1" <-> "OE2"
    Residue "l ARG   30": "NH1" <-> "NH2"
    Residue "l ARG   31": "NH1" <-> "NH2"
    Residue "l ARG   50": "NH1" <-> "NH2"
    Residue "l ARG   54": "NH1" <-> "NH2"
    Residue "l GLU   62": "OE1" <-> "OE2"
    Residue "l GLU   76": "OE1" <-> "OE2"
    Residue "l ARG   99": "NH1" <-> "NH2"
    Residue "l ASP  103": "OD1" <-> "OD2"
    Residue "m ARG    3": "NH1" <-> "NH2"
    Residue "m TYR   21": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "m GLU   41": "OE1" <-> "OE2"
    Residue "m ARG   46": "NH1" <-> "NH2"
    Residue "m ASP   49": "OD1" <-> "OD2"
    Residue "m ARG   57": "NH1" <-> "NH2"
    Residue "m ARG   79": "NH1" <-> "NH2"
    Residue "m ARG   98": "NH1" <-> "NH2"
    Residue "m ARG  101": "NH1" <-> "NH2"
    Residue "m ARG  107": "NH1" <-> "NH2"
    Residue "n GLU   26": "OE1" <-> "OE2"
    Residue "n GLU   39": "OE1" <-> "OE2"
    Residue "n ARG   59": "NH1" <-> "NH2"
    Residue "n ARG   61": "NH1" <-> "NH2"
    Residue "o ARG   58": "NH1" <-> "NH2"
    Residue "o ARG   64": "NH1" <-> "NH2"
    Residue "p ARG   46": "NH1" <-> "NH2"
    Residue "p GLU   87": "OE1" <-> "OE2"
    Residue "q ARG   40": "NH1" <-> "NH2"
    Residue "q ARG   41": "NH1" <-> "NH2"
    Residue "r TYR   23": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "r ASP   27": "OD1" <-> "OD2"
    Residue "r GLU   35": "OE1" <-> "OE2"
    Residue "r ARG   43": "NH1" <-> "NH2"
    Residue "r ARG   53": "NH1" <-> "NH2"
    Residue "r ARG   63": "NH1" <-> "NH2"
    Residue "r ASP   72": "OD1" <-> "OD2"
    Residue "s GLU   20": "OE1" <-> "OE2"
    Residue "s ARG   28": "NH1" <-> "NH2"
    Residue "s ARG   81": "NH1" <-> "NH2"
    Residue "t ARG   12": "NH1" <-> "NH2"
    Residue "t ARG   18": "NH1" <-> "NH2"
    Residue "t ARG   29": "NH1" <-> "NH2"
    Residue "t ARG   34": "NH1" <-> "NH2"
    Residue "t ARG   78": "NH1" <-> "NH2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib"
  Total number of atoms: 50850
  Number of models: 1
  Model: ""
    Number of chains: 20
    Chain: "sN"
      Number of atoms: 32782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1528, 32782
          Classifications: {'RNA': 1528}
          Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 109, 'rna2p_pyr': 84, 'rna3p': 8, 'rna3p_pur': 754, 'rna3p_pyr': 572}
          Link IDs: {'rna2p': 193, 'rna3p': 1334}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 6
    Chain: "b"
      Number of atoms: 1769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1769
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 7, 'TRANS': 217}
    Chain: "c"
      Number of atoms: 1690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1690
          Classifications: {'peptide': 215}
          Link IDs: {'PTRANS': 7, 'TRANS': 207}
    Chain: "d"
      Number of atoms: 1631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1631
          Classifications: {'peptide': 207}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 200}
    Chain: "e"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1129
          Classifications: {'peptide': 155}
          Link IDs: {'PTRANS': 4, 'TRANS': 150}
    Chain: "f"
      Number of atoms: 793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 793
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "g"
      Number of atoms: 1047
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 1047
          Classifications: {'peptide': 133}
          Link IDs: {'PTRANS': 6, 'TRANS': 126}
    Chain: "h"
      Number of atoms: 985
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 985
          Classifications: {'peptide': 130}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 125}
    Chain: "i"
      Number of atoms: 995
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 995
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 3, 'TRANS': 123}
    Chain: "j"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 801
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 5, 'TRANS': 94}
    Chain: "k"
      Number of atoms: 862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 862
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 109}
    Chain: "l"
      Number of atoms: 945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 945
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 6, 'TRANS': 115}
    Chain: "m"
      Number of atoms: 903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 903
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 5, 'TRANS': 109}
    Chain: "n"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 792
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "o"
      Number of atoms: 705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 705
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
    Chain: "p"
      Number of atoms: 649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 649
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 3, 'TRANS': 79}
    Chain: "q"
      Number of atoms: 630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 630
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 2, 'TRANS': 77}
    Chain: "r"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 438
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 2, 'TRANS': 50}
    Chain: "s"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 646
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 5, 'TRANS': 76}
    Chain: "t"
      Number of atoms: 658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 658
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
  Time building chain proxies: 23.36, per 1000 atoms: 0.46
  Number of scatterers: 50850
  At special positions: 0
  Unit cell: (139.384, 191.52, 256.424, 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      61     16.00
     P    1527     15.00
     O   13879      8.00
     N    9466      7.00
     C   25917      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS l  34 " - pdb=" SG  CYS l  53 " distance=2.03

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 27.31
  Conformation dependent library (CDL) restraints added in 3.1 seconds
  

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4270

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      81 helices and 20 sheets defined
      38.7% alpha, 15.8% beta
      467 base pairs and 777 stacking pairs defined.
    Time for finding SS restraints: 22.43
  Creating SS restraints...
    Processing helix  chain 'b' and resid 9 through 14
    Processing helix  chain 'b' and resid 45 through 65
      Proline residue:  b  50  - end of helix
      removed outlier: 3.966A  pdb=" N   LYS b  65 " --> pdb=" O   GLN b  61 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 76 through 89
      removed outlier: 4.180A  pdb=" N   ASN b  80 " --> pdb=" O   ARG b  76 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   ILE b  81 " --> pdb=" O   ALA b  77 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   GLU b  84 " --> pdb=" O   ASN b  80 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 106 through 123
      removed outlier: 3.979A  pdb=" N   GLN b 111 " --> pdb=" O   LYS b 107 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   SER b 112 " --> pdb=" O   THR b 108 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER b 123 " --> pdb=" O   LEU b 119 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 133 through 149
      removed outlier: 3.535A  pdb=" N   ARG b 148 " --> pdb=" O   GLU b 144 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   SER b 149 " --> pdb=" O   LYS b 145 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 172 through 181
    Processing helix  chain 'b' and resid 209 through 226
      removed outlier: 4.141A  pdb=" N   GLY b 226 " --> pdb=" O   ALA b 222 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 9 through 11
      No H-bonds generated for 'chain 'c' and resid 9 through 11'
    Processing helix  chain 'c' and resid 29 through 46
      removed outlier: 3.709A  pdb=" N   LYS c  35 " --> pdb=" O   GLU c  31 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS c  45 " --> pdb=" O   GLU c  41 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 48 through 50
      No H-bonds generated for 'chain 'c' and resid 48 through 50'
    Processing helix  chain 'c' and resid 73 through 76
      No H-bonds generated for 'chain 'c' and resid 73 through 76'
    Processing helix  chain 'c' and resid 82 through 94
    Processing helix  chain 'c' and resid 113 through 126
      removed outlier: 3.938A  pdb=" N   LYS c 126 " --> pdb=" O   SER c 122 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 130 through 143
    Processing helix  chain 'c' and resid 157 through 159
      No H-bonds generated for 'chain 'c' and resid 157 through 159'
    Processing helix  chain 'c' and resid 210 through 214
    Processing helix  chain 'd' and resid 9 through 15
      removed outlier: 3.523A  pdb=" N   ARG d  14 " --> pdb=" O   LYS d  10 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 28 through 32
      removed outlier: 3.589A  pdb=" N   THR d  32 " --> pdb=" O   PHE d  28 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'd' and resid 28 through 32'
    Processing helix  chain 'd' and resid 52 through 67
      removed outlier: 3.596A  pdb=" N   ARG d  64 " --> pdb=" O   LYS d  60 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 71 through 83
    Processing helix  chain 'd' and resid 88 through 97
      removed outlier: 3.959A  pdb=" N   LEU d  92 " --> pdb=" O   THR d  88 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   LEU d  93 " --> pdb=" O   GLY d  89 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 100 through 107
    Processing helix  chain 'd' and resid 113 through 121
    Processing helix  chain 'd' and resid 155 through 166
      removed outlier: 3.807A  pdb=" N   ALA d 160 " --> pdb=" O   ARG d 156 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLN d 166 " --> pdb=" O   GLU d 162 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 199 through 206
    Processing helix  chain 'e' and resid 55 through 67
    Processing helix  chain 'e' and resid 108 through 117
      removed outlier: 3.957A  pdb=" N   VAL e 113 " --> pdb=" O   ALA e 109 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA e 116 " --> pdb=" O   ALA e 112 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 132 through 144
      removed outlier: 3.841A  pdb=" N   ARG e 144 " --> pdb=" O   PHE e 140 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 149 through 156
    Processing helix  chain 'e' and resid 160 through 163
      No H-bonds generated for 'chain 'e' and resid 160 through 163'
    Processing helix  chain 'f' and resid 12 through 18
      removed outlier: 4.283A  pdb=" N   ASP f  16 " --> pdb=" O   ASP f  13 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL f  18 " --> pdb=" O   SER f  15 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 22 through 28
      removed outlier: 4.753A  pdb=" N   ILE f  26 " --> pdb=" O   VAL f  22 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   GLN f  28 " --> pdb=" O   ARG f  24 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 30 through 32
      No H-bonds generated for 'chain 'f' and resid 30 through 32'
    Processing helix  chain 'f' and resid 71 through 80
      removed outlier: 4.679A  pdb=" N   LEU f  77 " --> pdb=" O   GLU f  73 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   PHE f  78 " --> pdb=" O   LEU f  74 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   TYR f  80 " --> pdb=" O   GLU f  76 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 21 through 30
    Processing helix  chain 'g' and resid 36 through 53
      removed outlier: 3.580A  pdb=" N   GLU g  52 " --> pdb=" O   GLU g  48 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LYS g  53 " --> pdb=" O   ARG g  49 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 58 through 69
      removed outlier: 4.445A  pdb=" N   GLU g  63 " --> pdb=" O   VAL g  59 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   THR g  64 " --> pdb=" O   GLU g  60 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL g  69 " --> pdb=" O   THR g  65 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 93 through 110
      removed outlier: 3.895A  pdb=" N   ASP g 106 " --> pdb=" O   ARG g 102 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ALA g 109 " --> pdb=" O   VAL g 105 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 116 through 129
    Processing helix  chain 'g' and resid 133 through 137
    Processing helix  chain 'h' and resid 7 through 19
    Processing helix  chain 'h' and resid 31 through 43
    Processing helix  chain 'h' and resid 96 through 99
    Processing helix  chain 'h' and resid 114 through 120
    Processing helix  chain 'i' and resid 33 through 36
      No H-bonds generated for 'chain 'i' and resid 33 through 36'
    Processing helix  chain 'i' and resid 40 through 52
      removed outlier: 3.724A  pdb=" N   VAL i  46 " --> pdb=" O   ALA i  42 " (cutoff:3.500A)
      Proline residue:  i  49  - end of helix
    Processing helix  chain 'i' and resid 70 through 88
    Processing helix  chain 'i' and resid 90 through 99
      Proline residue:  i  94  - end of helix
      removed outlier: 3.659A  pdb=" N   ARG i  97 " --> pdb=" O   PRO i  94 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLN i  98 " --> pdb=" O   VAL i  95 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 15 through 32
      removed outlier: 3.786A  pdb=" N   THR j  32 " --> pdb=" O   THR j  28 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 83 through 89
      removed outlier: 4.063A  pdb=" N   MET j  88 " --> pdb=" O   VAL j  84 " (cutoff:3.500A)
    Processing helix  chain 'k' and resid 54 through 57
    Processing helix  chain 'k' and resid 59 through 76
      removed outlier: 3.871A  pdb=" N   VAL k  64 " --> pdb=" O   PHE k  60 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA k  69 " --> pdb=" O   ALA k  65 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA k  72 " --> pdb=" O   VAL k  68 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ASP k  75 " --> pdb=" O   LYS k  71 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   TYR k  76 " --> pdb=" O   ALA k  72 " (cutoff:3.500A)
    Processing helix  chain 'k' and resid 94 through 102
      removed outlier: 3.675A  pdb=" N   ALA k 101 " --> pdb=" O   ARG k  97 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL k 102 " --> pdb=" O   ALA k  98 " (cutoff:3.500A)
    Processing helix  chain 'l' and resid 4 through 9
    Processing helix  chain 'm' and resid 15 through 21
      removed outlier: 3.650A  pdb=" N   THR m  20 " --> pdb=" O   VAL m  16 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   TYR m  21 " --> pdb=" O   ILE m  17 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 27 through 37
    Processing helix  chain 'm' and resid 50 through 62
      removed outlier: 4.050A  pdb=" N   ALA m  55 " --> pdb=" O   ALA m  51 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLU m  59 " --> pdb=" O   ALA m  55 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LYS m  62 " --> pdb=" O   ALA m  58 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 66 through 83
      removed outlier: 3.555A  pdb=" N   ARG m  70 " --> pdb=" O   GLU m  66 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 86 through 94
      removed outlier: 5.147A  pdb=" N   ARG m  93 " --> pdb=" O   LEU m  89 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   SER m  94 " --> pdb=" O   ARG m  90 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 4 through 19
    Processing helix  chain 'n' and resid 21 through 32
    Processing helix  chain 'n' and resid 38 through 50
    Processing helix  chain 'n' and resid 53 through 55
      No H-bonds generated for 'chain 'n' and resid 53 through 55'
    Processing helix  chain 'n' and resid 57 through 59
      No H-bonds generated for 'chain 'n' and resid 57 through 59'
    Processing helix  chain 'n' and resid 81 through 90
      removed outlier: 3.523A  pdb=" N   ASP n  86 " --> pdb=" O   ASN n  82 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 5 through 15
    Processing helix  chain 'o' and resid 25 through 44
      removed outlier: 4.168A  pdb=" N   GLY o  41 " --> pdb=" O   ASN o  37 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   HIS o  42 " --> pdb=" O   ASP o  38 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   LYS o  44 " --> pdb=" O   GLN o  40 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 50 through 73
      removed outlier: 3.583A  pdb=" N   GLY o  55 " --> pdb=" O   HIS o  51 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 75 through 85
    Processing helix  chain 'p' and resid 72 through 80
    Processing helix  chain 'p' and resid 87 through 99
    Processing helix  chain 'r' and resid 26 through 32
      removed outlier: 3.989A  pdb=" N   TYR r  32 " --> pdb=" O   THR r  28 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 42 through 45
      No H-bonds generated for 'chain 'r' and resid 42 through 45'
    Processing helix  chain 'r' and resid 49 through 64
    Processing helix  chain 's' and resid 13 through 25
    Processing helix  chain 's' and resid 42 through 44
      No H-bonds generated for 'chain 's' and resid 42 through 44'
    Processing helix  chain 's' and resid 64 through 66
      No H-bonds generated for 'chain 's' and resid 64 through 66'
    Processing helix  chain 's' and resid 71 through 74
      removed outlier: 3.582A  pdb=" N   PHE s  74 " --> pdb=" O   LEU s  71 " (cutoff:3.500A)
      No H-bonds generated for 'chain 's' and resid 71 through 74'
    Processing helix  chain 't' and resid 5 through 41
      removed outlier: 3.530A  pdb=" N   LEU t  24 " --> pdb=" O   HIS t  20 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 44 through 64
      Proline residue:  t  56  - end of helix
    Processing helix  chain 't' and resid 69 through 86
      removed outlier: 3.694A  pdb=" N   LEU t  86 " --> pdb=" O   GLN t  82 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'b' and resid 69 through 72
      removed outlier: 7.694A  pdb=" N   ALA b 162 " --> pdb=" O   LEU b  70 " (cutoff:3.500A)
      removed outlier: 8.741A  pdb=" N   VAL b  72 " --> pdb=" O   ALA b 162 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   PHE b 164 " --> pdb=" O   VAL b  72 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   VAL b 165 " --> pdb=" O   PRO b 184 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   ILE b 186 " --> pdb=" O   VAL b 165 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   TYR b 200 " --> pdb=" O   GLY b 187 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   VAL b 189 " --> pdb=" O   TYR b 200 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   ILE b 202 " --> pdb=" O   VAL b 189 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  A
    Processing sheet with id=  B, first strand: chain 'b' and resid 33 through 36
      removed outlier: 7.300A  pdb=" N   ILE b  42 " --> pdb=" O   PHE b  34 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'c' and resid 99 through 105
      removed outlier: 6.433A  pdb=" N   ALA c  64 " --> pdb=" O   GLN c 100 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   SER c 102 " --> pdb=" O   ALA c  64 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   VAL c  66 " --> pdb=" O   SER c 102 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   ASN c 104 " --> pdb=" O   VAL c  66 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ILE c  68 " --> pdb=" O   ASN c 104 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASN c  54 " --> pdb=" O   SER c  69 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'c' and resid 164 through 171
    Processing sheet with id=  E, first strand: chain 'd' and resid 130 through 132
      removed outlier: 4.563A  pdb=" N   ILE d 125 " --> pdb=" O   VAL d 132 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'e' and resid 70 through 72
      removed outlier: 6.249A  pdb=" N   VAL e  37 " --> pdb=" O   LEU e  14 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   LEU e  14 " --> pdb=" O   VAL e  37 " (cutoff:3.500A)
      removed outlier: 7.474A  pdb=" N   GLY e  39 " --> pdb=" O   GLU e  12 " (cutoff:3.500A)
      removed outlier: 5.070A  pdb=" N   GLU e  12 " --> pdb=" O   GLY e  39 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'e' and resid 84 through 88
    Processing sheet with id=  H, first strand: chain 'f' and resid 88 through 92
      removed outlier: 3.676A  pdb=" N   HIS f   3 " --> pdb=" O   ARG f  92 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE f  60 " --> pdb=" O   LEU f   8 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY f  43 " --> pdb=" O   TYR f  59 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   LEU f  61 " --> pdb=" O   ASP f  41 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   ASP f  41 " --> pdb=" O   LEU f  61 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'g' and resid 74 through 76
      removed outlier: 3.904A  pdb=" N   LYS g  76 " --> pdb=" O   VAL g  87 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   VAL g  87 " --> pdb=" O   LYS g  76 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'h' and resid 24 through 28
      removed outlier: 3.783A  pdb=" N   ASN h  48 " --> pdb=" O   THR h  63 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'h' and resid 76 through 78
      removed outlier: 7.141A  pdb=" N   ILE h 104 " --> pdb=" O   ILE h 127 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   PHE h 129 " --> pdb=" O   ILE h 102 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   ILE h 102 " --> pdb=" O   PHE h 129 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'i' and resid 4 through 9
    Processing sheet with id=  M, first strand: chain 'j' and resid 96 through 100
      removed outlier: 4.652A  pdb=" N   LYS j  71 " --> pdb=" O   MET j  42 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'j' and resid 45 through 52
    Processing sheet with id=  O, first strand: chain 'k' and resid 82 through 86
    Processing sheet with id=  P, first strand: chain 'l' and resid 95 through 97
      removed outlier: 6.460A  pdb=" N   ARG l  54 " --> pdb=" O   THR l  35 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   VAL l  37 " --> pdb=" O   VAL l  52 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   VAL l  52 " --> pdb=" O   VAL l  37 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   THR l  39 " --> pdb=" O   ARG l  50 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ARG l  50 " --> pdb=" O   THR l  39 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   LYS l  51 " --> pdb=" O   ILE l  67 " (cutoff:3.500A)
    Processing sheet with id=  Q, first strand: chain 'p' and resid 20 through 27
      removed outlier: 3.857A  pdb=" N   GLY p  55 " --> pdb=" O   ILE p  37 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL p  39 " --> pdb=" O   ARG p  53 " (cutoff:3.500A)
      removed outlier: 5.802A  pdb=" N   ARG p  53 " --> pdb=" O   VAL p  39 " (cutoff:3.500A)
    Processing sheet with id=  R, first strand: chain 'q' and resid 74 through 76
      removed outlier: 16.839A  pdb=" N   THR q   8 " --> pdb=" O   ARG q  29 " (cutoff:3.500A)
      removed outlier: 13.312A  pdb=" N   ARG q  29 " --> pdb=" O   THR q   8 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   THR q  10 " --> pdb=" O   GLU q  27 " (cutoff:3.500A)
      removed outlier: 5.549A  pdb=" N   GLU q  27 " --> pdb=" O   THR q  10 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   VAL q  23 " --> pdb=" O   VAL q  14 " (cutoff:3.500A)
    Processing sheet with id=  S, first strand: chain 'q' and resid 59 through 61
      removed outlier: 6.541A  pdb=" N   THR q  61 " --> pdb=" O   VAL q  79 " (cutoff:3.500A)
      removed outlier: 5.686A  pdb=" N   VAL q  79 " --> pdb=" O   THR q  61 " (cutoff:3.500A)
    Processing sheet with id=  T, first strand: chain 's' and resid 30 through 33
      removed outlier: 7.403A  pdb=" N   THR s  48 " --> pdb=" O   ILE s  31 " (cutoff:3.500A)
      removed outlier: 8.236A  pdb=" N   THR s  33 " --> pdb=" O   THR s  48 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   SER s  50 " --> pdb=" O   THR s  33 " (cutoff:3.500A)

    724 hydrogen bonds defined for protein.
    2085 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      1171 hydrogen bonds
      1822 hydrogen bond angles
      0 basepair planarities
      467 basepair parallelities
      777 stacking parallelities
  Total time for adding SS restraints: 47.77

  Time building geometry restraints manager: 29.02 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 4949
        1.31 -     1.44: 23893
        1.44 -     1.56: 23022
        1.56 -     1.69: 3054
        1.69 -     1.82: 111
  Bond restraints: 55029
  Sorted by residual:
  bond pdb=" N6  MA6sN1516 "
       pdb=" C9  MA6sN1516 "
    ideal  model  delta    sigma   weight residual
    1.517  1.443  0.074 2.00e-02 2.50e+03 1.36e+01
  bond pdb=" N6  MA6sN1515 "
       pdb=" C9  MA6sN1515 "
    ideal  model  delta    sigma   weight residual
    1.517  1.444  0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" C   VAL b  49 "
       pdb=" N   PRO b  50 "
    ideal  model  delta    sigma   weight residual
    1.336  1.366 -0.030 1.20e-02 6.94e+03 6.44e+00
  bond pdb=" N3  UR3sN1495 "
       pdb=" C3U UR3sN1495 "
    ideal  model  delta    sigma   weight residual
    1.490  1.442  0.048 2.00e-02 2.50e+03 5.65e+00
  bond pdb=" CA  CYS l  53 "
       pdb=" CB  CYS l  53 "
    ideal  model  delta    sigma   weight residual
    1.532  1.563 -0.031 1.82e-02 3.02e+03 2.90e+00
  ... (remaining 55024 not shown)

  Histogram of bond angle deviations from ideal:
       99.50 -   107.26: 9505
      107.26 -   115.01: 35970
      115.01 -   122.76: 26914
      122.76 -   130.52: 8902
      130.52 -   138.27: 598
  Bond angle restraints: 81889
  Sorted by residual:
  angle pdb=" C1' 2MGsN 963 "
        pdb=" N9  2MGsN 963 "
        pdb=" C8  2MGsN 963 "
      ideal   model   delta    sigma   weight residual
     110.07  132.65  -22.58 3.00e+00 1.11e-01 5.66e+01
  angle pdb=" C1' 2MGsN1204 "
        pdb=" N9  2MGsN1204 "
        pdb=" C8  2MGsN1204 "
      ideal   model   delta    sigma   weight residual
     110.07  132.15  -22.08 3.00e+00 1.11e-01 5.42e+01
  angle pdb=" C1' 2MGsN 963 "
        pdb=" N9  2MGsN 963 "
        pdb=" C4  2MGsN 963 "
      ideal   model   delta    sigma   weight residual
     138.70  119.04   19.66 3.00e+00 1.11e-01 4.29e+01
  angle pdb=" C1' 2MGsN1204 "
        pdb=" N9  2MGsN1204 "
        pdb=" C4  2MGsN1204 "
      ideal   model   delta    sigma   weight residual
     138.70  119.51   19.19 3.00e+00 1.11e-01 4.09e+01
  angle pdb=" C3'   UsN 989 "
        pdb=" O3'   UsN 989 "
        pdb=" P     GsN 990 "
      ideal   model   delta    sigma   weight residual
     120.20  125.65   -5.45 1.50e+00 4.44e-01 1.32e+01
  ... (remaining 81884 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 28716
       35.97 -    71.95: 851
       71.95 -   107.92: 64
      107.92 -   143.90: 3
      143.90 -   179.87: 19
  Dihedral angle restraints: 29653
    sinusoidal: 23031
      harmonic: 6622
  Sorted by residual:
  dihedral pdb=" O4'   CsN 326 "
           pdb=" C1'   CsN 326 "
           pdb=" N1    CsN 326 "
           pdb=" C2    CsN 326 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   38.05  161.95     1      1.50e+01 4.44e-03 8.32e+01
  dihedral pdb=" O4'   CsN 717 "
           pdb=" C1'   CsN 717 "
           pdb=" N1    CsN 717 "
           pdb=" C2    CsN 717 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   41.10  158.90     1      1.50e+01 4.44e-03 8.25e+01
  dihedral pdb=" O4'   UsN 419 "
           pdb=" C1'   UsN 419 "
           pdb=" N1    UsN 419 "
           pdb=" C2    UsN 419 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   43.61  156.39     1      1.50e+01 4.44e-03 8.18e+01
  ... (remaining 29650 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 9838
       0.057 -    0.113: 493
       0.113 -    0.170: 57
       0.170 -    0.226: 2
       0.226 -    0.283: 2
  Chirality restraints: 10392
  Sorted by residual:
  chirality pdb=" C1* PSUsN 513 "
            pdb=" O4* PSUsN 513 "
            pdb=" C2* PSUsN 513 "
            pdb=" C5  PSUsN 513 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.27    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" C3'   UsN1123 "
            pdb=" C4'   UsN1123 "
            pdb=" O3'   UsN1123 "
            pdb=" C2'   UsN1123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.51   -0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" C3'   UsN 989 "
            pdb=" C4'   UsN 989 "
            pdb=" O3'   UsN 989 "
            pdb=" C2'   UsN 989 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.56   -0.19 2.00e-01 2.50e+01 8.91e-01
  ... (remaining 10389 not shown)

  Planarity restraints: 4722
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C5' 2MGsN 963 "    0.040 2.00e-02 2.50e+03   5.80e-01 7.56e+03
        pdb=" C4' 2MGsN 963 "    0.435 2.00e-02 2.50e+03
        pdb=" O4' 2MGsN 963 "    0.635 2.00e-02 2.50e+03
        pdb=" C3' 2MGsN 963 "   -0.592 2.00e-02 2.50e+03
        pdb=" O3' 2MGsN 963 "   -0.587 2.00e-02 2.50e+03
        pdb=" C2' 2MGsN 963 "   -0.202 2.00e-02 2.50e+03
        pdb=" O2' 2MGsN 963 "    0.928 2.00e-02 2.50e+03
        pdb=" C1' 2MGsN 963 "    0.225 2.00e-02 2.50e+03
        pdb=" N9  2MGsN 963 "   -0.883 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C5' 2MGsN1204 "    0.028 2.00e-02 2.50e+03   5.65e-01 7.19e+03
        pdb=" C4' 2MGsN1204 "    0.434 2.00e-02 2.50e+03
        pdb=" O4' 2MGsN1204 "    0.633 2.00e-02 2.50e+03
        pdb=" C3' 2MGsN1204 "   -0.588 2.00e-02 2.50e+03
        pdb=" O3' 2MGsN1204 "   -0.553 2.00e-02 2.50e+03
        pdb=" C2' 2MGsN1204 "   -0.218 2.00e-02 2.50e+03
        pdb=" O2' 2MGsN1204 "    0.894 2.00e-02 2.50e+03
        pdb=" C1' 2MGsN1204 "    0.229 2.00e-02 2.50e+03
        pdb=" N9  2MGsN1204 "   -0.858 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C5' 7MGsN 524 "   -0.027 2.00e-02 2.50e+03   5.63e-01 7.13e+03
        pdb=" C4' 7MGsN 524 "   -0.431 2.00e-02 2.50e+03
        pdb=" O4' 7MGsN 524 "   -0.627 2.00e-02 2.50e+03
        pdb=" C3' 7MGsN 524 "    0.588 2.00e-02 2.50e+03
        pdb=" O3' 7MGsN 524 "    0.550 2.00e-02 2.50e+03
        pdb=" C2' 7MGsN 524 "    0.218 2.00e-02 2.50e+03
        pdb=" O2' 7MGsN 524 "   -0.893 2.00e-02 2.50e+03
        pdb=" C1' 7MGsN 524 "   -0.230 2.00e-02 2.50e+03
        pdb=" N9  7MGsN 524 "    0.853 2.00e-02 2.50e+03
  ... (remaining 4719 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 1078
        2.61 -     3.18: 41212
        3.18 -     3.76: 100087
        3.76 -     4.33: 130223
        4.33 -     4.90: 177183
  Nonbonded interactions: 449783
  Sorted by model distance:
  nonbonded pdb=" O2    UsN 202 "
            pdb=" O6    GsN 208 "
     model   vdw
     2.039 2.432
  nonbonded pdb=" N1    AsN  75 "
            pdb=" O6    GsN  92 "
     model   vdw
     2.122 2.496
  nonbonded pdb=" O2    UsN 602 "
            pdb=" O6    GsN 630 "
     model   vdw
     2.130 2.432
  nonbonded pdb=" N7    GsN1157 "
            pdb=" N2    GsN1179 "
     model   vdw
     2.136 2.560
  nonbonded pdb=" N2    GsN 503 "
            pdb=" O2    CsN 522 "
     model   vdw
     2.140 2.496
  ... (remaining 449778 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             7.880
  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:             0.040
  Extract box with map and model:          31.010
  Check model and map are aligned:         0.760
  Set scattering table:                    0.420
  Process input model:                     163.650
  Find NCS groups from input model:        1.090
  Set up NCS constraints:                  0.140
  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:3.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  208.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
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   0.074  55029  Z= 0.111
  Angle     :  0.467  22.580  81889  Z= 0.251
  Chirality :  0.027   0.283  10392
  Planarity :  0.017   0.580   4722
  Dihedral  : 14.327 179.874  25380
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer Outliers :  0.05 %
  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: -1.40 (0.16), residues: 2273
  helix: -0.91 (0.15), residues: 881
  sheet:  0.30 (0.27), residues: 373
  loop : -1.32 (0.18), residues: 1019

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

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

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  545 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 544
  time to evaluate  : 3.289 
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: 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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 545
  average time/residue: 0.7422
  time to fit residues: 633.8757
Evaluate side-chains
  310 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 309
  time to evaluate  : 3.022 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.4254
  time to fit residues: 4.1390
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 317 optimal weight:    4.9990
   chunk 284 optimal weight:    6.9990
   chunk 158 optimal weight:    9.9990
   chunk 97 optimal weight:   10.0000
   chunk 192 optimal weight:   10.0000
   chunk 152 optimal weight:    1.9990
   chunk 294 optimal weight:    0.9980
   chunk 114 optimal weight:   10.0000
   chunk 179 optimal weight:    8.9990
   chunk 219 optimal weight:    4.9990
   chunk 341 optimal weight:    0.1980
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
b   5 ASN
** b  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b  57 ASN
b 120 GLN
b 122 GLN
b 180 ASN
** c   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
c  28 GLN
c  88 GLN
** c 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
d  44 GLN
d  73 GLN
** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d 138 GLN
d 154 GLN
** e  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
e 121 ASN
** f  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
f  52 ASN
** f  55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
g  28 ASN
** g  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
h   4 GLN
h  38 ASN
h  98 GLN
i  73 GLN
j  56 HIS
j  58 ASN
** j  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
l  72 HIS
** m  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
n  82 ASN
o  42 HIS
o  50 HIS
q  32 HIS
** s  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
s  65 HIS
s  83 HIS
t  13 GLN
t  21 ASN

Total number of N/Q/H flips: 29

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.042  55029  Z= 0.214
  Angle     :  0.609  13.674  81889  Z= 0.324
  Chirality :  0.032   0.362  10392
  Planarity :  0.006   0.116   4722
  Dihedral  : 14.544 179.895  20875
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 18.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer Outliers :  0.05 %
  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: -0.56 (0.17), residues: 2273
  helix:  0.05 (0.17), residues: 898
  sheet:  0.54 (0.27), residues: 372
  loop : -1.04 (0.19), residues: 1003

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

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

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 396
  time to evaluate  : 3.144 
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: 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: 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
  outliers start: 1
  outliers final: 0
  residues processed: 397
  average time/residue: 0.6761
  time to fit residues: 437.4735
Evaluate side-chains
  291 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 3.806 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 3.2747
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 189 optimal weight:    9.9990
   chunk 105 optimal weight:   10.0000
   chunk 284 optimal weight:    9.9990
   chunk 232 optimal weight:    8.9990
   chunk 94 optimal weight:   10.0000
   chunk 342 optimal weight:    5.9990
   chunk 369 optimal weight:    6.9990
   chunk 304 optimal weight:   10.0000
   chunk 339 optimal weight:    9.9990
   chunk 116 optimal weight:   10.0000
   chunk 274 optimal weight:    4.9990
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
b  17 HIS
b  85 GLN
b  91 GLN
** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d  73 GLN
** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
i 124 GLN
j  23 GLN
** j  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
k  21 HIS
k  37 GLN
** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** l   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
p  77 HIS
** r  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
r  61 GLN
s  52 HIS
** s  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** s  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.5481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.008   0.137  55029  Z= 0.514
  Angle     :  1.065  13.481  81889  Z= 0.542
  Chirality :  0.050   0.563  10392
  Planarity :  0.009   0.142   4722
  Dihedral  : 17.145 178.711  20875
  Min Nonbonded Distance : 1.743

Molprobity Statistics.
  All-atom Clashscore : 46.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer Outliers :  0.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.25 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.17), residues: 2273
  helix: -0.82 (0.16), residues: 831
  sheet: -0.16 (0.26), residues: 382
  loop : -1.22 (0.19), residues: 1060

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

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

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 317
  time to evaluate  : 2.891 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 0
  residues processed: 320
  average time/residue: 0.6697
  time to fit residues: 352.2683
Evaluate side-chains
  248 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 3.001 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 3.2955
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 337 optimal weight:    2.9990
   chunk 257 optimal weight:    1.9990
   chunk 177 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 163 optimal weight:    0.9980
   chunk 229 optimal weight:    5.9990
   chunk 343 optimal weight:    0.2980
   chunk 363 optimal weight:    3.9990
   chunk 179 optimal weight:   20.0000
   chunk 325 optimal weight:    0.7980
   chunk 97 optimal weight:   10.0000
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
b  85 GLN
b 111 GLN
c  28 GLN
c 139 GLN
d  73 GLN
** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
h  98 GLN
i  73 GLN
** j  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** j  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** l  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
m  52 GLN
** q  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.4923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.060  55029  Z= 0.166
  Angle     :  0.641  12.927  81889  Z= 0.343
  Chirality :  0.035   0.478  10392
  Planarity :  0.006   0.121   4722
  Dihedral  : 16.085 179.954  20875
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 19.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer Outliers :  0.05 %
  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: -0.59 (0.17), residues: 2273
  helix:  0.15 (0.17), residues: 865
  sheet: -0.02 (0.27), residues: 370
  loop : -0.92 (0.19), residues: 1038

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

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

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 361
  time to evaluate  : 2.798 
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: 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
  outliers start: 1
  outliers final: 0
  residues processed: 362
  average time/residue: 0.6331
  time to fit residues: 378.7934
Evaluate side-chains
  277 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 3.059 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 4.1360
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 302 optimal weight:    0.0370
   chunk 206 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   chunk 270 optimal weight:    9.9990
   chunk 149 optimal weight:   20.0000
   chunk 310 optimal weight:    9.9990
   chunk 251 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 185 optimal weight:    0.5980
   chunk 326 optimal weight:    0.8980
   chunk 91 optimal weight:    7.9990
   overall best weight:    2.1062

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

Flipped N/Q/H residues before XYZ refinement:
** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  28 GLN
c  88 GLN
** c 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
e 120 HIS
** f  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
h  98 GLN
** j  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
j  78 GLN
** j  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** l  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
m   8 ASN
m  52 GLN
r  61 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.5134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.037  55029  Z= 0.188
  Angle     :  0.623  12.469  81889  Z= 0.334
  Chirality :  0.034   0.472  10392
  Planarity :  0.006   0.123   4722
  Dihedral  : 15.881 179.193  20875
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 22.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer Outliers :  0.05 %
  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: -0.41 (0.17), residues: 2273
  helix:  0.37 (0.17), residues: 866
  sheet:  0.02 (0.27), residues: 366
  loop : -0.86 (0.19), residues: 1041

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

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

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  365 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 364
  time to evaluate  : 2.916 
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: 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
  outliers start: 1
  outliers final: 0
  residues processed: 364
  average time/residue: 0.6312
  time to fit residues: 379.4456
Evaluate side-chains
  285 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 2.759 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 3.0983
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 122 optimal weight:   10.0000
   chunk 327 optimal weight:    0.6980
   chunk 71 optimal weight:   10.0000
   chunk 213 optimal weight:    5.9990
   chunk 89 optimal weight:   10.0000
   chunk 363 optimal weight:    5.9990
   chunk 301 optimal weight:   10.0000
   chunk 168 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 120 optimal weight:   10.0000
   chunk 190 optimal weight:    6.9990
   overall best weight:    4.9388

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

Flipped N/Q/H residues before XYZ refinement:
b  44 ASN
** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  28 GLN
** c 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d  42 HIS
** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** j  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
j  23 GLN
** j  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** j  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
m   8 ASN
m  52 GLN
n  54 ASN
** q  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** s  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.6183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.059  55029  Z= 0.361
  Angle     :  0.815  12.118  81889  Z= 0.424
  Chirality :  0.042   0.536  10392
  Planarity :  0.007   0.125   4722
  Dihedral  : 16.727 179.347  20875
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 35.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer Outliers :  0.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.17), residues: 2273
  helix: -0.25 (0.17), residues: 861
  sheet: -0.40 (0.27), residues: 356
  loop : -1.14 (0.19), residues: 1056

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

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

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 336
  time to evaluate  : 2.791 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 336
  average time/residue: 0.6546
  time to fit residues: 363.6072
Evaluate side-chains
  269 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 2.930 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 3.4113
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 350 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 207 optimal weight:    9.9990
   chunk 265 optimal weight:    2.9990
   chunk 205 optimal weight:    1.9990
   chunk 306 optimal weight:    9.9990
   chunk 203 optimal weight:   10.0000
   chunk 362 optimal weight:    0.9990
   chunk 226 optimal weight:    9.9990
   chunk 220 optimal weight:    0.6980
   chunk 167 optimal weight:    6.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 170 HIS
c  28 GLN
** c 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
f  28 GLN
** f  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
g  21 GLN
j  20 GLN
** j  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
j  78 GLN
** j  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
k 118 ASN
** l  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
m   8 ASN
** m  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
q  31 GLN
t  21 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.6133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.040  55029  Z= 0.208
  Angle     :  0.654  12.322  81889  Z= 0.348
  Chirality :  0.036   0.501  10392
  Planarity :  0.006   0.123   4722
  Dihedral  : 16.320 179.889  20875
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 23.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer Outliers :  0.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.17), residues: 2273
  helix:  0.28 (0.17), residues: 861
  sheet: -0.30 (0.27), residues: 358
  loop : -1.08 (0.19), residues: 1054

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

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

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  356 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 354
  time to evaluate  : 3.284 
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: 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
  outliers start: 2
  outliers final: 0
  residues processed: 355
  average time/residue: 0.6563
  time to fit residues: 384.0603
Evaluate side-chains
  285 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 2.878 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 3.1912
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 224 optimal weight:    7.9990
   chunk 144 optimal weight:   20.0000
   chunk 216 optimal weight:    0.9990
   chunk 109 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 70 optimal weight:   20.0000
   chunk 230 optimal weight:    7.9990
   chunk 246 optimal weight:    8.9990
   chunk 179 optimal weight:    0.5980
   chunk 33 optimal weight:   10.0000
   chunk 284 optimal weight:    0.7980
   overall best weight:    3.2786

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

Flipped N/Q/H residues before XYZ refinement:
b  91 GLN
** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  28 GLN
** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
g  21 GLN
h  98 GLN
** j  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** j  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** l  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
m   8 ASN
m  52 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.6529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.056  55029  Z= 0.258
  Angle     :  0.705  12.095  81889  Z= 0.371
  Chirality :  0.037   0.521  10392
  Planarity :  0.006   0.124   4722
  Dihedral  : 16.501 179.473  20875
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 28.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer Outliers :  0.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.17), residues: 2273
  helix:  0.16 (0.17), residues: 864
  sheet: -0.38 (0.27), residues: 359
  loop : -1.07 (0.19), residues: 1050

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

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

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  343 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 342
  time to evaluate  : 3.303 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 342
  average time/residue: 0.6579
  time to fit residues: 374.7096
Evaluate side-chains
  280 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 3.052 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 3.3550
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 329 optimal weight:    0.7980
   chunk 347 optimal weight:    8.9990
   chunk 316 optimal weight:    0.9980
   chunk 337 optimal weight:    1.9990
   chunk 203 optimal weight:    0.9980
   chunk 147 optimal weight:   20.0000
   chunk 265 optimal weight:    0.9990
   chunk 103 optimal weight:   10.0000
   chunk 305 optimal weight:    2.9990
   chunk 319 optimal weight:    5.9990
   chunk 336 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
b 111 GLN
c  28 GLN
** c 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d 102 ASN
** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d 177 HIS
** f  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
g  21 GLN
h  38 ASN
h  98 GLN
** i  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
j  20 GLN
j  56 HIS
** j  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** l  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
m   8 ASN
m  52 GLN
** n  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.6322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.033  55029  Z= 0.138
  Angle     :  0.599  12.526  81889  Z= 0.320
  Chirality :  0.033   0.455  10392
  Planarity :  0.005   0.120   4722
  Dihedral  : 15.913 179.727  20875
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 17.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer Outliers :  0.16 %
  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: -0.32 (0.18), residues: 2273
  helix:  0.64 (0.18), residues: 859
  sheet: -0.12 (0.27), residues: 360
  loop : -0.91 (0.19), residues: 1054

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

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

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  377 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 374
  time to evaluate  : 3.309 
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: 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
  outliers start: 3
  outliers final: 1
  residues processed: 376
  average time/residue: 0.6561
  time to fit residues: 406.4505
Evaluate side-chains
  295 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 294
  time to evaluate  : 2.996 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.5337
  time to fit residues: 4.4334
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 221 optimal weight:    8.9990
   chunk 357 optimal weight:   10.0000
   chunk 217 optimal weight:    7.9990
   chunk 169 optimal weight:    1.9990
   chunk 248 optimal weight:    9.9990
   chunk 374 optimal weight:    2.9990
   chunk 344 optimal weight:    1.9990
   chunk 298 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 230 optimal weight:   10.0000
   chunk 182 optimal weight:    2.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  28 GLN
** c 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d 118 GLN
** f  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
g  21 GLN
h  98 GLN
** j  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
m   8 ASN
m  52 GLN
q  31 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.6662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.045  55029  Z= 0.233
  Angle     :  0.664  12.165  81889  Z= 0.350
  Chirality :  0.035   0.485  10392
  Planarity :  0.006   0.121   4722
  Dihedral  : 16.157 179.297  20875
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 25.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer Outliers :  0.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.18), residues: 2273
  helix:  0.47 (0.18), residues: 864
  sheet: -0.23 (0.27), residues: 354
  loop : -0.96 (0.20), residues: 1055

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

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

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4546 Ramachandran restraints generated.
    2273 Oldfield, 0 Emsley, 2273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  343 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 342
  time to evaluate  : 3.143 
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: 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
  outliers start: 1
  outliers final: 0
  residues processed: 342
  average time/residue: 0.6784
  time to fit residues: 380.3584
Evaluate side-chains
  278 residues out of total 1891 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 278
  time to evaluate  : 2.898 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 3.2770
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 236 optimal weight:    5.9990
   chunk 317 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 275 optimal weight:    9.9990
   chunk 44 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   chunk 298 optimal weight:    0.5980
   chunk 125 optimal weight:   10.0000
   chunk 306 optimal weight:    4.9990
   chunk 37 optimal weight:    7.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    4.1188

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

Flipped N/Q/H residues before XYZ refinement:
** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  28 GLN
** c 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
g  21 GLN
h  98 GLN
j  20 GLN
** j  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
m   8 ASN
m  52 GLN
n  54 ASN
q  31 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.065402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.047445 restraints weight = 458600.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.047027 restraints weight = 397163.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.046949 restraints weight = 315632.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.7326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.049  55029  Z= 0.302
  Angle     :  0.759  11.981  81889  Z= 0.396
  Chirality :  0.039   0.529  10392
  Planarity :  0.007   0.122   4722
  Dihedral  : 16.760 179.540  20875
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 32.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer Outliers :  0.11 %
  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: -0.87 (0.17), residues: 2273
  helix:  0.13 (0.17), residues: 856
  sheet: -0.35 (0.28), residues: 330
  loop : -1.18 (0.19), residues: 1087

===============================================================================
Job complete
usr+sys time: 8567.29 seconds
wall clock time: 160 minutes 37.94 seconds (9637.94 seconds total)