Starting phenix.real_space_refine
on Thu Nov 16 12:36:10 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/11_2023/5tc1_8397.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/11_2023/5tc1_8397.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/11_2023/5tc1_8397.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/11_2023/5tc1_8397.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/11_2023/5tc1_8397.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/11_2023/5tc1_8397.pdb"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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     242      5.49       5
     S      43      5.16       5
     C    8768      2.51       5
     N    2671      2.21       5
     O    3669      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "M ARG    2": "NH1" <-> "NH2"
    Residue "M ARG    9": "NH1" <-> "NH2"
    Residue "M ARG   43": "NH1" <-> "NH2"
    Residue "M ARG   62": "NH1" <-> "NH2"
    Residue "M ARG  147": "NH1" <-> "NH2"
    Residue "M ARG  168": "NH1" <-> "NH2"
    Residue "M ARG  177": "NH1" <-> "NH2"
    Residue "M ARG  188": "NH1" <-> "NH2"
    Residue "M ARG  229": "NH1" <-> "NH2"
    Residue "M ARG  232": "NH1" <-> "NH2"
    Residue "M ARG  260": "NH1" <-> "NH2"
    Residue "M ARG  358": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib"
  Total number of atoms: 15393
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 965
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 122}
    Chain: "B"
      Number of atoms: 965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 965
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 122}
    Chain: "C"
      Number of atoms: 965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 965
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 122}
    Chain: "D"
      Number of atoms: 965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 965
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 122}
    Chain: "E"
      Number of atoms: 965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 965
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 122}
    Chain: "F"
      Number of atoms: 965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 965
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 122}
    Chain: "G"
      Number of atoms: 898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 898
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 112}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 965
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 122}
    Chain: "M"
      Number of atoms: 2608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2608
          Classifications: {'peptide': 330}
          Link IDs: {'PTRANS': 13, 'TRANS': 316}
          Chain breaks: 4
    Chain: "R"
      Number of atoms: 5132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 5132
          Classifications: {'RNA': 242}
          Modifications used: {'rna2p_pur': 27, 'rna2p_pyr': 34, 'rna3p_pur': 92, 'rna3p_pyr': 89}
          Link IDs: {'rna2p': 61, 'rna3p': 180}
          Chain breaks: 15
  Residues with excluded nonbonded symmetry interactions: 17
    residue:
      pdb=" P     A R1748 " occ=0.80
      ... (20 atoms not shown)
      pdb=" C4    A R1748 " occ=0.80
    residue:
      pdb=" P     U R1749 " occ=0.80
      ... (18 atoms not shown)
      pdb=" C6    U R1749 " occ=0.80
    residue:
      pdb=" P     G R1750 " occ=0.80
      ... (21 atoms not shown)
      pdb=" C4    G R1750 " occ=0.80
    residue:
      pdb=" P     A R1751 " occ=0.80
      ... (20 atoms not shown)
      pdb=" C4    A R1751 " occ=0.80
    residue:
      pdb=" P     G R1752 " occ=0.80
      ... (21 atoms not shown)
      pdb=" C4    G R1752 " occ=0.80
    residue:
      pdb=" P     G R1753 " occ=0.80
      ... (21 atoms not shown)
      pdb=" C4    G R1753 " occ=0.80
    residue:
      pdb=" P     A R1754 " occ=0.80
      ... (20 atoms not shown)
      pdb=" C4    A R1754 " occ=0.80
    residue:
      pdb=" P     U R1755 " occ=0.80
      ... (18 atoms not shown)
      pdb=" C6    U R1755 " occ=0.80
    residue:
      pdb=" P     U R1756 " occ=0.80
      ... (18 atoms not shown)
      pdb=" C6    U R1756 " occ=0.80
    residue:
      pdb=" P     A R1757 " occ=0.80
      ... (20 atoms not shown)
      pdb=" C4    A R1757 " occ=0.80
    residue:
      pdb=" P     C R1758 " occ=0.80
      ... (18 atoms not shown)
      pdb=" C6    C R1758 " occ=0.80
    residue:
      pdb=" P     C R1759 " occ=0.80
      ... (18 atoms not shown)
      pdb=" C6    C R1759 " occ=0.80
    ... (remaining 5 not shown)
  Time building chain proxies: 9.00, per 1000 atoms: 0.58
  Number of scatterers: 15393
  At special positions: 0
  Unit cell: (206.7, 216.24, 261.82, 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      43     16.00
     P     242     15.00
     O    3669      8.00
     N    2671      7.00
     C    8768      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 7.25
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2522

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 9 sheets defined
      26.6% alpha, 40.5% beta
      17 base pairs and 71 stacking pairs defined.
    Time for finding SS restraints: 4.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 29
    Processing helix  chain 'A' and resid 97 through 111
      removed outlier: 3.829A  pdb=" N   LEU A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 123
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.603A  pdb=" N   GLY B  28 " --> pdb=" O   PHE B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 112
      removed outlier: 3.692A  pdb=" N   VAL B 105 " --> pdb=" O   CYS B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 123
      removed outlier: 3.532A  pdb=" N   ILE B 122 " --> pdb=" O   ILE B 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 25 through 29
      removed outlier: 3.847A  pdb=" N   GLY C  28 " --> pdb=" O   PHE C  25 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 41
      removed outlier: 3.623A  pdb=" N   ALA C  41 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 112
      removed outlier: 3.554A  pdb=" N   LEU C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 123
    Processing helix  chain 'D' and resid 25 through 27
      No H-bonds generated for 'chain 'D' and resid 25 through 27'
    Processing helix  chain 'D' and resid 97 through 112
      removed outlier: 3.603A  pdb=" N   LEU D 103 " --> pdb=" O   SER D  99 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU D 112 " --> pdb=" O   MET D 108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 116 through 124
      removed outlier: 3.514A  pdb=" N   ALA D 123 " --> pdb=" O   PRO D 119 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA D 124 " --> pdb=" O   SER D 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 81
      removed outlier: 3.552A  pdb=" N   ALA E  81 " --> pdb=" O   PRO E  78 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 78 through 81'
    Processing helix  chain 'E' and resid 97 through 112
      removed outlier: 3.585A  pdb=" N   LEU E 103 " --> pdb=" O   SER E  99 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU E 111 " --> pdb=" O   ALA E 107 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 118 through 123
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.890A  pdb=" N   GLY F  28 " --> pdb=" O   PHE F  25 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 97 through 112
      removed outlier: 3.687A  pdb=" N   ILE F 104 " --> pdb=" O   ASP F 100 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU F 112 " --> pdb=" O   MET F 108 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 116 through 124
      removed outlier: 3.530A  pdb=" N   ALA F 124 " --> pdb=" O   SER F 120 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 25 through 29
      removed outlier: 4.044A  pdb=" N   GLY G  28 " --> pdb=" O   PHE G  25 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 37 through 41
      removed outlier: 3.573A  pdb=" N   ALA G  41 " --> pdb=" O   ARG G  38 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 97 through 112
      removed outlier: 3.949A  pdb=" N   LEU G 103 " --> pdb=" O   SER G  99 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 116 through 123
      removed outlier: 3.623A  pdb=" N   ALA G 123 " --> pdb=" O   PRO G 119 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 25 through 29
      removed outlier: 4.362A  pdb=" N   GLY H  28 " --> pdb=" O   PHE H  25 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 97 through 110
      removed outlier: 3.590A  pdb=" N   LEU H 103 " --> pdb=" O   SER H  99 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE H 104 " --> pdb=" O   ASP H 100 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL H 105 " --> pdb=" O   CYS H 101 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 116 through 123
    Processing helix  chain 'M' and resid 98 through 104
      removed outlier: 3.696A  pdb=" N   CYS M 101 " --> pdb=" O   ALA M  98 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   TYR M 102 " --> pdb=" O   ARG M  99 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   SER M 103 " --> pdb=" O   SER M 100 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU M 104 " --> pdb=" O   CYS M 101 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 98 through 104'
    Processing helix  chain 'M' and resid 117 through 135
      removed outlier: 4.056A  pdb=" N   ARG M 123 " --> pdb=" O   ASN M 119 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LYS M 131 " --> pdb=" O   GLU M 127 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR M 133 " --> pdb=" O   LEU M 129 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 140 through 145
    Processing helix  chain 'M' and resid 145 through 150
    Processing helix  chain 'M' and resid 152 through 169
      removed outlier: 3.580A  pdb=" N   GLN M 156 " --> pdb=" O   GLN M 152 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ALA M 159 " --> pdb=" O   THR M 155 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   VAL M 161 " --> pdb=" O   THR M 157 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA M 166 " --> pdb=" O   LYS M 162 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 171 through 176
    Processing helix  chain 'M' and resid 191 through 199
      removed outlier: 3.717A  pdb=" N   LEU M 199 " --> pdb=" O   ARG M 195 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 199 through 220
      Proline residue:  M 205  - end of helix
      removed outlier: 3.663A  pdb=" N   GLN M 211 " --> pdb=" O   MET M 207 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   MET M 216 " --> pdb=" O   GLY M 212 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU M 217 " --> pdb=" O   ALA M 213 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 221 through 224
    Processing helix  chain 'M' and resid 294 through 300
      removed outlier: 3.741A  pdb=" N   ASP M 298 " --> pdb=" O   SER M 294 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 300 through 312
      removed outlier: 3.503A  pdb=" N   MET M 306 " --> pdb=" O   PRO M 302 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLU M 308 " --> pdb=" O   GLY M 304 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   THR M 311 " --> pdb=" O   LEU M 307 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 379 through 388
      removed outlier: 3.722A  pdb=" N   ILE M 387 " --> pdb=" O   ALA M 383 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10
      removed outlier: 6.710A  pdb=" N   VAL A  18 " --> pdb=" O   LEU A   9 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   GLU A  31 " --> pdb=" O   SER A  23 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LYS A  61 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ARG A  56 " --> pdb=" O   THR A  91 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   THR A  91 " --> pdb=" O   ARG A  56 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   TYR A  58 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   GLU A  89 " --> pdb=" O   TYR A  58 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ILE A  60 " --> pdb=" O   ASN A  87 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   ASN A  87 " --> pdb=" O   ILE A  60 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   VAL A  62 " --> pdb=" O   TYR A  85 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   TYR A  85 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   VAL A  64 " --> pdb=" O   ARG A  83 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   ARG A  83 " --> pdb=" O   VAL A  64 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LYS A  66 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL A  79 " --> pdb=" O   ALA A  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 7 through 10
      removed outlier: 7.131A  pdb=" N   VAL B  18 " --> pdb=" O   LEU B   9 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   GLU B  31 " --> pdb=" O   SER B  23 " (cutoff:3.500A)
      removed outlier: 8.376A  pdb=" N   ARG D  83 " --> pdb=" O   PRO B  93 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   GLU D  76 " --> pdb=" O   VAL D  72 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   VAL D  72 " --> pdb=" O   GLU D  76 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   GLN D  70 " --> pdb=" O   PRO D  78 " (cutoff:3.500A)
      removed outlier: 5.489A  pdb=" N   ALA D  80 " --> pdb=" O   ALA D  68 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ALA D  68 " --> pdb=" O   ALA D  80 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   TRP D  82 " --> pdb=" O   LYS D  66 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ARG D  49 " --> pdb=" O   LYS D  57 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   GLU D  31 " --> pdb=" O   SER D  23 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   VAL D  18 " --> pdb=" O   LEU D   9 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 7 through 10
      removed outlier: 6.891A  pdb=" N   VAL C  18 " --> pdb=" O   LEU C   9 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   GLU C  31 " --> pdb=" O   SER C  23 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LYS C  61 " --> pdb=" O   THR C  45 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   TRP C  82 " --> pdb=" O   LYS C  66 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ALA C  68 " --> pdb=" O   ALA C  80 " (cutoff:3.500A)
      removed outlier: 5.154A  pdb=" N   ALA C  80 " --> pdb=" O   ALA C  68 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   GLN C  70 " --> pdb=" O   PRO C  78 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   VAL C  72 " --> pdb=" O   GLU C  76 " (cutoff:3.500A)
      removed outlier: 5.650A  pdb=" N   GLU C  76 " --> pdb=" O   VAL C  72 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 7 through 10
      removed outlier: 5.262A  pdb=" N   VAL E   8 " --> pdb=" O   VAL E  20 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   VAL E  20 " --> pdb=" O   VAL E   8 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL E  10 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   GLU E  31 " --> pdb=" O   SER E  23 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   PHE E  25 " --> pdb=" O   VAL E  29 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   VAL E  29 " --> pdb=" O   PHE E  25 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA E  30 " --> pdb=" O   CYS E  46 " (cutoff:3.500A)
      removed outlier: 8.691A  pdb=" N   ARG F  83 " --> pdb=" O   PRO E  93 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   GLU F  76 " --> pdb=" O   VAL F  72 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   VAL F  72 " --> pdb=" O   GLU F  76 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   GLN F  70 " --> pdb=" O   PRO F  78 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   ALA F  80 " --> pdb=" O   ALA F  68 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ALA F  68 " --> pdb=" O   ALA F  80 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   TRP F  82 " --> pdb=" O   LYS F  66 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LYS F  61 " --> pdb=" O   THR F  45 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   GLU F  31 " --> pdb=" O   SER F  23 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   VAL F  18 " --> pdb=" O   LEU F   9 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE F   7 " --> pdb=" O   VAL F  20 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 7 through 10
      removed outlier: 5.262A  pdb=" N   VAL E   8 " --> pdb=" O   VAL E  20 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   VAL E  20 " --> pdb=" O   VAL E   8 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL E  10 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   GLU E  31 " --> pdb=" O   SER E  23 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   PHE E  25 " --> pdb=" O   VAL E  29 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   VAL E  29 " --> pdb=" O   PHE E  25 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA E  30 " --> pdb=" O   CYS E  46 " (cutoff:3.500A)
      removed outlier: 8.195A  pdb=" N   ARG E  83 " --> pdb=" O   PRO F  93 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LYS F  61 " --> pdb=" O   THR F  45 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   GLU F  31 " --> pdb=" O   SER F  23 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   VAL F  18 " --> pdb=" O   LEU F   9 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE F   7 " --> pdb=" O   VAL F  20 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 7 through 10
      removed outlier: 6.858A  pdb=" N   VAL G  18 " --> pdb=" O   LEU G   9 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   GLU G  31 " --> pdb=" O   SER G  23 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   CYS G  46 " --> pdb=" O   ALA G  30 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LYS G  61 " --> pdb=" O   THR G  45 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG G  49 " --> pdb=" O   LYS G  57 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   SER G  51 " --> pdb=" O   ASN G  55 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ASN G  55 " --> pdb=" O   SER G  51 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU G  90 " --> pdb=" O   TYR G  58 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 7 through 10
      removed outlier: 6.662A  pdb=" N   VAL H  18 " --> pdb=" O   LEU H   9 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   GLU H  31 " --> pdb=" O   SER H  23 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LYS H  43 " --> pdb=" O   GLU H  63 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LYS H  61 " --> pdb=" O   THR H  45 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   GLN H  70 " --> pdb=" O   PRO H  78 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'M' and resid 38 through 39
      removed outlier: 6.745A  pdb=" N   LYS M 350 " --> pdb=" O   THR M  68 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA M 351 " --> pdb=" O   SER M 331 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE M 327 " --> pdb=" O   ALA M 355 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   TRP M 264 " --> pdb=" O   MET M 319 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   GLY M 321 " --> pdb=" O   VAL M 262 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   VAL M 262 " --> pdb=" O   GLY M 321 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   VAL M 323 " --> pdb=" O   ARG M 260 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ARG M 260 " --> pdb=" O   VAL M 323 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ASP M 325 " --> pdb=" O   SER M 258 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   SER M 258 " --> pdb=" O   ASP M 325 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ILE M 327 " --> pdb=" O   ASN M 256 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   ASN M 256 " --> pdb=" O   ILE M 327 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   GLY M 329 " --> pdb=" O   THR M 254 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   THR M 254 " --> pdb=" O   GLY M 329 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE M 261 " --> pdb=" O   ARG M 232 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'M' and resid 44 through 45
      removed outlier: 4.067A  pdb=" N   PHE M  44 " --> pdb=" O   SER M  61 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   SER M  61 " --> pdb=" O   PHE M  44 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   TYR M  60 " --> pdb=" O   ARG M 358 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA M 351 " --> pdb=" O   SER M 331 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE M 327 " --> pdb=" O   ALA M 355 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   ALA M 369 " --> pdb=" O   CYS M 316 " (cutoff:3.500A)

    469 hydrogen bonds defined for protein.
    1284 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      39 hydrogen bonds
      78 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      71 stacking parallelities
  Total time for adding SS restraints: 4.57

  Time building geometry restraints manager: 7.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3967
        1.34 -     1.45: 4322
        1.45 -     1.57: 7348
        1.57 -     1.69: 468
        1.69 -     1.81: 67
  Bond restraints: 16172
  Sorted by residual:
  bond pdb=" C   LEU M 104 "
       pdb=" N   PHE M 105 "
    ideal  model  delta    sigma   weight residual
    1.330  1.232  0.098 1.47e-02 4.63e+03 4.49e+01
  bond pdb=" C   VAL E  20 "
       pdb=" N   ALA E  21 "
    ideal  model  delta    sigma   weight residual
    1.331  1.390 -0.059 1.59e-02 3.96e+03 1.37e+01
  bond pdb=" C   TYR F 129 "
       pdb=" O   TYR F 129 "
    ideal  model  delta    sigma   weight residual
    1.231  1.277 -0.046 2.00e-02 2.50e+03 5.40e+00
  bond pdb=" C   TYR F 129 "
       pdb=" OXT TYR F 129 "
    ideal  model  delta    sigma   weight residual
    1.231  1.277 -0.046 2.00e-02 2.50e+03 5.26e+00
  bond pdb=" C   ILE G 118 "
       pdb=" N   PRO G 119 "
    ideal  model  delta    sigma   weight residual
    1.335  1.350 -0.015 9.40e-03 1.13e+04 2.53e+00
  ... (remaining 16167 not shown)

  Histogram of bond angle deviations from ideal:
       97.86 -   106.34: 1551
      106.34 -   114.83: 10158
      114.83 -   123.31: 9862
      123.31 -   131.79: 1429
      131.79 -   140.27: 100
  Bond angle restraints: 23100
  Sorted by residual:
  angle pdb=" C   LEU M 104 "
        pdb=" N   PHE M 105 "
        pdb=" CA  PHE M 105 "
      ideal   model   delta    sigma   weight residual
     120.68  140.27  -19.59 1.52e+00 4.33e-01 1.66e+02
  angle pdb=" C   LEU M 179 "
        pdb=" N   ALA M 180 "
        pdb=" CA  ALA M 180 "
      ideal   model   delta    sigma   weight residual
     122.40  127.50   -5.10 1.45e+00 4.76e-01 1.24e+01
  angle pdb=" N   VAL B  67 "
        pdb=" CA  VAL B  67 "
        pdb=" C   VAL B  67 "
      ideal   model   delta    sigma   weight residual
     112.96  109.49    3.47 1.00e+00 1.00e+00 1.21e+01
  angle pdb=" C   ASN M 110 "
        pdb=" N   LEU M 111 "
        pdb=" CA  LEU M 111 "
      ideal   model   delta    sigma   weight residual
     123.05  128.30   -5.25 1.57e+00 4.06e-01 1.12e+01
  angle pdb=" C   ALA H  26 "
        pdb=" N   ASN H  27 "
        pdb=" CA  ASN H  27 "
      ideal   model   delta    sigma   weight residual
     122.40  127.18   -4.78 1.45e+00 4.76e-01 1.09e+01
  ... (remaining 23095 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.56: 8702
       35.56 -    71.12: 361
       71.12 -   106.68: 33
      106.68 -   142.24: 3
      142.24 -   177.80: 14
  Dihedral angle restraints: 9113
    sinusoidal: 5210
      harmonic: 3903
  Sorted by residual:
  dihedral pdb=" C4'   U R2479 "
           pdb=" C3'   U R2479 "
           pdb=" C2'   U R2479 "
           pdb=" C1'   U R2479 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   36.21  -71.21     1      8.00e+00 1.56e-02 1.02e+02
  dihedral pdb=" C4'   U R2844 "
           pdb=" C3'   U R2844 "
           pdb=" C2'   U R2844 "
           pdb=" C1'   U R2844 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   36.16  -71.16     1      8.00e+00 1.56e-02 1.02e+02
  dihedral pdb=" C4'   U R1755 "
           pdb=" C3'   U R1755 "
           pdb=" C2'   U R1755 "
           pdb=" C1'   U R1755 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   36.12  -71.12     1      8.00e+00 1.56e-02 1.01e+02
  ... (remaining 9110 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1962
       0.054 -    0.109: 422
       0.109 -    0.163: 289
       0.163 -    0.217: 195
       0.217 -    0.271: 3
  Chirality restraints: 2871
  Sorted by residual:
  chirality pdb=" CB  VAL H  20 "
            pdb=" CA  VAL H  20 "
            pdb=" CG1 VAL H  20 "
            pdb=" CG2 VAL H  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CB  VAL F  20 "
            pdb=" CA  VAL F  20 "
            pdb=" CG1 VAL F  20 "
            pdb=" CG2 VAL F  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CB  VAL A  20 "
            pdb=" CA  VAL A  20 "
            pdb=" CG1 VAL A  20 "
            pdb=" CG2 VAL A  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 2868 not shown)

  Planarity restraints: 2074
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL F  64 "   -0.045 5.00e-02 4.00e+02   6.75e-02 7.30e+00
        pdb=" N   PRO F  65 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO F  65 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO F  65 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU M 204 "    0.045 5.00e-02 4.00e+02   6.71e-02 7.20e+00
        pdb=" N   PRO M 205 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO M 205 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO M 205 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL H  64 "   -0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO H  65 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO H  65 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO H  65 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 2071 not shown)

  Histogram of nonbonded interaction distances:
        1.13 -     1.88: 14
        1.88 -     2.64: 394
        2.64 -     3.39: 19273
        3.39 -     4.15: 37897
        4.15 -     4.90: 61108
  Nonbonded interactions: 118686
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG E  56 "
            pdb=" OD1 ASN F 125 "
     model   vdw
     1.126 2.520
  nonbonded pdb=" OG  SER M  58 "
            pdb=" O6    G R3555 "
     model   vdw
     1.430 2.440
  nonbonded pdb=" O   ALA B   1 "
            pdb=" CE2 TYR D 129 "
     model   vdw
     1.444 3.340
  nonbonded pdb=" CB  ALA B   1 "
            pdb=" OH  TYR D 129 "
     model   vdw
     1.483 3.460
  nonbonded pdb=" OD1 ASP E 114 "
            pdb=" NE2 GLN F 109 "
     model   vdw
     1.649 2.520
  ... (remaining 118681 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 67 or resid 78 through 129))
  selection = (chain 'B' and (resid 1 through 67 or resid 78 through 129))
  selection = (chain 'C' and (resid 1 through 67 or resid 78 through 129))
  selection = (chain 'D' and (resid 1 through 67 or resid 78 through 129))
  selection = (chain 'E' and (resid 1 through 67 or resid 78 through 129))
  selection = (chain 'F' and (resid 1 through 67 or resid 78 through 129))
  selection = chain 'G'
  selection = (chain 'H' and (resid 1 through 67 or resid 78 through 129))
}

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=0.80 max=1.00 mean=0.98
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:             1.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          7.900
  Check model and map are aligned:         0.240
  Set scattering table:                    0.140
  Process input model:                     46.780
  Find NCS groups from input model:        0.750
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   60.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
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      :  0.006   0.098  16172  Z= 0.367
  Angle     :  0.870  19.587  23100  Z= 0.562
  Chirality :  0.075   0.271   2871
  Planarity :  0.007   0.068   2074
  Dihedral  : 18.344 177.798   6591
  Min Nonbonded Distance : 1.126

Molprobity Statistics.
  All-atom Clashscore : 33.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.25 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.80 (0.19), residues: 1324
  helix: -4.62 (0.09), residues: 332
  sheet: -0.77 (0.25), residues: 423
  loop : -2.45 (0.21), residues: 569

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 333
  time to evaluate  : 1.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 335
  average time/residue: 0.2635
  time to fit residues: 129.5678
Evaluate side-chains
  198 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 197
  time to evaluate  : 1.387 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.1796
  time to fit residues: 2.0637
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:   20.0000
   chunk 115 optimal weight:    9.9990
   chunk 63 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 77 optimal weight:    0.8980
   chunk 61 optimal weight:    8.9990
   chunk 119 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 88 optimal weight:    7.9990
   chunk 138 optimal weight:   20.0000
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 116 ASN
B   3 ASN
B 116 ASN
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  98 ASN
D  36 ASN
D 116 ASN
F   6 GLN
F 116 ASN
G  54 GLN
** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  70 GLN
M  11 ASN
** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 352 GLN
M 357 HIS
M 389 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  16172  Z= 0.287
  Angle     :  0.684   8.244  23100  Z= 0.361
  Chirality :  0.044   0.281   2871
  Planarity :  0.005   0.050   2074
  Dihedral  : 18.841 179.313   4301
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 10.79 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.21), residues: 1324
  helix: -2.76 (0.19), residues: 325
  sheet: -0.45 (0.24), residues: 441
  loop : -1.79 (0.24), residues: 558

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 187
  time to evaluate  : 1.330 
Fit side-chains
  outliers start: 32
  outliers final: 25
  residues processed: 210
  average time/residue: 0.2518
  time to fit residues: 81.9136
Evaluate side-chains
  179 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 1.358 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1438
  time to fit residues: 8.3646
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 114 optimal weight:    5.9990
   chunk 93 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 138 optimal weight:   20.0000
   chunk 149 optimal weight:   20.0000
   chunk 123 optimal weight:    8.9990
   chunk 137 optimal weight:   30.0000
   chunk 47 optimal weight:    2.9990
   chunk 110 optimal weight:   20.0000
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   3 ASN
D 116 ASN
E 116 ASN
M 109 GLN
M 211 GLN
M 221 HIS
M 252 GLN
M 282 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  16172  Z= 0.338
  Angle     :  0.642   7.201  23100  Z= 0.341
  Chirality :  0.043   0.342   2871
  Planarity :  0.005   0.046   2074
  Dihedral  : 18.034 177.245   4301
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 12.58 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.79 (0.22), residues: 1324
  helix: -1.58 (0.24), residues: 325
  sheet: -0.23 (0.24), residues: 441
  loop : -1.63 (0.25), residues: 558

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 168
  time to evaluate  : 1.381 
Fit side-chains
   revert: symmetry clash
  outliers start: 30
  outliers final: 18
  residues processed: 187
  average time/residue: 0.2230
  time to fit residues: 66.5765
Evaluate side-chains
  168 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 1.326 
Switching outliers to nearest non-outliers
  outliers start: 18
  outliers final: 0
  residues processed: 18
  average time/residue: 0.1345
  time to fit residues: 6.1185
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 136 optimal weight:   20.0000
   chunk 103 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0050
   chunk 92 optimal weight:   10.0000
   chunk 138 optimal weight:   20.0000
   chunk 146 optimal weight:   20.0000
   chunk 72 optimal weight:   10.0000
   chunk 131 optimal weight:   30.0000
   chunk 39 optimal weight:    7.9990
   overall best weight:    4.8002

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   3 ASN
C  36 ASN
D 116 ASN
G  40 GLN
M 211 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  16172  Z= 0.247
  Angle     :  0.570   8.293  23100  Z= 0.299
  Chirality :  0.041   0.318   2871
  Planarity :  0.004   0.042   2074
  Dihedral  : 17.300 178.373   4301
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 15.17 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.29 (0.22), residues: 1324
  helix: -1.00 (0.27), residues: 324
  sheet:  0.10 (0.24), residues: 448
  loop : -1.49 (0.26), residues: 552

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 164
  time to evaluate  : 1.433 
Fit side-chains
  outliers start: 14
  outliers final: 7
  residues processed: 170
  average time/residue: 0.2328
  time to fit residues: 62.7759
Evaluate side-chains
  159 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 152
  time to evaluate  : 1.397 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1447
  time to fit residues: 3.5402
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 122 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 109 optimal weight:   20.0000
   chunk 60 optimal weight:   10.0000
   chunk 125 optimal weight:    7.9990
   chunk 101 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 75 optimal weight:    2.9990
   chunk 131 optimal weight:   30.0000
   chunk 37 optimal weight:    3.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 ASN
E  50 GLN
E 109 GLN
M 379 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.4100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  16172  Z= 0.279
  Angle     :  0.581   7.209  23100  Z= 0.303
  Chirality :  0.041   0.290   2871
  Planarity :  0.004   0.047   2074
  Dihedral  : 17.119 178.259   4301
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.79 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.01 (0.23), residues: 1324
  helix: -0.66 (0.28), residues: 324
  sheet:  0.30 (0.25), residues: 429
  loop : -1.38 (0.25), residues: 571

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 1.459 
Fit side-chains
  outliers start: 22
  outliers final: 13
  residues processed: 172
  average time/residue: 0.2572
  time to fit residues: 70.2512
Evaluate side-chains
  165 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 152
  time to evaluate  : 1.352 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.1512
  time to fit residues: 5.3878
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 132 optimal weight:   20.0000
   chunk 29 optimal weight:    9.9990
   chunk 86 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   chunk 147 optimal weight:   40.0000
   chunk 122 optimal weight:    6.9990
   chunk 68 optimal weight:    6.9990
   chunk 12 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 ASN
D   6 GLN
D 116 ASN
E  50 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.4276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  16172  Z= 0.297
  Angle     :  0.588   7.270  23100  Z= 0.307
  Chirality :  0.041   0.362   2871
  Planarity :  0.004   0.043   2074
  Dihedral  : 17.018 178.030   4301
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.32 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.93 (0.23), residues: 1324
  helix: -0.58 (0.28), residues: 324
  sheet:  0.35 (0.25), residues: 416
  loop : -1.29 (0.25), residues: 584

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 1.368 
Fit side-chains
  outliers start: 20
  outliers final: 9
  residues processed: 168
  average time/residue: 0.2293
  time to fit residues: 60.8788
Evaluate side-chains
  156 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 147
  time to evaluate  : 1.490 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.1509
  time to fit residues: 4.3533
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 141 optimal weight:   30.0000
   chunk 16 optimal weight:    9.9990
   chunk 83 optimal weight:   10.0000
   chunk 107 optimal weight:    8.9990
   chunk 123 optimal weight:   20.0000
   chunk 82 optimal weight:    0.6980
   chunk 146 optimal weight:   20.0000
   chunk 91 optimal weight:    7.9990
   chunk 89 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 90 optimal weight:    0.0270
   overall best weight:    3.7444

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
C  36 ASN
D 116 ASN
E  50 GLN
H  27 ASN
M  45 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.4430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  16172  Z= 0.201
  Angle     :  0.523   6.328  23100  Z= 0.273
  Chirality :  0.039   0.310   2871
  Planarity :  0.004   0.041   2074
  Dihedral  : 16.731 179.716   4301
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 17.57 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.60 (0.23), residues: 1324
  helix: -0.25 (0.29), residues: 324
  sheet:  0.55 (0.26), residues: 411
  loop : -1.13 (0.26), residues: 589

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 160
  time to evaluate  : 1.388 
Fit side-chains
  outliers start: 12
  outliers final: 8
  residues processed: 166
  average time/residue: 0.2451
  time to fit residues: 62.9868
Evaluate side-chains
  163 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 1.330 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1423
  time to fit residues: 3.7596
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 58 optimal weight:    8.9990
   chunk 87 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 93 optimal weight:    3.9990
   chunk 99 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 115 optimal weight:   20.0000
   chunk 133 optimal weight:   20.0000
   chunk 140 optimal weight:   10.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
C  36 ASN
D 116 ASN
E  50 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.4497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  16172  Z= 0.267
  Angle     :  0.560   6.385  23100  Z= 0.292
  Chirality :  0.040   0.312   2871
  Planarity :  0.004   0.042   2074
  Dihedral  : 16.685 178.706   4301
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 17.66 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.62 (0.23), residues: 1324
  helix: -0.24 (0.29), residues: 324
  sheet:  0.56 (0.26), residues: 411
  loop : -1.17 (0.26), residues: 589

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 154
  time to evaluate  : 1.517 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 157
  average time/residue: 0.2628
  time to fit residues: 64.9216
Evaluate side-chains
  153 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 149
  time to evaluate  : 1.415 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1396
  time to fit residues: 2.6816
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:   20.0000
   chunk 136 optimal weight:   20.0000
   chunk 140 optimal weight:   20.0000
   chunk 82 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0980
   chunk 107 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 123 optimal weight:   20.0000
   chunk 129 optimal weight:   30.0000
   chunk 89 optimal weight:    1.9990
   chunk 144 optimal weight:   30.0000
   overall best weight:    4.0190

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
A  87 ASN
C  36 ASN
D 116 ASN
E  50 GLN
M 252 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.4615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16172  Z= 0.211
  Angle     :  0.517   6.149  23100  Z= 0.269
  Chirality :  0.039   0.290   2871
  Planarity :  0.004   0.041   2074
  Dihedral  : 16.514 179.894   4301
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 17.40 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.49 (0.23), residues: 1324
  helix: -0.05 (0.29), residues: 324
  sheet:  0.64 (0.26), residues: 409
  loop : -1.14 (0.26), residues: 591

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 154
  time to evaluate  : 1.247 
Fit side-chains
  outliers start: 13
  outliers final: 8
  residues processed: 161
  average time/residue: 0.2490
  time to fit residues: 62.0042
Evaluate side-chains
  159 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 151
  time to evaluate  : 1.257 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1447
  time to fit residues: 3.7623
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 68 optimal weight:    5.9990
   chunk 100 optimal weight:    0.7980
   chunk 151 optimal weight:   20.0000
   chunk 139 optimal weight:   20.0000
   chunk 120 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   chunk 73 optimal weight:    9.9990
   chunk 95 optimal weight:    0.0870
   chunk 128 optimal weight:   20.0000
   overall best weight:    3.9764

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
C  36 ASN
M 252 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.4680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16172  Z= 0.210
  Angle     :  0.520   6.377  23100  Z= 0.270
  Chirality :  0.039   0.312   2871
  Planarity :  0.004   0.041   2074
  Dihedral  : 16.429 179.810   4301
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 17.75 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.37 (0.23), residues: 1324
  helix:  0.07 (0.29), residues: 324
  sheet:  0.72 (0.26), residues: 409
  loop : -1.09 (0.26), residues: 591

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 158
  time to evaluate  : 1.478 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 159
  average time/residue: 0.2528
  time to fit residues: 62.1243
Evaluate side-chains
  155 residues out of total 1121 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 153
  time to evaluate  : 1.396 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1389
  time to fit residues: 2.2470
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 36 optimal weight:    8.9990
   chunk 111 optimal weight:    9.9990
   chunk 17 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 120 optimal weight:    9.9990
   chunk 50 optimal weight:   10.0000
   chunk 124 optimal weight:   20.0000
   chunk 15 optimal weight:    8.9990
   chunk 22 optimal weight:    4.9990
   chunk 106 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
A  40 GLN
A  87 ASN
A 116 ASN
D 116 ASN
M 252 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.120699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.096650 restraints weight = 28847.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.098130 restraints weight = 15746.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.098835 restraints weight = 11622.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|
r_final: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.4690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  16172  Z= 0.350
  Angle     :  0.604   6.782  23100  Z= 0.314
  Chirality :  0.042   0.365   2871
  Planarity :  0.005   0.043   2074
  Dihedral  : 16.602 178.287   4301
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 18.20 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.68 (0.23), residues: 1324
  helix: -0.27 (0.28), residues: 324
  sheet:  0.52 (0.26), residues: 410
  loop : -1.23 (0.25), residues: 590

===============================================================================
Job complete
usr+sys time: 2721.70 seconds
wall clock time: 51 minutes 14.67 seconds (3074.67 seconds total)