Starting phenix.real_space_refine
on Tue Mar 19 07:57:40 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/03_2024/6umm_20820.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/03_2024/6umm_20820.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/03_2024/6umm_20820.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/03_2024/6umm_20820.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/03_2024/6umm_20820.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/03_2024/6umm_20820.pdb"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C   15131      2.51       5
     N    4240      2.21       5
     O    4227      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   27": "NH1" <-> "NH2"
    Residue "A ARG   64": "NH1" <-> "NH2"
    Residue "A ASP   67": "OD1" <-> "OD2"
    Residue "A ASP   72": "OD1" <-> "OD2"
    Residue "A ARG   75": "NH1" <-> "NH2"
    Residue "A ASP   98": "OD1" <-> "OD2"
    Residue "A ARG  118": "NH1" <-> "NH2"
    Residue "A ARG  119": "NH1" <-> "NH2"
    Residue "A ASP  130": "OD1" <-> "OD2"
    Residue "A ARG  153": "NH1" <-> "NH2"
    Residue "A ARG  154": "NH1" <-> "NH2"
    Residue "A GLU  161": "OE1" <-> "OE2"
    Residue "A ASP  190": "OD1" <-> "OD2"
    Residue "A ASP  203": "OD1" <-> "OD2"
    Residue "A GLU  207": "OE1" <-> "OE2"
    Residue "A GLU  219": "OE1" <-> "OE2"
    Residue "A GLU  225": "OE1" <-> "OE2"
    Residue "A PHE  226": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  246": "NH1" <-> "NH2"
    Residue "A ARG  260": "NH1" <-> "NH2"
    Residue "B ARG   11": "NH1" <-> "NH2"
    Residue "B ASP   19": "OD1" <-> "OD2"
    Residue "B GLU   26": "OE1" <-> "OE2"
    Residue "B ASP  111": "OD1" <-> "OD2"
    Residue "B ARG  123": "NH1" <-> "NH2"
    Residue "B ARG  125": "NH1" <-> "NH2"
    Residue "B PHE  204": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  211": "OD1" <-> "OD2"
    Residue "B ARG  239": "NH1" <-> "NH2"
    Residue "B ASP  378": "OD1" <-> "OD2"
    Residue "B TYR  391": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  406": "NH1" <-> "NH2"
    Residue "B TYR  439": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  444": "NH1" <-> "NH2"
    Residue "B ARG  445": "NH1" <-> "NH2"
    Residue "B PHE  449": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  455": "OD1" <-> "OD2"
    Residue "B ARG  475": "NH1" <-> "NH2"
    Residue "C ASP   19": "OD1" <-> "OD2"
    Residue "C GLU   26": "OE1" <-> "OE2"
    Residue "C PHE   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  114": "OD1" <-> "OD2"
    Residue "C PHE  119": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  123": "NH1" <-> "NH2"
    Residue "C ARG  155": "NH1" <-> "NH2"
    Residue "C PHE  165": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  212": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  312": "NH1" <-> "NH2"
    Residue "C ASP  405": "OD1" <-> "OD2"
    Residue "C ARG  406": "NH1" <-> "NH2"
    Residue "C ASP  437": "OD1" <-> "OD2"
    Residue "C TYR  439": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  469": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  474": "OD1" <-> "OD2"
    Residue "D PHE   13": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG   29": "NH1" <-> "NH2"
    Residue "D PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG   65": "NH1" <-> "NH2"
    Residue "D PHE   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG    3": "NH1" <-> "NH2"
    Residue "E GLU   25": "OE1" <-> "OE2"
    Residue "E ARG  112": "NH1" <-> "NH2"
    Residue "E ARG  123": "NH1" <-> "NH2"
    Residue "E GLU  132": "OE1" <-> "OE2"
    Residue "E GLU  134": "OE1" <-> "OE2"
    Residue "E ARG  144": "NH1" <-> "NH2"
    Residue "E ARG  151": "NH1" <-> "NH2"
    Residue "E PHE  155": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP  168": "OD1" <-> "OD2"
    Residue "E GLU  179": "OE1" <-> "OE2"
    Residue "E ASP  181": "OD1" <-> "OD2"
    Residue "E ARG  191": "NH1" <-> "NH2"
    Residue "E ARG  198": "NH1" <-> "NH2"
    Residue "E ASP  208": "OD1" <-> "OD2"
    Residue "E GLU  223": "OE1" <-> "OE2"
    Residue "E ARG  225": "NH1" <-> "NH2"
    Residue "E ASP  240": "OD1" <-> "OD2"
    Residue "E ASP  268": "OD1" <-> "OD2"
    Residue "E ASP  274": "OD1" <-> "OD2"
    Residue "E ARG  280": "NH1" <-> "NH2"
    Residue "E ARG  290": "NH1" <-> "NH2"
    Residue "E ARG  292": "NH1" <-> "NH2"
    Residue "E ASP  299": "OD1" <-> "OD2"
    Residue "E ARG  300": "NH1" <-> "NH2"
    Residue "E ASP  322": "OD1" <-> "OD2"
    Residue "E ARG  349": "NH1" <-> "NH2"
    Residue "E GLU  350": "OE1" <-> "OE2"
    Residue "E TYR  352": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP  354": "OD1" <-> "OD2"
    Residue "E ARG  361": "NH1" <-> "NH2"
    Residue "E ARG  366": "NH1" <-> "NH2"
    Residue "E ARG  395": "NH1" <-> "NH2"
    Residue "E ARG  399": "NH1" <-> "NH2"
    Residue "F ARG   27": "NH1" <-> "NH2"
    Residue "F ARG   64": "NH1" <-> "NH2"
    Residue "F ASP   67": "OD1" <-> "OD2"
    Residue "F ASP   72": "OD1" <-> "OD2"
    Residue "F ARG   75": "NH1" <-> "NH2"
    Residue "F ASP   98": "OD1" <-> "OD2"
    Residue "F ARG  118": "NH1" <-> "NH2"
    Residue "F ARG  119": "NH1" <-> "NH2"
    Residue "F ASP  127": "OD1" <-> "OD2"
    Residue "F ARG  153": "NH1" <-> "NH2"
    Residue "F ARG  154": "NH1" <-> "NH2"
    Residue "F GLU  161": "OE1" <-> "OE2"
    Residue "F ASP  173": "OD1" <-> "OD2"
    Residue "F GLU  182": "OE1" <-> "OE2"
    Residue "F ASP  190": "OD1" <-> "OD2"
    Residue "F ASP  206": "OD1" <-> "OD2"
    Residue "F GLU  211": "OE1" <-> "OE2"
    Residue "F GLU  219": "OE1" <-> "OE2"
    Residue "F PHE  226": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG  246": "NH1" <-> "NH2"
    Residue "F ARG  260": "NH1" <-> "NH2"
    Residue "G ARG   11": "NH1" <-> "NH2"
    Residue "G ASP   19": "OD1" <-> "OD2"
    Residue "G ASP   20": "OD1" <-> "OD2"
    Residue "G GLU   32": "OE1" <-> "OE2"
    Residue "G GLU   37": "OE1" <-> "OE2"
    Residue "G ASP   80": "OD1" <-> "OD2"
    Residue "G GLU  110": "OE1" <-> "OE2"
    Residue "G ASP  114": "OD1" <-> "OD2"
    Residue "G ARG  123": "NH1" <-> "NH2"
    Residue "G ARG  125": "NH1" <-> "NH2"
    Residue "G ASP  160": "OD1" <-> "OD2"
    Residue "G ASP  211": "OD1" <-> "OD2"
    Residue "G ARG  239": "NH1" <-> "NH2"
    Residue "G ARG  295": "NH1" <-> "NH2"
    Residue "G ASP  405": "OD1" <-> "OD2"
    Residue "G ARG  406": "NH1" <-> "NH2"
    Residue "G TYR  407": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ARG  444": "NH1" <-> "NH2"
    Residue "G ARG  445": "NH1" <-> "NH2"
    Residue "G ASP  455": "OD1" <-> "OD2"
    Residue "G ARG  475": "NH1" <-> "NH2"
    Residue "H ASP   19": "OD1" <-> "OD2"
    Residue "H PHE   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ASP   84": "OD1" <-> "OD2"
    Residue "H GLU  121": "OE1" <-> "OE2"
    Residue "H ARG  123": "NH1" <-> "NH2"
    Residue "H ARG  155": "NH1" <-> "NH2"
    Residue "H ASP  211": "OD1" <-> "OD2"
    Residue "H ASP  306": "OD1" <-> "OD2"
    Residue "H ARG  312": "NH1" <-> "NH2"
    Residue "H ARG  406": "NH1" <-> "NH2"
    Residue "H ASP  437": "OD1" <-> "OD2"
    Residue "H TYR  439": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ASP  474": "OD1" <-> "OD2"
    Residue "I ASP   62": "OD1" <-> "OD2"
    Residue "I ARG   65": "NH1" <-> "NH2"
    Residue "I ARG   69": "NH1" <-> "NH2"
    Residue "J ARG    3": "NH1" <-> "NH2"
    Residue "J GLU   25": "OE1" <-> "OE2"
    Residue "J ARG   32": "NH1" <-> "NH2"
    Residue "J GLU   95": "OE1" <-> "OE2"
    Residue "J ASP  103": "OD1" <-> "OD2"
    Residue "J ARG  112": "NH1" <-> "NH2"
    Residue "J ASP  113": "OD1" <-> "OD2"
    Residue "J GLU  121": "OE1" <-> "OE2"
    Residue "J ARG  123": "NH1" <-> "NH2"
    Residue "J ARG  144": "NH1" <-> "NH2"
    Residue "J ASP  149": "OD1" <-> "OD2"
    Residue "J ARG  151": "NH1" <-> "NH2"
    Residue "J PHE  155": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J ASP  168": "OD1" <-> "OD2"
    Residue "J ASP  181": "OD1" <-> "OD2"
    Residue "J ARG  191": "NH1" <-> "NH2"
    Residue "J ARG  198": "NH1" <-> "NH2"
    Residue "J GLU  220": "OE1" <-> "OE2"
    Residue "J ARG  225": "NH1" <-> "NH2"
    Residue "J ARG  280": "NH1" <-> "NH2"
    Residue "J ARG  290": "NH1" <-> "NH2"
    Residue "J ARG  292": "NH1" <-> "NH2"
    Residue "J ARG  300": "NH1" <-> "NH2"
    Residue "J ASP  322": "OD1" <-> "OD2"
    Residue "J GLU  345": "OE1" <-> "OE2"
    Residue "J ARG  349": "NH1" <-> "NH2"
    Residue "J TYR  352": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J ARG  361": "NH1" <-> "NH2"
    Residue "J ASP  364": "OD1" <-> "OD2"
    Residue "J ARG  366": "NH1" <-> "NH2"
    Residue "J ARG  395": "NH1" <-> "NH2"
    Residue "J ARG  399": "NH1" <-> "NH2"
    Residue "J ASP  401": "OD1" <-> "OD2"
  Time to flip residues: 0.09s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 23658
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 2169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2169
          Classifications: {'peptide': 285}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 268}
    Chain: "B"
      Number of atoms: 3162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 441, 3162
          Classifications: {'peptide': 441}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 25, 'TRANS': 415}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3238
          Classifications: {'peptide': 452}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 422}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 644
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 76}
    Chain: "E"
      Number of atoms: 2698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2698
          Classifications: {'peptide': 343}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 313}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 2169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2169
          Classifications: {'peptide': 285}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 268}
    Chain: "G"
      Number of atoms: 3162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 441, 3162
          Classifications: {'peptide': 441}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 25, 'TRANS': 415}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 3238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3238
          Classifications: {'peptide': 452}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 422}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 480
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 480
          Classifications: {'peptide': 61}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 58}
    Chain: "J"
      Number of atoms: 2698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2698
          Classifications: {'peptide': 343}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 313}
          Chain breaks: 1
  Time building chain proxies: 12.69, per 1000 atoms: 0.54
  Number of scatterers: 23658
  At special positions: 0
  Unit cell: (188.6, 141.86, 154.98, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    4227      8.00
     N    4240      7.00
     C   15131      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: 9.63
  Conformation dependent library (CDL) restraints added in 4.3 seconds
  

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5908

  Finding SS restraints...
    Secondary structure from input PDB file:
      114 helices and 19 sheets defined
      58.3% alpha, 11.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 17
    Processing helix  chain 'A' and resid 23 through 41
    Processing helix  chain 'A' and resid 48 through 65
    Processing helix  chain 'A' and resid 89 through 95
      removed outlier: 3.671A  pdb=" N   VAL A  93 " --> pdb=" O   GLN A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 139
      removed outlier: 3.793A  pdb=" N   LEU A 135 " --> pdb=" O   ASN A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 163
    Processing helix  chain 'A' and resid 204 through 214
    Processing helix  chain 'A' and resid 263 through 270
    Processing helix  chain 'B' and resid 34 through 47
      removed outlier: 3.796A  pdb=" N   ILE B  38 " --> pdb=" O   PRO B  34 " (cutoff:3.500A)
      Proline residue:  B  40  - end of helix
    Processing helix  chain 'B' and resid 111 through 120
    Processing helix  chain 'B' and resid 121 through 124
    Processing helix  chain 'B' and resid 127 through 159
      removed outlier: 3.803A  pdb=" N   HIS B 131 " --> pdb=" O   TRP B 127 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ILE B 132 " --> pdb=" O   GLY B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 181
      removed outlier: 3.675A  pdb=" N   LEU B 179 " --> pdb=" O   VAL B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 196
    Processing helix  chain 'B' and resid 196 through 206
    Processing helix  chain 'B' and resid 213 through 234
      removed outlier: 3.553A  pdb=" N   GLY B 234 " --> pdb=" O   ILE B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 264
    Processing helix  chain 'B' and resid 267 through 285
      removed outlier: 3.556A  pdb=" N   ILE B 271 " --> pdb=" O   SER B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 294
    Processing helix  chain 'B' and resid 319 through 351
    Processing helix  chain 'B' and resid 356 through 374
      removed outlier: 3.556A  pdb=" N   TRP B 360 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL B 363 " --> pdb=" O   ALA B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 404
      removed outlier: 4.396A  pdb=" N   SER B 390 " --> pdb=" O   LEU B 386 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   TYR B 391 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 430
    Processing helix  chain 'B' and resid 430 through 435
    Processing helix  chain 'B' and resid 436 through 439
      removed outlier: 3.540A  pdb=" N   TYR B 439 " --> pdb=" O   PRO B 436 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 436 through 439'
    Processing helix  chain 'B' and resid 440 through 455
    Processing helix  chain 'B' and resid 457 through 466
      removed outlier: 3.984A  pdb=" N   VAL B 461 " --> pdb=" O   SER B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 473
    Processing helix  chain 'C' and resid 34 through 47
      Proline residue:  C  40  - end of helix
    Processing helix  chain 'C' and resid 82 through 87
    Processing helix  chain 'C' and resid 115 through 123
      removed outlier: 3.926A  pdb=" N   ARG C 123 " --> pdb=" O   PHE C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 158
    Processing helix  chain 'C' and resid 161 through 182
    Processing helix  chain 'C' and resid 185 through 196
      removed outlier: 3.543A  pdb=" N   ALA C 189 " --> pdb=" O   SER C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 208
      removed outlier: 3.889A  pdb=" N   LEU C 206 " --> pdb=" O   ALA C 202 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   VAL C 208 " --> pdb=" O   PHE C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 233
      removed outlier: 3.587A  pdb=" N   VAL C 217 " --> pdb=" O   GLY C 213 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ALA C 233 " --> pdb=" O   LEU C 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 239 through 264
      removed outlier: 3.753A  pdb=" N   VAL C 243 " --> pdb=" O   ARG C 239 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TRP C 264 " --> pdb=" O   ALA C 260 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 285
    Processing helix  chain 'C' and resid 285 through 294
    Processing helix  chain 'C' and resid 313 through 351
      removed outlier: 3.667A  pdb=" N   LEU C 317 " --> pdb=" O   PRO C 313 " (cutoff:3.500A)
      Proline residue:  C 321  - end of helix
    Processing helix  chain 'C' and resid 356 through 373
    Processing helix  chain 'C' and resid 374 through 376
      No H-bonds generated for 'chain 'C' and resid 374 through 376'
    Processing helix  chain 'C' and resid 379 through 404
      removed outlier: 4.648A  pdb=" N   SER C 390 " --> pdb=" O   LEU C 386 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   TYR C 391 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 407 through 430
    Processing helix  chain 'C' and resid 435 through 439
    Processing helix  chain 'C' and resid 440 through 466
      removed outlier: 4.443A  pdb=" N   ILE C 459 " --> pdb=" O   ASP C 455 " (cutoff:3.500A)
      Proline residue:  C 460  - end of helix
    Processing helix  chain 'C' and resid 467 through 474
    Processing helix  chain 'D' and resid 34 through 54
    Processing helix  chain 'D' and resid 62 through 92
    Processing helix  chain 'E' and resid 95 through 130
    Processing helix  chain 'E' and resid 134 through 139
      removed outlier: 3.540A  pdb=" N   ILE E 139 " --> pdb=" O   LEU E 136 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 183 through 197
    Processing helix  chain 'E' and resid 210 through 212
      No H-bonds generated for 'chain 'E' and resid 210 through 212'
    Processing helix  chain 'E' and resid 220 through 237
    Processing helix  chain 'E' and resid 258 through 264
    Processing helix  chain 'E' and resid 285 through 298
      Proline residue:  E 295  - end of helix
    Processing helix  chain 'E' and resid 386 through 399
      removed outlier: 3.953A  pdb=" N   ARG E 399 " --> pdb=" O   ARG E 395 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 17
    Processing helix  chain 'F' and resid 23 through 41
    Processing helix  chain 'F' and resid 48 through 65
    Processing helix  chain 'F' and resid 89 through 96
    Processing helix  chain 'F' and resid 132 through 137
    Processing helix  chain 'F' and resid 143 through 163
    Processing helix  chain 'F' and resid 204 through 215
      removed outlier: 3.638A  pdb=" N   VAL F 208 " --> pdb=" O   ARG F 204 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 263 through 271
    Processing helix  chain 'G' and resid 34 through 37
    Processing helix  chain 'G' and resid 38 through 47
    Processing helix  chain 'G' and resid 112 through 121
      removed outlier: 3.585A  pdb=" N   GLU G 121 " --> pdb=" O   VAL G 117 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 128 through 159
    Processing helix  chain 'G' and resid 161 through 181
      removed outlier: 3.805A  pdb=" N   PHE G 165 " --> pdb=" O   LEU G 161 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 185 through 208
      removed outlier: 3.664A  pdb=" N   ALA G 189 " --> pdb=" O   SER G 185 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   VAL G 198 " --> pdb=" O   VAL G 194 " (cutoff:3.500A)
      Proline residue:  G 199  - end of helix
      removed outlier: 3.993A  pdb=" N   VAL G 208 " --> pdb=" O   PHE G 204 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 213 through 235
      removed outlier: 3.616A  pdb=" N   VAL G 217 " --> pdb=" O   GLY G 213 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 240 through 264
    Processing helix  chain 'G' and resid 267 through 285
      removed outlier: 3.501A  pdb=" N   ILE G 271 " --> pdb=" O   SER G 267 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 285 through 294
    Processing helix  chain 'G' and resid 319 through 349
    Processing helix  chain 'G' and resid 356 through 374
    Processing helix  chain 'G' and resid 379 through 404
      removed outlier: 3.518A  pdb=" N   TRP G 385 " --> pdb=" O   ALA G 381 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   SER G 390 " --> pdb=" O   LEU G 386 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   TYR G 391 " --> pdb=" O   LEU G 387 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 406 through 430
      removed outlier: 3.552A  pdb=" N   ALA G 410 " --> pdb=" O   ARG G 406 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 430 through 435
      removed outlier: 3.634A  pdb=" N   ALA G 434 " --> pdb=" O   ASN G 430 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 440 through 466
      removed outlier: 5.280A  pdb=" N   ILE G 459 " --> pdb=" O   ASP G 455 " (cutoff:3.500A)
      Proline residue:  G 460  - end of helix
    Processing helix  chain 'G' and resid 469 through 474
    Processing helix  chain 'H' and resid 34 through 47
      removed outlier: 3.980A  pdb=" N   ILE H  38 " --> pdb=" O   PRO H  34 " (cutoff:3.500A)
      Proline residue:  H  40  - end of helix
      removed outlier: 3.518A  pdb=" N   GLN H  47 " --> pdb=" O   GLN H  43 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 82 through 87
    Processing helix  chain 'H' and resid 115 through 123
    Processing helix  chain 'H' and resid 128 through 158
    Processing helix  chain 'H' and resid 160 through 181
      removed outlier: 4.408A  pdb=" N   GLN H 164 " --> pdb=" O   ASP H 160 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 182 through 184
      No H-bonds generated for 'chain 'H' and resid 182 through 184'
    Processing helix  chain 'H' and resid 186 through 196
    Processing helix  chain 'H' and resid 196 through 206
    Processing helix  chain 'H' and resid 213 through 233
      removed outlier: 4.021A  pdb=" N   VAL H 217 " --> pdb=" O   GLY H 213 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA H 233 " --> pdb=" O   LEU H 229 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 239 through 264
      removed outlier: 3.534A  pdb=" N   TRP H 264 " --> pdb=" O   ALA H 260 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 267 through 285
      removed outlier: 3.527A  pdb=" N   ILE H 271 " --> pdb=" O   SER H 267 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLN H 285 " --> pdb=" O   ILE H 281 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 285 through 294
    Processing helix  chain 'H' and resid 313 through 351
      removed outlier: 3.531A  pdb=" N   LEU H 317 " --> pdb=" O   PRO H 313 " (cutoff:3.500A)
      Proline residue:  H 321  - end of helix
    Processing helix  chain 'H' and resid 356 through 373
    Processing helix  chain 'H' and resid 380 through 404
      removed outlier: 3.846A  pdb=" N   ALA H 384 " --> pdb=" O   ALA H 380 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   SER H 390 " --> pdb=" O   LEU H 386 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   TYR H 391 " --> pdb=" O   LEU H 387 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 407 through 430
    Processing helix  chain 'H' and resid 435 through 439
    Processing helix  chain 'H' and resid 440 through 466
      removed outlier: 4.331A  pdb=" N   ILE H 459 " --> pdb=" O   ASP H 455 " (cutoff:3.500A)
      Proline residue:  H 460  - end of helix
    Processing helix  chain 'H' and resid 468 through 475
    Processing helix  chain 'I' and resid 34 through 51
    Processing helix  chain 'I' and resid 62 through 92
    Processing helix  chain 'J' and resid 95 through 130
    Processing helix  chain 'J' and resid 132 through 136
    Processing helix  chain 'J' and resid 183 through 197
    Processing helix  chain 'J' and resid 210 through 212
      No H-bonds generated for 'chain 'J' and resid 210 through 212'
    Processing helix  chain 'J' and resid 220 through 237
    Processing helix  chain 'J' and resid 255 through 260
      removed outlier: 4.226A  pdb=" N   TRP J 260 " --> pdb=" O   GLY J 256 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 261 through 263
      No H-bonds generated for 'chain 'J' and resid 261 through 263'
    Processing helix  chain 'J' and resid 285 through 294
    Processing helix  chain 'J' and resid 295 through 297
      No H-bonds generated for 'chain 'J' and resid 295 through 297'
    Processing helix  chain 'J' and resid 324 through 328
      removed outlier: 3.623A  pdb=" N   ILE J 328 " --> pdb=" O   PRO J 325 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 386 through 398
    Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 169
      removed outlier: 4.401A  pdb=" N   VAL A  79 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   SER A 120 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99
      removed outlier: 7.305A  pdb=" N   ASP A 105 " --> pdb=" O   GLY A 228 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   GLY A 228 " --> pdb=" O   ASP A 105 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLU A 219 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   VAL A 237 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL A 199 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS A 181 " --> pdb=" O   ALA A 188 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 183
      removed outlier: 3.647A  pdb=" N   LYS A 181 " --> pdb=" O   ALA A 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 169
      removed outlier: 4.401A  pdb=" N   VAL A  79 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   ASP A 127 " --> pdb=" O   CYS A 104 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   CYS A 104 " --> pdb=" O   ASP A 127 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   ASP A 105 " --> pdb=" O   GLY A 228 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   GLY A 228 " --> pdb=" O   ASP A 105 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLU A 219 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   VAL A 237 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL A 199 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 67 through 71
      removed outlier: 8.836A  pdb=" N   LEU B  94 " --> pdb=" O   ARG B  11 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ALA B  13 " --> pdb=" O   LEU B  94 " (cutoff:3.500A)
      removed outlier: 8.086A  pdb=" N   LEU B  96 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   LEU B  15 " --> pdb=" O   LEU B  96 " (cutoff:3.500A)
      removed outlier: 9.457A  pdb=" N   ALA B  98 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 14
    Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 70
    Processing sheet with id=AA8, first strand: chain 'E' and resid 22 through 24
      removed outlier: 6.039A  pdb=" N   ILE E  22 " --> pdb=" O   LYS E 172 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'E' and resid 157 through 166
      removed outlier: 6.793A  pdb=" N   VAL E 157 " --> pdb=" O   ASP E 208 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ASP E 208 " --> pdb=" O   VAL E 157 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ARG E 159 " --> pdb=" O   GLY E 206 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   GLY E 206 " --> pdb=" O   ARG E 159 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   GLY E 161 " --> pdb=" O   PRO E 204 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   HIS E 163 " --> pdb=" O   ASP E 202 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ASP E 202 " --> pdb=" O   HIS E 163 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 246 through 249
      removed outlier: 6.225A  pdb=" N   ALA E 247 " --> pdb=" O   VAL E 317 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   VAL E 316 " --> pdb=" O   ILE E 340 " (cutoff:3.500A)
      removed outlier: 7.854A  pdb=" N   ARG E 342 " --> pdb=" O   VAL E 316 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   LEU E 318 " --> pdb=" O   ARG E 342 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   LEU E 360 " --> pdb=" O   ARG E 214 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   THR E 216 " --> pdb=" O   LEU E 360 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   VAL E 362 " --> pdb=" O   THR E 216 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   ILE E 218 " --> pdb=" O   VAL E 362 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   ILE E 359 " --> pdb=" O   TRP E 370 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 166 through 168
      removed outlier: 3.868A  pdb=" N   SER F 120 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS F 106 " --> pdb=" O   THR F 125 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   SER F 229 " --> pdb=" O   GLU F 232 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   VAL F 237 " --> pdb=" O   VAL F 199 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 98 through 99
    Processing sheet with id=AB4, first strand: chain 'F' and resid 181 through 182
    Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 71
      removed outlier: 8.471A  pdb=" N   LEU G  94 " --> pdb=" O   ARG G  11 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   ALA G  13 " --> pdb=" O   LEU G  94 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   LEU G  96 " --> pdb=" O   ALA G  13 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   LEU G  15 " --> pdb=" O   LEU G  96 " (cutoff:3.500A)
      removed outlier: 9.179A  pdb=" N   ALA G  98 " --> pdb=" O   LEU G  15 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ARG G  23 " --> pdb=" O   ALA G  16 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 24 through 30
      removed outlier: 3.918A  pdb=" N   LEU H  96 " --> pdb=" O   LEU H  15 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'J' and resid 23 through 24
    Processing sheet with id=AB8, first strand: chain 'J' and resid 157 through 163
      removed outlier: 6.938A  pdb=" N   THR J 205 " --> pdb=" O   ALA J 160 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   ARG J 162 " --> pdb=" O   ALA J 203 " (cutoff:3.500A)
      removed outlier: 5.657A  pdb=" N   ALA J 203 " --> pdb=" O   ARG J 162 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'J' and resid 216 through 219
      removed outlier: 5.824A  pdb=" N   THR J 216 " --> pdb=" O   LEU J 360 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   VAL J 362 " --> pdb=" O   THR J 216 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   ILE J 218 " --> pdb=" O   VAL J 362 " (cutoff:3.500A)
      removed outlier: 5.204A  pdb=" N   ILE J 359 " --> pdb=" O   TRP J 370 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'J' and resid 246 through 248
      removed outlier: 6.429A  pdb=" N   ALA J 247 " --> pdb=" O   VAL J 317 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   LEU J 314 " --> pdb=" O   THR J 338 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   ILE J 340 " --> pdb=" O   LEU J 314 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   VAL J 316 " --> pdb=" O   ILE J 340 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1

    1531 hydrogen bonds defined for protein.
    4485 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 7.79

  Time building geometry restraints manager: 10.34 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: 7885
        1.34 -     1.45: 3036
        1.45 -     1.57: 13116
        1.57 -     1.69: 0
        1.69 -     1.81: 104
  Bond restraints: 24141
  Sorted by residual:
  bond pdb=" C   LEU A 270 "
       pdb=" N   ASN A 271 "
    ideal  model  delta    sigma   weight residual
    1.327  1.246  0.081 2.31e-02 1.87e+03 1.23e+01
  bond pdb=" N   VAL G 350 "
       pdb=" CA  VAL G 350 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.92e+00
  bond pdb=" N   LEU G 349 "
       pdb=" CA  LEU G 349 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.10e-02 8.26e+03 7.90e+00
  bond pdb=" N   ARG C 312 "
       pdb=" CA  ARG C 312 "
    ideal  model  delta    sigma   weight residual
    1.452  1.489 -0.037 1.41e-02 5.03e+03 6.75e+00
  bond pdb=" N   SER G 351 "
       pdb=" CA  SER G 351 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.030 1.22e-02 6.72e+03 6.00e+00
  ... (remaining 24136 not shown)

  Histogram of bond angle deviations from ideal:
       98.64 -   105.74: 737
      105.74 -   112.84: 14013
      112.84 -   119.93: 7508
      119.93 -   127.03: 10420
      127.03 -   134.13: 423
  Bond angle restraints: 33101
  Sorted by residual:
  angle pdb=" N   ILE E 328 "
        pdb=" CA  ILE E 328 "
        pdb=" C   ILE E 328 "
      ideal   model   delta    sigma   weight residual
     113.71  107.40    6.31 9.50e-01 1.11e+00 4.41e+01
  angle pdb=" N   ARG J 151 "
        pdb=" CA  ARG J 151 "
        pdb=" C   ARG J 151 "
      ideal   model   delta    sigma   weight residual
     114.64  105.58    9.06 1.52e+00 4.33e-01 3.55e+01
  angle pdb=" N   ILE J 328 "
        pdb=" CA  ILE J 328 "
        pdb=" C   ILE J 328 "
      ideal   model   delta    sigma   weight residual
     111.62  108.19    3.43 7.90e-01 1.60e+00 1.88e+01
  angle pdb=" N   ASP H  19 "
        pdb=" CA  ASP H  19 "
        pdb=" C   ASP H  19 "
      ideal   model   delta    sigma   weight residual
     114.39  108.40    5.99 1.45e+00 4.76e-01 1.71e+01
  angle pdb=" N   TRP E 258 "
        pdb=" CA  TRP E 258 "
        pdb=" C   TRP E 258 "
      ideal   model   delta    sigma   weight residual
     114.64  108.46    6.18 1.52e+00 4.33e-01 1.66e+01
  ... (remaining 33096 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 13337
       17.86 -    35.71: 913
       35.71 -    53.57: 130
       53.57 -    71.43: 43
       71.43 -    89.28: 24
  Dihedral angle restraints: 14447
    sinusoidal: 5342
      harmonic: 9105
  Sorted by residual:
  dihedral pdb=" CA  SER D  15 "
           pdb=" C   SER D  15 "
           pdb=" N   ARG D  16 "
           pdb=" CA  ARG D  16 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.17  -21.83     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" CA  ARG E 349 "
           pdb=" C   ARG E 349 "
           pdb=" N   GLU E 350 "
           pdb=" CA  GLU E 350 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.32   20.68     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  ASP E 364 "
           pdb=" C   ASP E 364 "
           pdb=" N   GLY E 365 "
           pdb=" CA  GLY E 365 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.40  -20.60     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 14444 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 3260
       0.053 -    0.106: 689
       0.106 -    0.159: 104
       0.159 -    0.212: 5
       0.212 -    0.265: 1
  Chirality restraints: 4059
  Sorted by residual:
  chirality pdb=" CB  ILE H 459 "
            pdb=" CA  ILE H 459 "
            pdb=" CG1 ILE H 459 "
            pdb=" CG2 ILE H 459 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CB  ILE J 180 "
            pdb=" CA  ILE J 180 "
            pdb=" CG1 ILE J 180 "
            pdb=" CG2 ILE J 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CB  VAL C 167 "
            pdb=" CA  VAL C 167 "
            pdb=" CG1 VAL C 167 "
            pdb=" CG2 VAL C 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.77e-01
  ... (remaining 4056 not shown)

  Planarity restraints: 4231
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 200 "   -0.010 2.00e-02 2.50e+03   2.12e-02 4.47e+00
        pdb=" C   VAL E 200 "    0.037 2.00e-02 2.50e+03
        pdb=" O   VAL E 200 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ARG E 201 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER H 435 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO H 436 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO H 436 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO H 436 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 441 "   -0.030 5.00e-02 4.00e+02   4.54e-02 3.30e+00
        pdb=" N   PRO C 442 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO C 442 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C 442 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 4228 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 3222
        2.74 -     3.28: 24920
        3.28 -     3.82: 39502
        3.82 -     4.36: 44139
        4.36 -     4.90: 76758
  Nonbonded interactions: 188541
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 352 "
            pdb=" OD1 ASN C 354 "
     model   vdw
     2.203 2.440
  nonbonded pdb=" O   THR C  82 "
            pdb=" OG1 THR C  85 "
     model   vdw
     2.227 2.440
  nonbonded pdb=" NH1 ARG J 225 "
            pdb=" OD2 ASP J 257 "
     model   vdw
     2.230 2.520
  nonbonded pdb=" OG  SER G  31 "
            pdb=" OD1 ASP G  84 "
     model   vdw
     2.231 2.440
  nonbonded pdb=" NE  ARG A 138 "
            pdb=" OE2 GLU C 110 "
     model   vdw
     2.237 2.520
  ... (remaining 188536 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'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'B' and (resid 7 through 49 or resid 67 through 475))
  selection = (chain 'C' and (resid 7 through 295 or resid 313 through 475))
  selection = (chain 'G' and (resid 7 through 49 or resid 67 through 475))
  selection = (chain 'H' and (resid 7 through 295 or resid 313 through 475))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             4.800
  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:             0.020
  Extract box with map and model:          19.460
  Check model and map are aligned:         0.380
  Set scattering table:                    0.240
  Process input model:                     62.560
  Find NCS groups from input model:        1.510
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   92.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6030
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   0.081  24141  Z= 0.429
  Angle     :  0.793  13.638  33101  Z= 0.455
  Chirality :  0.043   0.265   4059
  Planarity :  0.005   0.046   4231
  Dihedral  : 13.227  89.283   8539
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  7.66 %
    Favored  : 92.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.13), residues: 3148
  helix: -0.54 (0.11), residues: 1748
  sheet: -2.31 (0.25), residues: 283
  loop : -2.33 (0.16), residues: 1117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP H 293 
 HIS   0.008   0.002   HIS J 239 
 PHE   0.020   0.002   PHE I  88 
 TYR   0.027   0.002   TYR F  96 
 ARG   0.007   0.001   ARG J 198 

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

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

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  603 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 599
  time to evaluate  : 2.388 
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: B  289 LEU cc_start: 0.8386 (mt) cc_final: 0.8043 (mt)
REVERT: C  288 GLN cc_start: 0.7078 (pt0) cc_final: 0.6671 (pt0)
REVERT: E  228 ILE cc_start: 0.8167 (mt) cc_final: 0.7855 (mm)
REVERT: H  461 VAL cc_start: 0.7424 (t) cc_final: 0.7064 (t)
  outliers start: 4
  outliers final: 1
  residues processed: 600
  average time/residue: 0.3357
  time to fit residues: 320.3491
Evaluate side-chains
  368 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 367
  time to evaluate  : 2.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  201 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 316
   random chunks:
   chunk 266 optimal weight:    0.9990
   chunk 239 optimal weight:    2.9990
   chunk 132 optimal weight:    5.9990
   chunk 81 optimal weight:    0.7980
   chunk 161 optimal weight:    7.9990
   chunk 127 optimal weight:    9.9990
   chunk 247 optimal weight:    6.9990
   chunk 95 optimal weight:    5.9990
   chunk 150 optimal weight:    4.9990
   chunk 184 optimal weight:    8.9990
   chunk 286 optimal weight:    5.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A  26 GLN
A  89 GLN
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 154 HIS
** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 408 GLN
C 154 HIS
C 216 ASN
C 328 GLN
E 130 HIS
E 187 HIS
** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 271 ASN
E 313 HIS
F  74 HIS
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 271 ASN
G  47 GLN
G 328 GLN
** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 234 GLN
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 313 HIS

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6199
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  24141  Z= 0.237
  Angle     :  0.733  10.164  33101  Z= 0.355
  Chirality :  0.045   0.382   4059
  Planarity :  0.005   0.043   4231
  Dihedral  :  4.943  73.900   3456
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 18.38 %
    Favored  : 78.60 %
  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: -0.51 (0.15), residues: 3148
  helix:  0.65 (0.12), residues: 1761
  sheet: -1.81 (0.27), residues: 288
  loop : -1.45 (0.18), residues: 1099

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP E 231 
 HIS   0.007   0.001   HIS G 389 
 PHE   0.029   0.002   PHE G 165 
 TYR   0.026   0.002   TYR F  96 
 ARG   0.015   0.000   ARG A  52 

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

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

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  474 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 401
  time to evaluate  : 2.634 
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: A   59 MET cc_start: 0.7105 (mtp) cc_final: 0.6872 (tpp)
REVERT: E  228 ILE cc_start: 0.8516 (mt) cc_final: 0.8042 (mm)
REVERT: H   80 ASP cc_start: 0.7285 (p0) cc_final: 0.7075 (p0)
  outliers start: 73
  outliers final: 31
  residues processed: 441
  average time/residue: 0.3006
  time to fit residues: 215.2734
Evaluate side-chains
  360 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 329
  time to evaluate  : 2.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain C residue  143 LEU
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain C residue  360 TRP
Chi-restraints excluded: chain C residue  417 LEU
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain E residue  317 VAL
Chi-restraints excluded: chain F residue   10 LEU
Chi-restraints excluded: chain F residue   74 HIS
Chi-restraints excluded: chain F residue  109 ILE
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain G residue  362 ILE
Chi-restraints excluded: chain G residue  398 LEU
Chi-restraints excluded: chain H residue  118 ILE
Chi-restraints excluded: chain H residue  125 ARG
Chi-restraints excluded: chain H residue  143 LEU
Chi-restraints excluded: chain H residue  198 VAL
Chi-restraints excluded: chain H residue  360 TRP
Chi-restraints excluded: chain H residue  393 LEU
Chi-restraints excluded: chain H residue  459 ILE
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue  105 LEU
Chi-restraints excluded: chain J residue  317 VAL
Chi-restraints excluded: chain J residue  331 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 316
   random chunks:
   chunk 159 optimal weight:   40.0000
   chunk 89 optimal weight:    7.9990
   chunk 238 optimal weight:    0.0970
   chunk 195 optimal weight:   20.0000
   chunk 79 optimal weight:    2.9990
   chunk 287 optimal weight:    3.9990
   chunk 310 optimal weight:    0.1980
   chunk 256 optimal weight:    6.9990
   chunk 285 optimal weight:   20.0000
   chunk 98 optimal weight:    6.9990
   chunk 230 optimal weight:   10.0000
   overall best weight:    2.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  74 HIS
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  43 GLN
** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 408 GLN
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6244
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  24141  Z= 0.224
  Angle     :  0.740  12.811  33101  Z= 0.348
  Chirality :  0.044   0.334   4059
  Planarity :  0.005   0.055   4231
  Dihedral  :  4.654  71.878   3452
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 17.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 19.62 %
    Favored  : 76.41 %
  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: -0.04 (0.15), residues: 3148
  helix:  0.97 (0.12), residues: 1768
  sheet: -1.55 (0.27), residues: 294
  loop : -1.16 (0.18), residues: 1086

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.001   TRP E 231 
 HIS   0.014   0.001   HIS F  74 
 PHE   0.033   0.002   PHE C 244 
 TYR   0.023   0.002   TYR F  96 
 ARG   0.006   0.000   ARG H 123 

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

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

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  459 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 96
    poor density    : 363
  time to evaluate  : 2.479 
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: E  271 ASN cc_start: 0.7867 (p0) cc_final: 0.7663 (p0)
REVERT: H   80 ASP cc_start: 0.7324 (p0) cc_final: 0.7094 (p0)
  outliers start: 96
  outliers final: 54
  residues processed: 418
  average time/residue: 0.2838
  time to fit residues: 196.5406
Evaluate side-chains
  385 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 331
  time to evaluate  : 2.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   96 TYR
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  417 LEU
Chi-restraints excluded: chain C residue  143 LEU
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  354 ASN
Chi-restraints excluded: chain C residue  417 LEU
Chi-restraints excluded: chain C residue  459 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain E residue  317 VAL
Chi-restraints excluded: chain F residue   10 LEU
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   83 ASP
Chi-restraints excluded: chain F residue  109 ILE
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  155 LEU
Chi-restraints excluded: chain F residue  244 SER
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain G residue   43 GLN
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue  282 VAL
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  143 LEU
Chi-restraints excluded: chain H residue  150 LEU
Chi-restraints excluded: chain H residue  198 VAL
Chi-restraints excluded: chain H residue  245 THR
Chi-restraints excluded: chain H residue  360 TRP
Chi-restraints excluded: chain H residue  393 LEU
Chi-restraints excluded: chain H residue  430 ASN
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   67 GLN
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue  175 ASP
Chi-restraints excluded: chain J residue  246 VAL
Chi-restraints excluded: chain J residue  317 VAL
Chi-restraints excluded: chain J residue  331 LYS
Chi-restraints excluded: chain J residue  362 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 316
   random chunks:
   chunk 284 optimal weight:    2.9990
   chunk 216 optimal weight:    5.9990
   chunk 149 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 137 optimal weight:    0.1980
   chunk 193 optimal weight:    0.4980
   chunk 288 optimal weight:    0.9990
   chunk 305 optimal weight:    4.9990
   chunk 150 optimal weight:   20.0000
   chunk 273 optimal weight:    6.9990
   chunk 82 optimal weight:    8.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 GLN
C 126 GLN
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 389 HIS
E 234 GLN
** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  89 GLN
** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6244
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  24141  Z= 0.193
  Angle     :  0.739  13.423  33101  Z= 0.341
  Chirality :  0.044   0.281   4059
  Planarity :  0.004   0.047   4231
  Dihedral  :  4.540  69.602   3452
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 16.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 22.56 %
    Favored  : 74.21 %
  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:  0.28 (0.15), residues: 3148
  helix:  1.16 (0.12), residues: 1767
  sheet: -1.40 (0.27), residues: 294
  loop : -0.90 (0.19), residues: 1087

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.001   TRP E 231 
 HIS   0.004   0.001   HIS G 389 
 PHE   0.049   0.002   PHE C 401 
 TYR   0.020   0.002   TYR F  96 
 ARG   0.008   0.000   ARG J 349 

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

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

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  434 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 78
    poor density    : 356
  time to evaluate  : 2.071 
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: A   59 MET cc_start: 0.7181 (tpp) cc_final: 0.6768 (tpp)
REVERT: C  285 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7184 (mm-40)
REVERT: H   80 ASP cc_start: 0.7299 (p0) cc_final: 0.7040 (p0)
  outliers start: 78
  outliers final: 49
  residues processed: 404
  average time/residue: 0.2928
  time to fit residues: 195.6975
Evaluate side-chains
  368 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 319
  time to evaluate  : 2.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain C residue  143 LEU
Chi-restraints excluded: chain C residue  150 LEU
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  354 ASN
Chi-restraints excluded: chain C residue  459 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   85 CYS
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain E residue  317 VAL
Chi-restraints excluded: chain E residue  379 VAL
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   83 ASP
Chi-restraints excluded: chain F residue  109 ILE
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  244 SER
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue  191 SER
Chi-restraints excluded: chain G residue  398 LEU
Chi-restraints excluded: chain G residue  414 LEU
Chi-restraints excluded: chain G residue  417 LEU
Chi-restraints excluded: chain H residue  118 ILE
Chi-restraints excluded: chain H residue  125 ARG
Chi-restraints excluded: chain H residue  143 LEU
Chi-restraints excluded: chain H residue  198 VAL
Chi-restraints excluded: chain H residue  360 TRP
Chi-restraints excluded: chain H residue  393 LEU
Chi-restraints excluded: chain H residue  430 ASN
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   67 GLN
Chi-restraints excluded: chain J residue   19 LYS
Chi-restraints excluded: chain J residue  171 LEU
Chi-restraints excluded: chain J residue  246 VAL
Chi-restraints excluded: chain J residue  322 ASP
Chi-restraints excluded: chain J residue  331 LYS
Chi-restraints excluded: chain J residue  360 LEU
Chi-restraints excluded: chain J residue  362 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 316
   random chunks:
   chunk 254 optimal weight:    5.9990
   chunk 173 optimal weight:    9.9990
   chunk 4 optimal weight:    4.9990
   chunk 227 optimal weight:    5.9990
   chunk 126 optimal weight:   30.0000
   chunk 260 optimal weight:    7.9990
   chunk 211 optimal weight:    0.0980
   chunk 0 optimal weight:   30.0000
   chunk 155 optimal weight:    8.9990
   chunk 274 optimal weight:    9.9990
   chunk 77 optimal weight:   20.0000
   overall best weight:    5.0188

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  43 GLN
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 131 HIS
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 392 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6390
moved from start:          0.4121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  24141  Z= 0.287
  Angle     :  0.765  13.421  33101  Z= 0.368
  Chirality :  0.044   0.368   4059
  Planarity :  0.005   0.052   4231
  Dihedral  :  4.565  64.600   3452
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 21.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 23.47 %
    Favored  : 72.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.15), residues: 3148
  helix:  1.25 (0.12), residues: 1771
  sheet: -1.38 (0.27), residues: 290
  loop : -0.69 (0.19), residues: 1087

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP E 231 
 HIS   0.006   0.001   HIS G 389 
 PHE   0.017   0.002   PHE B 401 
 TYR   0.017   0.002   TYR D  28 
 ARG   0.007   0.001   ARG J 153 

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

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

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  441 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 107
    poor density    : 334
  time to evaluate  : 2.494 
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: A   59 MET cc_start: 0.7313 (tpp) cc_final: 0.6869 (tpp)
REVERT: C  269 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7797 (p0)
REVERT: C  285 GLN cc_start: 0.7688 (mm-40) cc_final: 0.6999 (mm-40)
REVERT: D   21 GLU cc_start: 0.7556 (mp0) cc_final: 0.7349 (pm20)
REVERT: G  443 MET cc_start: 0.7705 (mpp) cc_final: 0.7381 (mpp)
REVERT: H   80 ASP cc_start: 0.7407 (p0) cc_final: 0.7150 (p0)
  outliers start: 107
  outliers final: 72
  residues processed: 407
  average time/residue: 0.2850
  time to fit residues: 192.7077
Evaluate side-chains
  382 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 309
  time to evaluate  : 2.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain C residue   37 GLU
Chi-restraints excluded: chain C residue  130 THR
Chi-restraints excluded: chain C residue  143 LEU
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  289 LEU
Chi-restraints excluded: chain C residue  354 ASN
Chi-restraints excluded: chain C residue  417 LEU
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   85 CYS
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain E residue  317 VAL
Chi-restraints excluded: chain E residue  379 VAL
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   83 ASP
Chi-restraints excluded: chain F residue  109 ILE
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  244 SER
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain G residue   43 GLN
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue  191 SER
Chi-restraints excluded: chain G residue  232 MET
Chi-restraints excluded: chain G residue  256 LEU
Chi-restraints excluded: chain G residue  331 GLN
Chi-restraints excluded: chain G residue  398 LEU
Chi-restraints excluded: chain G residue  414 LEU
Chi-restraints excluded: chain G residue  417 LEU
Chi-restraints excluded: chain H residue  118 ILE
Chi-restraints excluded: chain H residue  125 ARG
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  143 LEU
Chi-restraints excluded: chain H residue  150 LEU
Chi-restraints excluded: chain H residue  198 VAL
Chi-restraints excluded: chain H residue  349 LEU
Chi-restraints excluded: chain H residue  360 TRP
Chi-restraints excluded: chain H residue  392 LEU
Chi-restraints excluded: chain H residue  393 LEU
Chi-restraints excluded: chain H residue  430 ASN
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   67 GLN
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue   19 LYS
Chi-restraints excluded: chain J residue  190 LEU
Chi-restraints excluded: chain J residue  246 VAL
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain J residue  317 VAL
Chi-restraints excluded: chain J residue  322 ASP
Chi-restraints excluded: chain J residue  362 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 316
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 275 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   chunk 179 optimal weight:    9.9990
   chunk 75 optimal weight:    6.9990
   chunk 305 optimal weight:    8.9990
   chunk 253 optimal weight:    0.9980
   chunk 141 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 101 optimal weight:    5.9990
   chunk 160 optimal weight:    7.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 126 GLN
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6407
moved from start:          0.4467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  24141  Z= 0.260
  Angle     :  0.776  13.259  33101  Z= 0.365
  Chirality :  0.044   0.331   4059
  Planarity :  0.005   0.048   4231
  Dihedral  :  4.532  59.590   3452
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 21.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 24.25 %
    Favored  : 71.61 %
  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:  0.57 (0.15), residues: 3148
  helix:  1.31 (0.12), residues: 1767
  sheet: -1.28 (0.27), residues: 289
  loop : -0.58 (0.19), residues: 1092

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.001   TRP E 231 
 HIS   0.005   0.001   HIS E 187 
 PHE   0.051   0.002   PHE C 401 
 TYR   0.017   0.002   TYR A  96 
 ARG   0.005   0.000   ARG J 300 

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

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

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  428 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 100
    poor density    : 328
  time to evaluate  : 2.642 
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: A   59 MET cc_start: 0.7333 (tpp) cc_final: 0.6879 (tpp)
REVERT: C  269 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7768 (p0)
REVERT: H   80 ASP cc_start: 0.7495 (p0) cc_final: 0.7257 (p0)
REVERT: H  249 VAL cc_start: 0.7806 (t) cc_final: 0.7603 (t)
  outliers start: 100
  outliers final: 72
  residues processed: 396
  average time/residue: 0.2796
  time to fit residues: 188.1684
Evaluate side-chains
  380 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 307
  time to evaluate  : 2.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain C residue   37 GLU
Chi-restraints excluded: chain C residue  130 THR
Chi-restraints excluded: chain C residue  143 LEU
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  289 LEU
Chi-restraints excluded: chain C residue  354 ASN
Chi-restraints excluded: chain C residue  417 LEU
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   85 CYS
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain E residue  317 VAL
Chi-restraints excluded: chain E residue  322 ASP
Chi-restraints excluded: chain E residue  379 VAL
Chi-restraints excluded: chain F residue   11 PHE
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   83 ASP
Chi-restraints excluded: chain F residue  109 ILE
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  244 SER
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain G residue   43 GLN
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue  191 SER
Chi-restraints excluded: chain G residue  331 GLN
Chi-restraints excluded: chain G residue  398 LEU
Chi-restraints excluded: chain G residue  414 LEU
Chi-restraints excluded: chain G residue  417 LEU
Chi-restraints excluded: chain H residue  118 ILE
Chi-restraints excluded: chain H residue  125 ARG
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  143 LEU
Chi-restraints excluded: chain H residue  198 VAL
Chi-restraints excluded: chain H residue  245 THR
Chi-restraints excluded: chain H residue  349 LEU
Chi-restraints excluded: chain H residue  356 SER
Chi-restraints excluded: chain H residue  360 TRP
Chi-restraints excluded: chain H residue  392 LEU
Chi-restraints excluded: chain H residue  393 LEU
Chi-restraints excluded: chain H residue  430 ASN
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   67 GLN
Chi-restraints excluded: chain J residue    1 MET
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue   19 LYS
Chi-restraints excluded: chain J residue  171 LEU
Chi-restraints excluded: chain J residue  175 ASP
Chi-restraints excluded: chain J residue  190 LEU
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain J residue  317 VAL
Chi-restraints excluded: chain J residue  322 ASP
Chi-restraints excluded: chain J residue  362 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 316
   random chunks:
   chunk 294 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0670
   chunk 174 optimal weight:   10.0000
   chunk 223 optimal weight:    0.4980
   chunk 172 optimal weight:    3.9990
   chunk 257 optimal weight:    2.9990
   chunk 170 optimal weight:    6.9990
   chunk 304 optimal weight:    0.2980
   chunk 190 optimal weight:    4.9990
   chunk 185 optimal weight:   20.0000
   chunk 140 optimal weight:   20.0000
   overall best weight:    1.5722

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

Flipped N/Q/H residues before XYZ refinement:
A 263 HIS
** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 126 GLN
** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  55 HIS
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6341
moved from start:          0.4589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  24141  Z= 0.190
  Angle     :  0.809  14.754  33101  Z= 0.364
  Chirality :  0.046   0.399   4059
  Planarity :  0.004   0.048   4231
  Dihedral  :  4.475  56.179   3452
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 19.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 26.16 %
    Favored  : 70.78 %
  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:  0.64 (0.15), residues: 3148
  helix:  1.37 (0.12), residues: 1758
  sheet: -1.16 (0.27), residues: 300
  loop : -0.57 (0.19), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.001   TRP E 231 
 HIS   0.006   0.001   HIS C 330 
 PHE   0.025   0.001   PHE B 401 
 TYR   0.016   0.002   TYR A  96 
 ARG   0.006   0.000   ARG C 312 

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

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

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  399 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 74
    poor density    : 325
  time to evaluate  : 2.631 
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: A   59 MET cc_start: 0.7312 (tpp) cc_final: 0.6830 (tpp)
REVERT: B    7 MET cc_start: 0.7200 (mtp) cc_final: 0.6984 (mpp)
REVERT: C  269 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7675 (p0)
REVERT: C  443 MET cc_start: 0.7734 (ptp) cc_final: 0.7523 (ptp)
REVERT: H   80 ASP cc_start: 0.7415 (p0) cc_final: 0.7167 (p0)
  outliers start: 74
  outliers final: 58
  residues processed: 379
  average time/residue: 0.2756
  time to fit residues: 176.7745
Evaluate side-chains
  363 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 59
    poor density    : 304
  time to evaluate  : 2.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain C residue  130 THR
Chi-restraints excluded: chain C residue  143 LEU
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  354 ASN
Chi-restraints excluded: chain C residue  417 LEU
Chi-restraints excluded: chain C residue  459 ILE
Chi-restraints excluded: chain C residue  469 PHE
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain E residue  317 VAL
Chi-restraints excluded: chain E residue  379 VAL
Chi-restraints excluded: chain F residue   11 PHE
Chi-restraints excluded: chain F residue   83 ASP
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  244 SER
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain G residue   43 GLN
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue  331 GLN
Chi-restraints excluded: chain G residue  414 LEU
Chi-restraints excluded: chain G residue  417 LEU
Chi-restraints excluded: chain H residue  125 ARG
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  143 LEU
Chi-restraints excluded: chain H residue  198 VAL
Chi-restraints excluded: chain H residue  349 LEU
Chi-restraints excluded: chain H residue  356 SER
Chi-restraints excluded: chain H residue  360 TRP
Chi-restraints excluded: chain H residue  392 LEU
Chi-restraints excluded: chain H residue  393 LEU
Chi-restraints excluded: chain H residue  430 ASN
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   67 GLN
Chi-restraints excluded: chain I residue   71 VAL
Chi-restraints excluded: chain J residue    1 MET
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue   19 LYS
Chi-restraints excluded: chain J residue  190 LEU
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain J residue  317 VAL
Chi-restraints excluded: chain J residue  322 ASP
Chi-restraints excluded: chain J residue  362 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 316
   random chunks:
   chunk 188 optimal weight:    0.9990
   chunk 121 optimal weight:    0.5980
   chunk 181 optimal weight:   20.0000
   chunk 91 optimal weight:    9.9990
   chunk 59 optimal weight:   30.0000
   chunk 193 optimal weight:    6.9990
   chunk 207 optimal weight:    6.9990
   chunk 150 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 239 optimal weight:    0.8980
   chunk 277 optimal weight:    9.9990
   overall best weight:    3.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6392
moved from start:          0.4804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  24141  Z= 0.232
  Angle     :  0.824  15.831  33101  Z= 0.378
  Chirality :  0.047   0.396   4059
  Planarity :  0.004   0.046   4231
  Dihedral  :  4.464  51.968   3452
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 21.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 26.86 %
    Favored  : 69.95 %
  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:  0.67 (0.15), residues: 3148
  helix:  1.38 (0.12), residues: 1755
  sheet: -1.10 (0.27), residues: 300
  loop : -0.54 (0.19), residues: 1093

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.001   TRP E 231 
 HIS   0.005   0.001   HIS C 330 
 PHE   0.017   0.001   PHE C 165 
 TYR   0.018   0.002   TYR A  96 
 ARG   0.005   0.000   ARG C 312 

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

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

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  383 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 77
    poor density    : 306
  time to evaluate  : 2.932 
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: A   59 MET cc_start: 0.7356 (tpp) cc_final: 0.7071 (tpp)
REVERT: B    7 MET cc_start: 0.7409 (mtp) cc_final: 0.7158 (mpp)
REVERT: C  269 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7669 (p0)
REVERT: H   80 ASP cc_start: 0.7508 (p0) cc_final: 0.7288 (p0)
  outliers start: 77
  outliers final: 65
  residues processed: 359
  average time/residue: 0.2859
  time to fit residues: 174.3303
Evaluate side-chains
  367 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 66
    poor density    : 301
  time to evaluate  : 2.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain C residue  130 THR
Chi-restraints excluded: chain C residue  143 LEU
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  417 LEU
Chi-restraints excluded: chain C residue  459 ILE
Chi-restraints excluded: chain C residue  469 PHE
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain E residue  317 VAL
Chi-restraints excluded: chain E residue  322 ASP
Chi-restraints excluded: chain E residue  379 VAL
Chi-restraints excluded: chain F residue   11 PHE
Chi-restraints excluded: chain F residue   83 ASP
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  244 SER
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain G residue   43 GLN
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue  331 GLN
Chi-restraints excluded: chain G residue  398 LEU
Chi-restraints excluded: chain G residue  414 LEU
Chi-restraints excluded: chain G residue  417 LEU
Chi-restraints excluded: chain H residue  125 ARG
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  143 LEU
Chi-restraints excluded: chain H residue  187 VAL
Chi-restraints excluded: chain H residue  198 VAL
Chi-restraints excluded: chain H residue  238 ASP
Chi-restraints excluded: chain H residue  349 LEU
Chi-restraints excluded: chain H residue  356 SER
Chi-restraints excluded: chain H residue  360 TRP
Chi-restraints excluded: chain H residue  392 LEU
Chi-restraints excluded: chain H residue  393 LEU
Chi-restraints excluded: chain H residue  430 ASN
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   67 GLN
Chi-restraints excluded: chain I residue   71 VAL
Chi-restraints excluded: chain J residue    1 MET
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue   19 LYS
Chi-restraints excluded: chain J residue  190 LEU
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain J residue  317 VAL
Chi-restraints excluded: chain J residue  322 ASP
Chi-restraints excluded: chain J residue  362 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 316
   random chunks:
   chunk 291 optimal weight:    2.9990
   chunk 266 optimal weight:    2.9990
   chunk 283 optimal weight:    0.9980
   chunk 170 optimal weight:    8.9990
   chunk 123 optimal weight:    1.9990
   chunk 222 optimal weight:    0.9990
   chunk 87 optimal weight:   10.0000
   chunk 256 optimal weight:    6.9990
   chunk 268 optimal weight:    6.9990
   chunk 282 optimal weight:    7.9990
   chunk 186 optimal weight:    0.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6339
moved from start:          0.4916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  24141  Z= 0.195
  Angle     :  0.842  16.839  33101  Z= 0.376
  Chirality :  0.048   0.422   4059
  Planarity :  0.004   0.047   4231
  Dihedral  :  4.409  48.116   3452
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 19.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 27.77 %
    Favored  : 69.66 %
  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:  0.70 (0.15), residues: 3148
  helix:  1.39 (0.12), residues: 1750
  sheet: -1.01 (0.27), residues: 300
  loop : -0.51 (0.19), residues: 1098

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.001   TRP E 231 
 HIS   0.006   0.001   HIS C 330 
 PHE   0.041   0.001   PHE C 244 
 TYR   0.020   0.002   TYR A  96 
 ARG   0.005   0.000   ARG C 312 

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

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

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  383 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 62
    poor density    : 321
  time to evaluate  : 2.619 
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: A   59 MET cc_start: 0.7328 (tpp) cc_final: 0.7019 (tpp)
REVERT: C  269 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7621 (p0)
REVERT: G  195 THR cc_start: 0.7587 (p) cc_final: 0.7385 (t)
REVERT: H   80 ASP cc_start: 0.7486 (p0) cc_final: 0.7268 (p0)
  outliers start: 62
  outliers final: 50
  residues processed: 368
  average time/residue: 0.2963
  time to fit residues: 185.3597
Evaluate side-chains
  359 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 308
  time to evaluate  : 2.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain C residue  143 LEU
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  417 LEU
Chi-restraints excluded: chain C residue  459 ILE
Chi-restraints excluded: chain C residue  469 PHE
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain E residue  317 VAL
Chi-restraints excluded: chain E residue  379 VAL
Chi-restraints excluded: chain F residue   11 PHE
Chi-restraints excluded: chain F residue   83 ASP
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  244 SER
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain G residue   43 GLN
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue  331 GLN
Chi-restraints excluded: chain G residue  414 LEU
Chi-restraints excluded: chain H residue   39 LEU
Chi-restraints excluded: chain H residue  125 ARG
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  143 LEU
Chi-restraints excluded: chain H residue  187 VAL
Chi-restraints excluded: chain H residue  356 SER
Chi-restraints excluded: chain H residue  360 TRP
Chi-restraints excluded: chain H residue  392 LEU
Chi-restraints excluded: chain H residue  393 LEU
Chi-restraints excluded: chain H residue  430 ASN
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   67 GLN
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue   19 LYS
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain J residue  317 VAL
Chi-restraints excluded: chain J residue  362 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 316
   random chunks:
   chunk 300 optimal weight:    4.9990
   chunk 183 optimal weight:   20.0000
   chunk 142 optimal weight:    5.9990
   chunk 208 optimal weight:   20.0000
   chunk 314 optimal weight:    8.9990
   chunk 289 optimal weight:    6.9990
   chunk 250 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 193 optimal weight:    4.9990
   chunk 153 optimal weight:   10.0000
   chunk 199 optimal weight:    9.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 187 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6497
moved from start:          0.5332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.086  24141  Z= 0.325
  Angle     :  0.876  16.402  33101  Z= 0.416
  Chirality :  0.048   0.414   4059
  Planarity :  0.005   0.048   4231
  Dihedral  :  4.569  42.237   3452
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 26.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 28.02 %
    Favored  : 69.50 %
  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:  0.70 (0.15), residues: 3148
  helix:  1.32 (0.12), residues: 1742
  sheet: -1.19 (0.26), residues: 314
  loop : -0.28 (0.20), residues: 1092

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP H 227 
 HIS   0.008   0.001   HIS C 330 
 PHE   0.021   0.002   PHE H 296 
 TYR   0.025   0.002   TYR A  96 
 ARG   0.011   0.001   ARG J 116 

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

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

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6296 Ramachandran restraints generated.
    3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 301
  time to evaluate  : 2.499 
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: A   59 MET cc_start: 0.7438 (tpp) cc_final: 0.7126 (tpp)
REVERT: B  414 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8193 (tt)
REVERT: C  269 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7728 (p0)
  outliers start: 60
  outliers final: 57
  residues processed: 345
  average time/residue: 0.2782
  time to fit residues: 162.5091
Evaluate side-chains
  352 residues out of total 2416 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 59
    poor density    : 293
  time to evaluate  : 2.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain C residue  143 LEU
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  289 LEU
Chi-restraints excluded: chain C residue  417 LEU
Chi-restraints excluded: chain C residue  459 ILE
Chi-restraints excluded: chain C residue  469 PHE
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   72 LEU
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain E residue  317 VAL
Chi-restraints excluded: chain E residue  379 VAL
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   83 ASP
Chi-restraints excluded: chain F residue  109 ILE
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain G residue   43 GLN
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue  331 GLN
Chi-restraints excluded: chain G residue  398 LEU
Chi-restraints excluded: chain G residue  414 LEU
Chi-restraints excluded: chain G residue  417 LEU
Chi-restraints excluded: chain H residue   39 LEU
Chi-restraints excluded: chain H residue  125 ARG
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  143 LEU
Chi-restraints excluded: chain H residue  187 VAL
Chi-restraints excluded: chain H residue  238 ASP
Chi-restraints excluded: chain H residue  356 SER
Chi-restraints excluded: chain H residue  360 TRP
Chi-restraints excluded: chain H residue  392 LEU
Chi-restraints excluded: chain H residue  393 LEU
Chi-restraints excluded: chain H residue  430 ASN
Chi-restraints excluded: chain H residue  458 LEU
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   67 GLN
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue   19 LYS
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain J residue  317 VAL
Chi-restraints excluded: chain J residue  362 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 316
   random chunks:
   chunk 267 optimal weight:    0.8980
   chunk 76 optimal weight:   20.0000
   chunk 231 optimal weight:    0.6980
   chunk 37 optimal weight:   20.0000
   chunk 69 optimal weight:    5.9990
   chunk 251 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   chunk 257 optimal weight:    8.9990
   chunk 31 optimal weight:    7.9990
   chunk 46 optimal weight:    4.9990
   chunk 220 optimal weight:    9.9990
   overall best weight:    3.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 348 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.043238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.036468 restraints weight = 230617.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.037131 restraints weight = 153095.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.037610 restraints weight = 117508.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.5408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080  24141  Z= 0.250
  Angle     :  0.856  16.720  33101  Z= 0.394
  Chirality :  0.048   0.403   4059
  Planarity :  0.005   0.047   4231
  Dihedral  :  4.515  39.965   3452
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 23.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 28.02 %
    Favored  : 69.25 %
  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:  0.73 (0.15), residues: 3148
  helix:  1.34 (0.12), residues: 1740
  sheet: -1.12 (0.27), residues: 296
  loop : -0.31 (0.19), residues: 1112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP C 227 
 HIS   0.006   0.001   HIS G 389 
 PHE   0.019   0.002   PHE A  11 
 TYR   0.025   0.002   TYR A  96 
 ARG   0.006   0.000   ARG D  65 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4916.04 seconds
wall clock time: 89 minutes 32.81 seconds (5372.81 seconds total)