Starting phenix.real_space_refine
on Tue Mar 19 12:34:35 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzz_22585/03_2024/7jzz_22585.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzz_22585/03_2024/7jzz_22585.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzz_22585/03_2024/7jzz_22585.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzz_22585/03_2024/7jzz_22585.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzz_22585/03_2024/7jzz_22585.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzz_22585/03_2024/7jzz_22585.pdb"
  }
  resolution = 3.2
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      60      5.49       5
     S      31      5.16       5
     C   15000      2.51       5
     N    4405      2.21       5
     O    4701      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   18": "OE1" <-> "OE2"
    Residue "A GLU   23": "OE1" <-> "OE2"
    Residue "A ASP   55": "OD1" <-> "OD2"
    Residue "A ARG   59": "NH1" <-> "NH2"
    Residue "A GLU  150": "OE1" <-> "OE2"
    Residue "A GLU  154": "OE1" <-> "OE2"
    Residue "A GLU  220": "OE1" <-> "OE2"
    Residue "A GLU  257": "OE1" <-> "OE2"
    Residue "A ARG  259": "NH1" <-> "NH2"
    Residue "A ARG  302": "NH1" <-> "NH2"
    Residue "A ASP  331": "OD1" <-> "OD2"
    Residue "A GLU  332": "OE1" <-> "OE2"
    Residue "A GLU  417": "OE1" <-> "OE2"
    Residue "A GLU  427": "OE1" <-> "OE2"
    Residue "A ASP  431": "OD1" <-> "OD2"
    Residue "B GLU    7": "OE1" <-> "OE2"
    Residue "B PHE   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG   46": "NH1" <-> "NH2"
    Residue "B ASP   53": "OD1" <-> "OD2"
    Residue "B ARG   85": "NH1" <-> "NH2"
    Residue "B GLU  100": "OE1" <-> "OE2"
    Residue "B ASP  116": "OD1" <-> "OD2"
    Residue "B GLU  125": "OE1" <-> "OE2"
    Residue "B GLU  132": "OE1" <-> "OE2"
    Residue "B ARG  151": "NH1" <-> "NH2"
    Residue "B GLU  167": "OE1" <-> "OE2"
    Residue "B ARG  169": "NH1" <-> "NH2"
    Residue "B ARG  174": "NH1" <-> "NH2"
    Residue "B ARG  175": "NH1" <-> "NH2"
    Residue "B GLU  190": "OE1" <-> "OE2"
    Residue "B GLU  198": "OE1" <-> "OE2"
    Residue "B ARG  201": "NH1" <-> "NH2"
    Residue "B GLU  206": "OE1" <-> "OE2"
    Residue "B ASP  215": "OD1" <-> "OD2"
    Residue "B PHE  221": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  243": "OD1" <-> "OD2"
    Residue "B GLU  266": "OE1" <-> "OE2"
    Residue "B ARG  268": "NH1" <-> "NH2"
    Residue "B ARG  271": "NH1" <-> "NH2"
    Residue "B ASP  272": "OD1" <-> "OD2"
    Residue "B ARG  278": "NH1" <-> "NH2"
    Residue "B GLU  281": "OE1" <-> "OE2"
    Residue "B ASP  300": "OD1" <-> "OD2"
    Residue "B TYR  304": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP    2": "OD1" <-> "OD2"
    Residue "C ASP   12": "OD1" <-> "OD2"
    Residue "C PHE   44": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU   87": "OE1" <-> "OE2"
    Residue "C GLU  110": "OE1" <-> "OE2"
    Residue "C ASP  121": "OD1" <-> "OD2"
    Residue "C GLU  124": "OE1" <-> "OE2"
    Residue "C ASP  133": "OD1" <-> "OD2"
    Residue "C ASP  140": "OD1" <-> "OD2"
    Residue "C PHE  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  169": "OE1" <-> "OE2"
    Residue "C PHE  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   33": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP   41": "OD1" <-> "OD2"
    Residue "D ASP  106": "OD1" <-> "OD2"
    Residue "D ASP  135": "OD1" <-> "OD2"
    Residue "D ARG  169": "NH1" <-> "NH2"
    Residue "D GLU  188": "OE1" <-> "OE2"
    Residue "D ASP  196": "OD1" <-> "OD2"
    Residue "D PHE  205": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  212": "OD1" <-> "OD2"
    Residue "D GLU  216": "OE1" <-> "OE2"
    Residue "D TYR  290": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  293": "OE1" <-> "OE2"
    Residue "D GLU  302": "OE1" <-> "OE2"
    Residue "D GLU  335": "OE1" <-> "OE2"
    Residue "E PHE   33": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU   57": "OE1" <-> "OE2"
    Residue "E ASP   99": "OD1" <-> "OD2"
    Residue "E ARG  169": "NH1" <-> "NH2"
    Residue "E ASP  253": "OD1" <-> "OD2"
    Residue "E ASP  256": "OD1" <-> "OD2"
    Residue "E ASP  270": "OD1" <-> "OD2"
    Residue "E TYR  290": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP  292": "OD1" <-> "OD2"
    Residue "E GLU  293": "OE1" <-> "OE2"
    Residue "E ASP  334": "OD1" <-> "OD2"
    Residue "E GLU  335": "OE1" <-> "OE2"
    Residue "F PHE   33": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU   57": "OE1" <-> "OE2"
    Residue "F ASP   80": "OD1" <-> "OD2"
    Residue "F ASP   99": "OD1" <-> "OD2"
    Residue "F ASP  130": "OD1" <-> "OD2"
    Residue "F ASP  147": "OD1" <-> "OD2"
    Residue "F ARG  169": "NH1" <-> "NH2"
    Residue "F ASP  208": "OD1" <-> "OD2"
    Residue "F ASP  212": "OD1" <-> "OD2"
    Residue "F ASP  270": "OD1" <-> "OD2"
    Residue "F ASP  292": "OD1" <-> "OD2"
    Residue "F GLU  302": "OE1" <-> "OE2"
    Residue "F GLU  335": "OE1" <-> "OE2"
    Residue "G PHE   33": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU   57": "OE1" <-> "OE2"
    Residue "G ASP   80": "OD1" <-> "OD2"
    Residue "G ASP   82": "OD1" <-> "OD2"
    Residue "G ASP  130": "OD1" <-> "OD2"
    Residue "G ARG  169": "NH1" <-> "NH2"
    Residue "G ASP  204": "OD1" <-> "OD2"
    Residue "G ASP  212": "OD1" <-> "OD2"
    Residue "G ASP  253": "OD1" <-> "OD2"
    Residue "G ASP  270": "OD1" <-> "OD2"
    Residue "G TYR  290": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU  293": "OE1" <-> "OE2"
    Residue "H ASP   53": "OD1" <-> "OD2"
    Residue "H GLU   65": "OE1" <-> "OE2"
    Residue "H ASP  130": "OD1" <-> "OD2"
    Residue "H ARG  169": "NH1" <-> "NH2"
    Residue "H ASP  196": "OD1" <-> "OD2"
    Residue "H ASP  204": "OD1" <-> "OD2"
    Residue "H GLU  216": "OE1" <-> "OE2"
    Residue "H TYR  290": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ASP  292": "OD1" <-> "OD2"
    Residue "H ASP  334": "OD1" <-> "OD2"
    Residue "I GLU   57": "OE1" <-> "OE2"
    Residue "I ASP  130": "OD1" <-> "OD2"
    Residue "I ASP  135": "OD1" <-> "OD2"
    Residue "I ASP  147": "OD1" <-> "OD2"
    Residue "I PHE  166": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ARG  169": "NH1" <-> "NH2"
    Residue "I GLU  188": "OE1" <-> "OE2"
    Residue "I ASP  204": "OD1" <-> "OD2"
    Residue "I GLU  216": "OE1" <-> "OE2"
    Residue "I ASP  240": "OD1" <-> "OD2"
    Residue "I ASP  256": "OD1" <-> "OD2"
    Residue "I ASP  270": "OD1" <-> "OD2"
    Residue "I ASP  292": "OD1" <-> "OD2"
    Residue "I ASP  334": "OD1" <-> "OD2"
    Residue "I GLU  335": "OE1" <-> "OE2"
    Residue "J GLU   81": "OE1" <-> "OE2"
    Residue "J GLU  100": "OE1" <-> "OE2"
    Residue "J GLU  119": "OE1" <-> "OE2"
    Residue "K GLU   81": "OE1" <-> "OE2"
    Residue "K GLU  100": "OE1" <-> "OE2"
    Residue "K GLU  119": "OE1" <-> "OE2"
  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: 24197
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 3088
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3088
          Classifications: {'peptide': 427}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 94}
          Link IDs: {'PTRANS': 24, 'TRANS': 402}
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 356
          Unresolved non-hydrogen angles: 457
          Unresolved non-hydrogen dihedrals: 297
          Unresolved non-hydrogen chiralities: 22
          Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 234
    Chain: "B"
      Number of atoms: 2411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2411
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 24, 'TRANS': 281}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1448
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 187, 1445
          Classifications: {'peptide': 187}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 54
      Conformer: "B"
        Number of residues, atoms: 187, 1445
          Classifications: {'peptide': 187}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 54
          bond proxies already assigned to first conformer: 1480
    Chain: "D"
      Number of atoms: 2307
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2307
          Classifications: {'peptide': 298}
          Link IDs: {'PTRANS': 10, 'TRANS': 287}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 2592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2592
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 12, 'TRANS': 322}
    Chain: "F"
      Number of atoms: 2592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2592
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 12, 'TRANS': 322}
    Chain: "G"
      Number of atoms: 2592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2592
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 12, 'TRANS': 322}
    Chain: "H"
      Number of atoms: 2554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2554
          Classifications: {'peptide': 330}
          Link IDs: {'PTRANS': 12, 'TRANS': 317}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 2592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2592
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 12, 'TRANS': 322}
    Chain: "J"
      Number of atoms: 374
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 374
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
    Chain: "K"
      Number of atoms: 374
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 374
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
    Chain: "M"
      Number of atoms: 1273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 1273
          Classifications: {'DNA': 1, 'RNA': 60}
          Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14}
          Link IDs: {'rna2p': 28, 'rna3p': 32}
          Unresolved chain link angles: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'  C:plan': 1, '  C:plan2': 1}
          Unresolved non-hydrogen planarities: 11
  Time building chain proxies: 13.84, per 1000 atoms: 0.57
  Number of scatterers: 24197
  At special positions: 0
  Unit cell: (131.25, 156.45, 148.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      31     16.00
     P      60     15.00
     O    4701      8.00
     N    4405      7.00
     C   15000      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: 9.49
  Conformation dependent library (CDL) restraints added in 4.9 seconds
  

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5534

  Finding SS restraints...
    Secondary structure from input PDB file:
      83 helices and 54 sheets defined
      33.3% alpha, 20.6% beta
      6 base pairs and 28 stacking pairs defined.
    Time for finding SS restraints: 8.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 31
    Processing helix  chain 'A' and resid 38 through 47
      removed outlier: 4.072A  pdb=" N   THR A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 60
    Processing helix  chain 'A' and resid 61 through 63
      No H-bonds generated for 'chain 'A' and resid 61 through 63'
    Processing helix  chain 'A' and resid 114 through 122
      removed outlier: 4.312A  pdb=" N   PHE A 118 " --> pdb=" O   ALA A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 136
      removed outlier: 3.766A  pdb=" N   GLU A 136 " --> pdb=" O   ASN A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 161
      removed outlier: 3.756A  pdb=" N   ALA A 152 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLY A 161 " --> pdb=" O   GLN A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 164
      No H-bonds generated for 'chain 'A' and resid 162 through 164'
    Processing helix  chain 'A' and resid 196 through 211
    Processing helix  chain 'A' and resid 212 through 225
      removed outlier: 3.668A  pdb=" N   ALA A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   SER A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 251
      removed outlier: 3.521A  pdb=" N   ILE A 251 " --> pdb=" O   PRO A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 258
      removed outlier: 4.070A  pdb=" N   GLU A 257 " --> pdb=" O   GLN A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 4.497A  pdb=" N   GLN A 273 " --> pdb=" O   PRO A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 289
    Processing helix  chain 'A' and resid 294 through 306
      removed outlier: 3.553A  pdb=" N   SER A 298 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   THR A 303 " --> pdb=" O   ARG A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 344
      removed outlier: 4.506A  pdb=" N   ALA A 317 " --> pdb=" O   HIS A 313 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLU A 344 " --> pdb=" O   LEU A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 349
    Processing helix  chain 'A' and resid 363 through 369
      removed outlier: 3.748A  pdb=" N   ALA A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 381
      removed outlier: 3.821A  pdb=" N   GLY A 381 " --> pdb=" O   ARG A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 396
      removed outlier: 4.080A  pdb=" N   ARG A 390 " --> pdb=" O   GLU A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 408
    Processing helix  chain 'A' and resid 409 through 430
    Processing helix  chain 'B' and resid 33 through 49
      removed outlier: 3.955A  pdb=" N   PHE B  37 " --> pdb=" O   SER B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 121
      removed outlier: 3.903A  pdb=" N   ASP B 120 " --> pdb=" O   ASP B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 135
    Processing helix  chain 'B' and resid 165 through 180
    Processing helix  chain 'B' and resid 189 through 204
      removed outlier: 3.901A  pdb=" N   LEU B 193 " --> pdb=" O   ARG B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 218
    Processing helix  chain 'C' and resid 16 through 36
      removed outlier: 3.503A  pdb=" N   LEU C  20 " --> pdb=" O   PRO C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 72
      removed outlier: 3.917A  pdb=" N   ALA C  72 " --> pdb=" O   ARG C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 77
      removed outlier: 3.506A  pdb=" N   LEU C  76 " --> pdb=" O   ARG C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 121
    Processing helix  chain 'C' and resid 123 through 131
    Processing helix  chain 'C' and resid 132 through 136
      removed outlier: 4.012A  pdb=" N   VAL C 135 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ALA C 136 " --> pdb=" O   ASP C 133 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 132 through 136'
    Processing helix  chain 'D' and resid 51 through 55
    Processing helix  chain 'D' and resid 130 through 148
    Processing helix  chain 'D' and resid 151 through 163
    Processing helix  chain 'D' and resid 208 through 223
      removed outlier: 3.788A  pdb=" N   ALA D 213 " --> pdb=" O   ALA D 209 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 284
    Processing helix  chain 'D' and resid 322 through 332
      removed outlier: 3.542A  pdb=" N   LEU D 326 " --> pdb=" O   ASP D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 338 through 352
    Processing helix  chain 'E' and resid 82 through 92
      removed outlier: 3.732A  pdb=" N   SER E  92 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 130 through 148
    Processing helix  chain 'E' and resid 151 through 163
    Processing helix  chain 'E' and resid 209 through 223
      removed outlier: 3.506A  pdb=" N   ALA E 213 " --> pdb=" O   ALA E 209 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 275 through 284
    Processing helix  chain 'E' and resid 293 through 297
      removed outlier: 3.627A  pdb=" N   LEU E 296 " --> pdb=" O   GLU E 293 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLY E 297 " --> pdb=" O   ASP E 294 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 293 through 297'
    Processing helix  chain 'E' and resid 322 through 332
    Processing helix  chain 'E' and resid 338 through 352
    Processing helix  chain 'F' and resid 51 through 55
    Processing helix  chain 'F' and resid 82 through 91
    Processing helix  chain 'F' and resid 130 through 148
    Processing helix  chain 'F' and resid 151 through 163
      removed outlier: 3.506A  pdb=" N   ARG F 155 " --> pdb=" O   ALA F 151 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 208 through 223
    Processing helix  chain 'F' and resid 275 through 284
    Processing helix  chain 'F' and resid 293 through 297
      removed outlier: 3.728A  pdb=" N   LEU F 296 " --> pdb=" O   GLU F 293 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY F 297 " --> pdb=" O   ASP F 294 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 293 through 297'
    Processing helix  chain 'F' and resid 322 through 332
    Processing helix  chain 'F' and resid 338 through 352
    Processing helix  chain 'G' and resid 82 through 91
    Processing helix  chain 'G' and resid 130 through 148
    Processing helix  chain 'G' and resid 151 through 163
    Processing helix  chain 'G' and resid 209 through 223
      removed outlier: 3.556A  pdb=" N   ALA G 213 " --> pdb=" O   ALA G 209 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 275 through 284
    Processing helix  chain 'G' and resid 322 through 332
    Processing helix  chain 'G' and resid 338 through 352
    Processing helix  chain 'H' and resid 51 through 55
    Processing helix  chain 'H' and resid 82 through 92
      removed outlier: 3.606A  pdb=" N   SER H  92 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 130 through 148
    Processing helix  chain 'H' and resid 150 through 163
      removed outlier: 3.526A  pdb=" N   ALA H 154 " --> pdb=" O   PHE H 150 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 208 through 223
    Processing helix  chain 'H' and resid 275 through 284
    Processing helix  chain 'H' and resid 322 through 331
      removed outlier: 3.566A  pdb=" N   LEU H 326 " --> pdb=" O   ASP H 322 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 338 through 352
    Processing helix  chain 'I' and resid 51 through 55
    Processing helix  chain 'I' and resid 82 through 90
    Processing helix  chain 'I' and resid 130 through 148
    Processing helix  chain 'I' and resid 152 through 163
    Processing helix  chain 'I' and resid 208 through 224
    Processing helix  chain 'I' and resid 275 through 284
    Processing helix  chain 'I' and resid 322 through 332
      removed outlier: 3.638A  pdb=" N   LEU I 326 " --> pdb=" O   ASP I 322 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 338 through 352
    Processing helix  chain 'J' and resid 109 through 121
    Processing helix  chain 'K' and resid 109 through 121
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66
    Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69
    Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192
      removed outlier: 6.251A  pdb=" N   ALA A 191 " --> pdb=" O   VAL B 280 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   ASN B 282 " --> pdb=" O   ALA A 191 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192
      removed outlier: 6.251A  pdb=" N   ALA A 191 " --> pdb=" O   VAL B 280 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   ASN B 282 " --> pdb=" O   ALA A 191 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLY B 254 " --> pdb=" O   LEU B 283 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   GLY B 285 " --> pdb=" O   PRO B 252 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   GLY B 287 " --> pdb=" O   PRO B 250 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   TRP B 289 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   LEU B 248 " --> pdb=" O   TRP B 289 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 267
      removed outlier: 5.861A  pdb=" N   LEU A 265 " --> pdb=" O   TRP B  29 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 61
      removed outlier: 4.012A  pdb=" N   VAL B  59 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   LEU B 110 " --> pdb=" O   VAL B  59 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 68
      removed outlier: 5.093A  pdb=" N   ALA B 103 " --> pdb=" O   ASN B  19 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ASN B  19 " --> pdb=" O   ALA B 103 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   SER B  16 " --> pdb=" O   LEU B 145 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 71
    Processing sheet with id=AA9, first strand: chain 'B' and resid 221 through 222
    Processing sheet with id=AB1, first strand: chain 'B' and resid 304 through 306
      removed outlier: 3.617A  pdb=" N   SER B 317 " --> pdb=" O   TYR B 304 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 43
      removed outlier: 3.501A  pdb=" N   HIS C   3 " --> pdb=" O   ALA C  62 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 41 through 43
      removed outlier: 3.501A  pdb=" N   HIS C   3 " --> pdb=" O   ALA C  62 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 97 through 98
    Processing sheet with id=AB5, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AB6, first strand: chain 'C' and resid 172 through 173
      removed outlier: 3.876A  pdb=" N   GLY C 172 " --> pdb=" O   LYS C 180 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 127 through 128
    Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 39
      removed outlier: 4.058A  pdb=" N   VAL D 228 " --> pdb=" O   VAL D 118 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ARG D 191 " --> pdb=" O   HIS D 183 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 39
    Processing sheet with id=AC1, first strand: chain 'D' and resid 64 through 66
    Processing sheet with id=AC2, first strand: chain 'D' and resid 248 through 249
      removed outlier: 4.300A  pdb=" N   THR D 264 " --> pdb=" O   GLU D 249 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 285 through 287
    Processing sheet with id=AC4, first strand: chain 'D' and resid 306 through 307
    Processing sheet with id=AC5, first strand: chain 'E' and resid 127 through 128
    Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 39
      removed outlier: 4.103A  pdb=" N   VAL E 228 " --> pdb=" O   VAL E 118 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   LEU E 229 " --> pdb=" O   ILE E 184 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   VAL E 177 " --> pdb=" O   ASP E 196 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   ASP E 196 " --> pdb=" O   VAL E 177 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL E 179 " --> pdb=" O   ARG E 194 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ARG E 194 " --> pdb=" O   VAL E 179 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ILE E 181 " --> pdb=" O   ALA E 192 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   ALA E 192 " --> pdb=" O   ILE E 181 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   HIS E 183 " --> pdb=" O   ALA E 190 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'E' and resid 38 through 39
    Processing sheet with id=AC8, first strand: chain 'E' and resid 63 through 70
    Processing sheet with id=AC9, first strand: chain 'E' and resid 248 through 249
      removed outlier: 4.417A  pdb=" N   THR E 264 " --> pdb=" O   GLU E 249 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'E' and resid 285 through 287
    Processing sheet with id=AD2, first strand: chain 'E' and resid 306 through 307
      removed outlier: 3.741A  pdb=" N   LYS E 312 " --> pdb=" O   VAL E 307 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'F' and resid 127 through 128
    Processing sheet with id=AD4, first strand: chain 'F' and resid 38 through 39
      removed outlier: 4.095A  pdb=" N   VAL F 228 " --> pdb=" O   VAL F 118 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   LEU F 229 " --> pdb=" O   ILE F 184 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   VAL F 177 " --> pdb=" O   ASP F 196 " (cutoff:3.500A)
      removed outlier: 4.972A  pdb=" N   ASP F 196 " --> pdb=" O   VAL F 177 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   VAL F 179 " --> pdb=" O   ARG F 194 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   ARG F 194 " --> pdb=" O   VAL F 179 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ILE F 181 " --> pdb=" O   ALA F 192 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   ALA F 192 " --> pdb=" O   ILE F 181 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   HIS F 183 " --> pdb=" O   ALA F 190 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'F' and resid 38 through 39
    Processing sheet with id=AD6, first strand: chain 'F' and resid 63 through 70
    Processing sheet with id=AD7, first strand: chain 'F' and resid 285 through 287
    Processing sheet with id=AD8, first strand: chain 'F' and resid 306 through 307
      removed outlier: 3.658A  pdb=" N   LYS F 312 " --> pdb=" O   VAL F 307 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'G' and resid 127 through 128
    Processing sheet with id=AE1, first strand: chain 'G' and resid 38 through 39
      removed outlier: 4.209A  pdb=" N   VAL G 228 " --> pdb=" O   VAL G 118 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   LEU G 229 " --> pdb=" O   ILE G 184 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   VAL G 177 " --> pdb=" O   ASP G 196 " (cutoff:3.500A)
      removed outlier: 4.890A  pdb=" N   ASP G 196 " --> pdb=" O   VAL G 177 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   VAL G 179 " --> pdb=" O   ARG G 194 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ARG G 194 " --> pdb=" O   VAL G 179 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   ILE G 181 " --> pdb=" O   ALA G 192 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ALA G 192 " --> pdb=" O   ILE G 181 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   HIS G 183 " --> pdb=" O   ALA G 190 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'G' and resid 38 through 39
    Processing sheet with id=AE3, first strand: chain 'G' and resid 64 through 70
      removed outlier: 4.284A  pdb=" N   PHE J 104 " --> pdb=" O   LEU G  95 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   THR G  97 " --> pdb=" O   PHE J 104 " (cutoff:3.500A)
      removed outlier: 11.660A  pdb=" N   CYS J 106 " --> pdb=" O   THR G  97 " (cutoff:3.500A)
      removed outlier: 14.496A  pdb=" N   ASP G  99 " --> pdb=" O   CYS J 106 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   PHE J 104 " --> pdb=" O   LYS J  94 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   LYS J  94 " --> pdb=" O   PHE J 104 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'G' and resid 248 through 249
      removed outlier: 4.600A  pdb=" N   THR G 264 " --> pdb=" O   GLU G 249 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'G' and resid 285 through 287
    Processing sheet with id=AE6, first strand: chain 'G' and resid 306 through 307
    Processing sheet with id=AE7, first strand: chain 'H' and resid 127 through 128
    Processing sheet with id=AE8, first strand: chain 'H' and resid 38 through 39
      removed outlier: 4.055A  pdb=" N   VAL H 228 " --> pdb=" O   VAL H 118 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   LEU H 229 " --> pdb=" O   ILE H 184 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ARG H 191 " --> pdb=" O   HIS H 183 " (cutoff:3.500A)
    Processing sheet with id=AE9, first strand: chain 'H' and resid 38 through 39
    Processing sheet with id=AF1, first strand: chain 'H' and resid 63 through 70
      removed outlier: 3.579A  pdb=" N   ASN H  94 " --> pdb=" O   GLY H  70 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ALA H 101 " --> pdb=" O   VAL H 244 " (cutoff:3.500A)
    Processing sheet with id=AF2, first strand: chain 'H' and resid 285 through 287
    Processing sheet with id=AF3, first strand: chain 'H' and resid 306 through 307
      removed outlier: 3.535A  pdb=" N   LYS H 312 " --> pdb=" O   VAL H 307 " (cutoff:3.500A)
    Processing sheet with id=AF4, first strand: chain 'I' and resid 127 through 128
    Processing sheet with id=AF5, first strand: chain 'I' and resid 38 through 39
      removed outlier: 4.697A  pdb=" N   LEU I 229 " --> pdb=" O   ILE I 184 " (cutoff:3.500A)
    Processing sheet with id=AF6, first strand: chain 'I' and resid 189 through 192
      removed outlier: 6.666A  pdb=" N   HIS I 183 " --> pdb=" O   ALA I 190 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   ALA I 192 " --> pdb=" O   ILE I 181 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ILE I 181 " --> pdb=" O   ALA I 192 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   LEU I 229 " --> pdb=" O   ILE I 184 " (cutoff:3.500A)
    Processing sheet with id=AF7, first strand: chain 'I' and resid 63 through 70
      removed outlier: 3.583A  pdb=" N   VAL I  68 " --> pdb=" O   GLN I  96 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   ALA I 101 " --> pdb=" O   VAL I 244 " (cutoff:3.500A)
    Processing sheet with id=AF8, first strand: chain 'I' and resid 63 through 70
      removed outlier: 3.583A  pdb=" N   VAL I  68 " --> pdb=" O   GLN I  96 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   THR I  97 " --> pdb=" O   PHE K 104 " (cutoff:3.500A)
      removed outlier: 11.844A  pdb=" N   CYS K 106 " --> pdb=" O   THR I  97 " (cutoff:3.500A)
      removed outlier: 14.427A  pdb=" N   ASP I  99 " --> pdb=" O   CYS K 106 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   PHE K 104 " --> pdb=" O   LYS K  94 " (cutoff:3.500A)
      removed outlier: 5.672A  pdb=" N   LYS K  94 " --> pdb=" O   PHE K 104 " (cutoff:3.500A)
    Processing sheet with id=AF9, first strand: chain 'I' and resid 285 through 287

    1022 hydrogen bonds defined for protein.
    2802 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      16 hydrogen bonds
      28 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      28 stacking parallelities
  Total time for adding SS restraints: 7.81

  Time building geometry restraints manager: 10.33 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 5057
        1.32 -     1.45: 6221
        1.45 -     1.57: 13363
        1.57 -     1.70: 120
        1.70 -     1.82: 46
  Bond restraints: 24807
  Sorted by residual:
  bond pdb=" O3'   A M  36 "
       pdb=" P     C M  37 "
    ideal  model  delta    sigma   weight residual
    1.607  1.675 -0.068 1.50e-02 4.44e+03 2.05e+01
  bond pdb=" C   LEU B 181 "
       pdb=" N   PRO B 182 "
    ideal  model  delta    sigma   weight residual
    1.337  1.378 -0.041 9.80e-03 1.04e+04 1.77e+01
  bond pdb=" CB  ARG G 237 "
       pdb=" CG  ARG G 237 "
    ideal  model  delta    sigma   weight residual
    1.520  1.432  0.088 3.00e-02 1.11e+03 8.56e+00
  bond pdb=" N   LEU H 250 "
       pdb=" CA  LEU H 250 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.22e-02 6.72e+03 7.35e+00
  bond pdb=" CB  ILE H 238 "
       pdb=" CG2 ILE H 238 "
    ideal  model  delta    sigma   weight residual
    1.521  1.437  0.084 3.30e-02 9.18e+02 6.47e+00
  ... (remaining 24802 not shown)

  Histogram of bond angle deviations from ideal:
       99.49 -   106.42: 987
      106.42 -   113.34: 13506
      113.34 -   120.26: 9339
      120.26 -   127.18: 9700
      127.18 -   134.11: 427
  Bond angle restraints: 33959
  Sorted by residual:
  angle pdb=" C   ILE F 251 "
        pdb=" N   LEU F 252 "
        pdb=" CA  LEU F 252 "
      ideal   model   delta    sigma   weight residual
     120.44  128.28   -7.84 1.30e+00 5.92e-01 3.63e+01
  angle pdb=" C   GLU D 188 "
        pdb=" N   VAL D 189 "
        pdb=" CA  VAL D 189 "
      ideal   model   delta    sigma   weight residual
     121.97  126.85   -4.88 1.00e+00 1.00e+00 2.38e+01
  angle pdb=" C   LYS H  77 "
        pdb=" N   THR H  78 "
        pdb=" CA  THR H  78 "
      ideal   model   delta    sigma   weight residual
     121.54  130.83   -9.29 1.91e+00 2.74e-01 2.36e+01
  angle pdb=" C   GLN A 124 "
        pdb=" N   TYR A 125 "
        pdb=" CA  TYR A 125 "
      ideal   model   delta    sigma   weight residual
     120.79  127.48   -6.69 1.39e+00 5.18e-01 2.32e+01
  angle pdb=" N   GLY H 356 "
        pdb=" CA  GLY H 356 "
        pdb=" C   GLY H 356 "
      ideal   model   delta    sigma   weight residual
     111.95  107.48    4.47 9.50e-01 1.11e+00 2.22e+01
  ... (remaining 33954 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.93: 14475
       35.93 -    71.86: 461
       71.86 -   107.79: 32
      107.79 -   143.72: 3
      143.72 -   179.65: 4
  Dihedral angle restraints: 14975
    sinusoidal: 6401
      harmonic: 8574
  Sorted by residual:
  dihedral pdb=" O4'   U M  21 "
           pdb=" C1'   U M  21 "
           pdb=" N1    U M  21 "
           pdb=" C2    U M  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   60.96  139.04     1      1.50e+01 4.44e-03 7.49e+01
  dihedral pdb=" O4'   U M  33 "
           pdb=" C1'   U M  33 "
           pdb=" N1    U M  33 "
           pdb=" C2    U M  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   72.55  127.45     1      1.50e+01 4.44e-03 6.86e+01
  dihedral pdb=" O4'   C M  37 "
           pdb=" C1'   C M  37 "
           pdb=" N1    C M  37 "
           pdb=" C2    C M  37 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   51.65 -179.65     1      1.70e+01 3.46e-03 6.64e+01
  ... (remaining 14972 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 2710
       0.053 -    0.106: 882
       0.106 -    0.158: 194
       0.158 -    0.211: 22
       0.211 -    0.264: 7
  Chirality restraints: 3815
  Sorted by residual:
  chirality pdb=" C3'   U M  33 "
            pdb=" C4'   U M  33 "
            pdb=" O3'   U M  33 "
            pdb=" C2'   U M  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.74    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CG  LEU B 197 "
            pdb=" CB  LEU B 197 "
            pdb=" CD1 LEU B 197 "
            pdb=" CD2 LEU B 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CB  ILE C  60 "
            pdb=" CA  ILE C  60 "
            pdb=" CG1 ILE C  60 "
            pdb=" CG2 ILE C  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.64e+00
  ... (remaining 3812 not shown)

  Planarity restraints: 4261
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER K  96 "    0.052 5.00e-02 4.00e+02   7.96e-02 1.01e+01
        pdb=" N   PRO K  97 "   -0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO K  97 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO K  97 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER J  96 "   -0.052 5.00e-02 4.00e+02   7.95e-02 1.01e+01
        pdb=" N   PRO J  97 "    0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO J  97 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO J  97 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 294 "    0.049 5.00e-02 4.00e+02   7.35e-02 8.63e+00
        pdb=" N   PRO A 295 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 295 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 295 "    0.041 5.00e-02 4.00e+02
  ... (remaining 4258 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 3690
        2.75 -     3.29: 21875
        3.29 -     3.82: 42249
        3.82 -     4.36: 51039
        4.36 -     4.90: 86828
  Nonbonded interactions: 205681
  Sorted by model distance:
  nonbonded pdb=" OH  TYR G 324 "
            pdb=" O   SER H  73 "
     model   vdw
     2.209 2.440
  nonbonded pdb=" OH  TYR E 324 "
            pdb=" O   SER F  73 "
     model   vdw
     2.227 2.440
  nonbonded pdb=" OH  TYR D 324 "
            pdb=" O   SER E  73 "
     model   vdw
     2.256 2.440
  nonbonded pdb=" OH  TYR H 324 "
            pdb=" O   SER I  73 "
     model   vdw
     2.260 2.440
  nonbonded pdb=" OH  TYR F 324 "
            pdb=" O   SER G  73 "
     model   vdw
     2.266 2.440
  ... (remaining 205676 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 'D'
  selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 
 358))
  selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 
 358))
  selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 
 358))
  selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 
 358))
  selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 
 358))
}
ncs_group {
  reference = chain 'J'
  selection = chain 'K'
}

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=0.37 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.810
  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:          5.190
  Check model and map are aligned:         0.440
  Set scattering table:                    0.270
  Process input model:                     71.260
  Find NCS groups from input model:        1.440
  Set up NCS constraints:                  0.120
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   82.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
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      :  0.010   0.088  24807  Z= 0.692
  Angle     :  0.977  10.390  33959  Z= 0.551
  Chirality :  0.054   0.264   3815
  Planarity :  0.007   0.080   4261
  Dihedral  : 17.227 179.653   9441
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  9.21 %
    Favored  : 90.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.74 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.65 (0.12), residues: 2949
  helix: -2.63 (0.11), residues: 917
  sheet: -1.09 (0.22), residues: 490
  loop : -2.79 (0.12), residues: 1542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP F  49 
 HIS   0.007   0.002   HIS D 343 
 PHE   0.020   0.002   PHE C 155 
 TYR   0.039   0.003   TYR H 304 
 ARG   0.019   0.001   ARG G 117 

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

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

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 332
  time to evaluate  : 2.554 
Fit side-chains
REVERT: A  200 HIS cc_start: 0.8299 (t-90) cc_final: 0.7685 (t-90)
REVERT: A  235 TYR cc_start: 0.8279 (m-80) cc_final: 0.7967 (m-80)
REVERT: A  331 ASP cc_start: 0.7145 (m-30) cc_final: 0.6454 (m-30)
REVERT: A  424 MET cc_start: 0.8076 (mmm) cc_final: 0.7745 (mtt)
REVERT: B  170 ARG cc_start: 0.7660 (ttp80) cc_final: 0.6780 (mtm110)
REVERT: B  189 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7882 (mtp85)
REVERT: B  218 ARG cc_start: 0.7608 (ptt180) cc_final: 0.7208 (ptt-90)
REVERT: B  268 ARG cc_start: 0.7511 (tpt170) cc_final: 0.7145 (ttt90)
REVERT: C   84 GLN cc_start: 0.7923 (pt0) cc_final: 0.7680 (pt0)
REVERT: C  110 GLU cc_start: 0.8138 (mp0) cc_final: 0.7929 (mp0)
REVERT: C  143 PHE cc_start: 0.7368 (p90) cc_final: 0.6611 (p90)
REVERT: D  294 ASP cc_start: 0.7660 (t0) cc_final: 0.7432 (t0)
REVERT: F   77 LYS cc_start: 0.8285 (mtpt) cc_final: 0.8066 (mtmt)
REVERT: F  258 LYS cc_start: 0.7346 (mmpt) cc_final: 0.6880 (mmpt)
REVERT: F  269 ARG cc_start: 0.7609 (ptp-170) cc_final: 0.7403 (ptp-170)
REVERT: H   72 ILE cc_start: 0.8914 (tp) cc_final: 0.8640 (tp)
REVERT: H   94 ASN cc_start: 0.8251 (p0) cc_final: 0.7287 (t0)
REVERT: I   99 ASP cc_start: 0.8349 (m-30) cc_final: 0.7877 (m-30)
REVERT: I  185 ARG cc_start: 0.7770 (tpp80) cc_final: 0.7386 (mmt90)
REVERT: I  249 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7871 (mt-10)
REVERT: I  261 LYS cc_start: 0.7860 (mttt) cc_final: 0.7537 (mttt)
REVERT: I  329 ASN cc_start: 0.7849 (m-40) cc_final: 0.7626 (m-40)
REVERT: J  114 ASN cc_start: 0.8355 (m-40) cc_final: 0.8052 (m-40)
REVERT: K   82 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8233 (ttmt)
REVERT: K   90 ASN cc_start: 0.8197 (t0) cc_final: 0.7680 (t0)
  outliers start: 14
  outliers final: 4
  residues processed: 341
  average time/residue: 0.4718
  time to fit residues: 228.6046
Evaluate side-chains
  229 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 225
  time to evaluate  : 2.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  300 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 298
   random chunks:
   chunk 251 optimal weight:    1.9990
   chunk 225 optimal weight:    1.9990
   chunk 125 optimal weight:    0.0980
   chunk 77 optimal weight:    3.9990
   chunk 152 optimal weight:    3.9990
   chunk 120 optimal weight:    1.9990
   chunk 233 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 142 optimal weight:    3.9990
   chunk 173 optimal weight:    0.9980
   chunk 270 optimal weight:    2.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 203 HIS
** B  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  29 HIS
C  84 GLN
** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 348 ASN
G 163 ASN
** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 159 HIS
H 348 ASN
** I  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 102 ASN
K 114 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  24807  Z= 0.215
  Angle     :  0.579   9.066  33959  Z= 0.303
  Chirality :  0.040   0.189   3815
  Planarity :  0.005   0.058   4261
  Dihedral  : 15.421 179.362   4201
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.69 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.74 %
    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: -2.21 (0.14), residues: 2949
  helix: -0.50 (0.15), residues: 922
  sheet: -0.55 (0.22), residues: 482
  loop : -2.46 (0.13), residues: 1545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP I  49 
 HIS   0.006   0.001   HIS A 203 
 PHE   0.024   0.001   PHE A 391 
 TYR   0.017   0.002   TYR C  97 
 ARG   0.008   0.000   ARG G 237 

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

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

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 261
  time to evaluate  : 2.635 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.5237 (OUTLIER) cc_final: 0.3419 (p-90)
REVERT: A  200 HIS cc_start: 0.8273 (t-90) cc_final: 0.7771 (t-90)
REVERT: A  235 TYR cc_start: 0.8130 (m-80) cc_final: 0.7755 (m-80)
REVERT: A  414 TRP cc_start: 0.6773 (t-100) cc_final: 0.6562 (t-100)
REVERT: B  170 ARG cc_start: 0.7748 (ttp80) cc_final: 0.6943 (mtm110)
REVERT: B  189 ARG cc_start: 0.8110 (mtp85) cc_final: 0.7909 (mtp85)
REVERT: B  218 ARG cc_start: 0.7376 (ptt180) cc_final: 0.7065 (ptt-90)
REVERT: C   44 PHE cc_start: 0.8516 (m-80) cc_final: 0.8262 (m-10)
REVERT: C  143 PHE cc_start: 0.7302 (p90) cc_final: 0.6478 (p90)
REVERT: D  294 ASP cc_start: 0.7710 (t0) cc_final: 0.7507 (t0)
REVERT: G  206 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7800 (mtmt)
REVERT: H   72 ILE cc_start: 0.8888 (tp) cc_final: 0.8662 (tp)
REVERT: H   94 ASN cc_start: 0.7927 (p0) cc_final: 0.7348 (t0)
REVERT: I   34 GLU cc_start: 0.8218 (tt0) cc_final: 0.7938 (tt0)
REVERT: I  185 ARG cc_start: 0.7759 (tpp80) cc_final: 0.7375 (tpp-160)
REVERT: J   99 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7563 (p-80)
REVERT: J  114 ASN cc_start: 0.8374 (m-40) cc_final: 0.8159 (m-40)
REVERT: K   82 LYS cc_start: 0.8687 (ttmt) cc_final: 0.8378 (tttm)
REVERT: K   90 ASN cc_start: 0.8400 (t0) cc_final: 0.7997 (t0)
REVERT: K   99 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.5767 (p-80)
  outliers start: 39
  outliers final: 27
  residues processed: 286
  average time/residue: 0.4162
  time to fit residues: 177.3711
Evaluate side-chains
  267 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 237
  time to evaluate  : 2.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain D residue   38 ASP
Chi-restraints excluded: chain E residue  304 TYR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue  143 THR
Chi-restraints excluded: chain F residue  304 TYR
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain G residue   68 VAL
Chi-restraints excluded: chain G residue  203 ARG
Chi-restraints excluded: chain G residue  237 ARG
Chi-restraints excluded: chain G residue  250 LEU
Chi-restraints excluded: chain G residue  304 TYR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain H residue  348 ASN
Chi-restraints excluded: chain I residue   71 THR
Chi-restraints excluded: chain J residue   99 HIS
Chi-restraints excluded: chain J residue  117 ILE
Chi-restraints excluded: chain K residue   99 HIS
Chi-restraints excluded: chain K residue  117 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 298
   random chunks:
   chunk 150 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   chunk 225 optimal weight:    0.7980
   chunk 184 optimal weight:    1.9990
   chunk 74 optimal weight:    9.9990
   chunk 271 optimal weight:    5.9990
   chunk 292 optimal weight:    6.9990
   chunk 241 optimal weight:    0.7980
   chunk 268 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 217 optimal weight:    0.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 203 HIS
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 102 ASN
I 159 HIS
I 183 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  24807  Z= 0.280
  Angle     :  0.568   6.997  33959  Z= 0.295
  Chirality :  0.040   0.261   3815
  Planarity :  0.004   0.050   4261
  Dihedral  : 15.213 179.648   4201
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.69 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.74 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.14), residues: 2949
  helix:  0.43 (0.16), residues: 923
  sheet: -0.27 (0.23), residues: 491
  loop : -2.29 (0.14), residues: 1535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E  49 
 HIS   0.010   0.001   HIS A 203 
 PHE   0.015   0.001   PHE D 245 
 TYR   0.013   0.002   TYR D 304 
 ARG   0.005   0.000   ARG G 237 

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

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

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 61
    poor density    : 249
  time to evaluate  : 2.684 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.5244 (OUTLIER) cc_final: 0.3744 (p-90)
REVERT: A  200 HIS cc_start: 0.8322 (t-90) cc_final: 0.7822 (t-90)
REVERT: A  228 TRP cc_start: 0.7732 (t-100) cc_final: 0.7478 (t-100)
REVERT: A  235 TYR cc_start: 0.8079 (m-80) cc_final: 0.7713 (m-80)
REVERT: B  170 ARG cc_start: 0.7749 (ttp80) cc_final: 0.6943 (mtm110)
REVERT: B  218 ARG cc_start: 0.7277 (ptt180) cc_final: 0.7015 (ptt-90)
REVERT: C    1 MET cc_start: 0.6270 (mtt) cc_final: 0.5645 (ttp)
REVERT: C  143 PHE cc_start: 0.7274 (p90) cc_final: 0.6380 (p90)
REVERT: C  186 TRP cc_start: 0.7667 (t-100) cc_final: 0.7450 (t-100)
REVERT: G  206 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7766 (mtmt)
REVERT: H   72 ILE cc_start: 0.8808 (tp) cc_final: 0.8588 (tp)
REVERT: H   94 ASN cc_start: 0.7939 (p0) cc_final: 0.7313 (t0)
REVERT: I   34 GLU cc_start: 0.8174 (tt0) cc_final: 0.7717 (tt0)
REVERT: I  185 ARG cc_start: 0.7801 (tpp80) cc_final: 0.7360 (tpp-160)
REVERT: I  254 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7592 (mppt)
REVERT: J   90 ASN cc_start: 0.8466 (t0) cc_final: 0.8005 (t0)
REVERT: J   99 HIS cc_start: 0.8116 (OUTLIER) cc_final: 0.7694 (p-80)
REVERT: J  114 ASN cc_start: 0.8279 (m-40) cc_final: 0.7996 (m-40)
REVERT: K   82 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8383 (tttm)
REVERT: K   90 ASN cc_start: 0.8620 (t0) cc_final: 0.8194 (t0)
REVERT: K   99 HIS cc_start: 0.8214 (OUTLIER) cc_final: 0.6002 (p-80)
  outliers start: 61
  outliers final: 40
  residues processed: 288
  average time/residue: 0.4046
  time to fit residues: 175.1356
Evaluate side-chains
  264 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 221
  time to evaluate  : 2.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   38 ASP
Chi-restraints excluded: chain D residue   99 ASP
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain E residue   82 ASP
Chi-restraints excluded: chain E residue  304 TYR
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue  143 THR
Chi-restraints excluded: chain F residue  304 TYR
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   68 VAL
Chi-restraints excluded: chain G residue  203 ARG
Chi-restraints excluded: chain G residue  237 ARG
Chi-restraints excluded: chain G residue  250 LEU
Chi-restraints excluded: chain G residue  304 TYR
Chi-restraints excluded: chain G residue  307 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  106 ASP
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain H residue  304 TYR
Chi-restraints excluded: chain I residue   44 MET
Chi-restraints excluded: chain I residue   71 THR
Chi-restraints excluded: chain I residue   73 SER
Chi-restraints excluded: chain I residue  109 THR
Chi-restraints excluded: chain I residue  143 THR
Chi-restraints excluded: chain J residue   99 HIS
Chi-restraints excluded: chain K residue   99 HIS
Chi-restraints excluded: chain K residue  117 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 298
   random chunks:
   chunk 267 optimal weight:    6.9990
   chunk 203 optimal weight:    0.9990
   chunk 140 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 129 optimal weight:    7.9990
   chunk 182 optimal weight:    0.8980
   chunk 272 optimal weight:    0.6980
   chunk 288 optimal weight:    5.9990
   chunk 142 optimal weight:   10.0000
   chunk 257 optimal weight:    5.9990
   chunk 77 optimal weight:    8.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
A  91 GLN
A 203 HIS
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 120 HIS
** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 148 GLN
E 342 GLN
F 148 GLN
F 159 HIS
F 242 GLN
** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 348 ASN
** I  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 102 ASN
I 148 GLN
I 348 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  24807  Z= 0.400
  Angle     :  0.617   7.467  33959  Z= 0.319
  Chirality :  0.042   0.211   3815
  Planarity :  0.004   0.053   4261
  Dihedral  : 15.155 178.868   4201
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.47 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.74 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.15), residues: 2949
  helix:  0.71 (0.16), residues: 922
  sheet: -0.18 (0.23), residues: 511
  loop : -2.26 (0.14), residues: 1516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP E  49 
 HIS   0.010   0.001   HIS C  29 
 PHE   0.016   0.002   PHE D 245 
 TYR   0.015   0.002   TYR G 290 
 ARG   0.007   0.000   ARG G 237 

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

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

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 75
    poor density    : 234
  time to evaluate  : 2.990 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.5222 (OUTLIER) cc_final: 0.3509 (p-90)
REVERT: A  178 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8348 (mt)
REVERT: A  200 HIS cc_start: 0.8336 (t-90) cc_final: 0.7825 (t-90)
REVERT: A  228 TRP cc_start: 0.7697 (t-100) cc_final: 0.7454 (t-100)
REVERT: A  235 TYR cc_start: 0.8077 (m-80) cc_final: 0.7787 (m-80)
REVERT: B  147 TRP cc_start: 0.8350 (t-100) cc_final: 0.7976 (t-100)
REVERT: B  170 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7010 (mtm110)
REVERT: C    1 MET cc_start: 0.6417 (mtt) cc_final: 0.5313 (ttp)
REVERT: C  143 PHE cc_start: 0.7290 (p90) cc_final: 0.6349 (p90)
REVERT: C  186 TRP cc_start: 0.7700 (t-100) cc_final: 0.7490 (t-100)
REVERT: D  146 ASN cc_start: 0.8392 (t0) cc_final: 0.8053 (t0)
REVERT: D  304 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.8333 (m-80)
REVERT: G   94 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8241 (p0)
REVERT: G  206 LYS cc_start: 0.8023 (mmmt) cc_final: 0.7765 (mtmt)
REVERT: H   72 ILE cc_start: 0.8791 (tp) cc_final: 0.8570 (tp)
REVERT: H   94 ASN cc_start: 0.7959 (p0) cc_final: 0.7315 (t0)
REVERT: I   34 GLU cc_start: 0.8196 (tt0) cc_final: 0.7746 (tt0)
REVERT: I  185 ARG cc_start: 0.7796 (tpp80) cc_final: 0.7431 (tpp-160)
REVERT: I  254 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7634 (mppt)
REVERT: J   99 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7743 (p-80)
REVERT: J  114 ASN cc_start: 0.8224 (m-40) cc_final: 0.8015 (m-40)
REVERT: K   82 LYS cc_start: 0.8844 (ttmt) cc_final: 0.8288 (ttmt)
REVERT: K   90 ASN cc_start: 0.8547 (t0) cc_final: 0.8210 (t0)
REVERT: K   99 HIS cc_start: 0.8431 (OUTLIER) cc_final: 0.6277 (p-80)
  outliers start: 75
  outliers final: 48
  residues processed: 282
  average time/residue: 0.4045
  time to fit residues: 171.3258
Evaluate side-chains
  283 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 229
  time to evaluate  : 2.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  414 TRP
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  159 ILE
Chi-restraints excluded: chain D residue   38 ASP
Chi-restraints excluded: chain D residue   99 ASP
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  304 TYR
Chi-restraints excluded: chain E residue   53 ASP
Chi-restraints excluded: chain E residue   82 ASP
Chi-restraints excluded: chain E residue  251 ILE
Chi-restraints excluded: chain E residue  304 TYR
Chi-restraints excluded: chain E residue  308 THR
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue  143 THR
Chi-restraints excluded: chain F residue  304 TYR
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain F residue  308 THR
Chi-restraints excluded: chain F residue  310 GLN
Chi-restraints excluded: chain G residue   68 VAL
Chi-restraints excluded: chain G residue   78 THR
Chi-restraints excluded: chain G residue   94 ASN
Chi-restraints excluded: chain G residue  203 ARG
Chi-restraints excluded: chain G residue  237 ARG
Chi-restraints excluded: chain G residue  250 LEU
Chi-restraints excluded: chain G residue  251 ILE
Chi-restraints excluded: chain G residue  304 TYR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  106 ASP
Chi-restraints excluded: chain H residue  188 GLU
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain H residue  304 TYR
Chi-restraints excluded: chain I residue   44 MET
Chi-restraints excluded: chain I residue   71 THR
Chi-restraints excluded: chain I residue  109 THR
Chi-restraints excluded: chain I residue  143 THR
Chi-restraints excluded: chain J residue   99 HIS
Chi-restraints excluded: chain J residue  117 ILE
Chi-restraints excluded: chain K residue   99 HIS
Chi-restraints excluded: chain K residue  117 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 298
   random chunks:
   chunk 239 optimal weight:    0.6980
   chunk 163 optimal weight:    0.6980
   chunk 4 optimal weight:    0.2980
   chunk 214 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 245 optimal weight:    3.9990
   chunk 199 optimal weight:    0.8980
   chunk 0 optimal weight:   30.0000
   chunk 147 optimal weight:    3.9990
   chunk 258 optimal weight:    0.8980
   chunk 72 optimal weight:   10.0000
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 203 HIS
** B  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 242 GLN
G  51 GLN
G 148 GLN
** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 348 ASN
I  96 GLN
I 102 ASN
I 310 GLN
J 110 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  24807  Z= 0.168
  Angle     :  0.527   7.709  33959  Z= 0.272
  Chirality :  0.039   0.171   3815
  Planarity :  0.004   0.047   4261
  Dihedral  : 15.016 179.572   4201
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 16.82 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.74 %
    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: -0.92 (0.15), residues: 2949
  helix:  1.17 (0.17), residues: 922
  sheet: -0.00 (0.23), residues: 498
  loop : -2.06 (0.15), residues: 1529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  10 
 HIS   0.009   0.001   HIS A 203 
 PHE   0.018   0.001   PHE D 245 
 TYR   0.011   0.001   TYR D 304 
 ARG   0.013   0.000   ARG B 218 

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

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

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 58
    poor density    : 260
  time to evaluate  : 2.798 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.5000 (OUTLIER) cc_final: 0.3522 (p-90)
REVERT: A  200 HIS cc_start: 0.8247 (t-90) cc_final: 0.7762 (t-90)
REVERT: A  228 TRP cc_start: 0.7706 (t-100) cc_final: 0.7471 (t-100)
REVERT: A  235 TYR cc_start: 0.7746 (m-80) cc_final: 0.7389 (m-80)
REVERT: B  170 ARG cc_start: 0.7640 (ttp80) cc_final: 0.6971 (mtm110)
REVERT: B  306 HIS cc_start: 0.7668 (m-70) cc_final: 0.7458 (m-70)
REVERT: C    1 MET cc_start: 0.6386 (mtt) cc_final: 0.5569 (ttp)
REVERT: C   56 GLU cc_start: 0.8014 (pm20) cc_final: 0.7329 (pm20)
REVERT: C  143 PHE cc_start: 0.7210 (p90) cc_final: 0.6284 (p90)
REVERT: D  146 ASN cc_start: 0.8345 (t0) cc_final: 0.8001 (t0)
REVERT: D  304 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8393 (m-80)
REVERT: F  258 LYS cc_start: 0.7350 (mmpt) cc_final: 0.7044 (mmpt)
REVERT: H   94 ASN cc_start: 0.7928 (p0) cc_final: 0.7191 (t0)
REVERT: I  254 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7711 (mppt)
REVERT: I  302 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7932 (mt-10)
REVERT: I  348 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8875 (t0)
REVERT: J   90 ASN cc_start: 0.8390 (t0) cc_final: 0.7997 (t0)
REVERT: J   99 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7641 (p-80)
REVERT: J  114 ASN cc_start: 0.8140 (m-40) cc_final: 0.7921 (m-40)
REVERT: K   82 LYS cc_start: 0.8864 (ttmt) cc_final: 0.8340 (ttmt)
REVERT: K   90 ASN cc_start: 0.8582 (t0) cc_final: 0.8298 (t0)
REVERT: K   99 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.6137 (p-80)
  outliers start: 58
  outliers final: 40
  residues processed: 296
  average time/residue: 0.3995
  time to fit residues: 178.7384
Evaluate side-chains
  277 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 231
  time to evaluate  : 2.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  414 TRP
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue  159 ILE
Chi-restraints excluded: chain D residue   38 ASP
Chi-restraints excluded: chain D residue  304 TYR
Chi-restraints excluded: chain E residue  188 GLU
Chi-restraints excluded: chain E residue  304 TYR
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue  250 LEU
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain F residue  304 TYR
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain F residue  308 THR
Chi-restraints excluded: chain G residue   68 VAL
Chi-restraints excluded: chain G residue   78 THR
Chi-restraints excluded: chain G residue   94 ASN
Chi-restraints excluded: chain G residue  203 ARG
Chi-restraints excluded: chain G residue  237 ARG
Chi-restraints excluded: chain G residue  251 ILE
Chi-restraints excluded: chain G residue  304 TYR
Chi-restraints excluded: chain G residue  307 VAL
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  106 ASP
Chi-restraints excluded: chain H residue  188 GLU
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain H residue  252 LEU
Chi-restraints excluded: chain H residue  304 TYR
Chi-restraints excluded: chain H residue  348 ASN
Chi-restraints excluded: chain I residue   44 MET
Chi-restraints excluded: chain I residue   71 THR
Chi-restraints excluded: chain I residue  302 GLU
Chi-restraints excluded: chain I residue  348 ASN
Chi-restraints excluded: chain J residue   99 HIS
Chi-restraints excluded: chain K residue   99 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 298
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 259 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 169 optimal weight:    0.5980
   chunk 71 optimal weight:    4.9990
   chunk 288 optimal weight:    3.9990
   chunk 239 optimal weight:    3.9990
   chunk 133 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 95 optimal weight:    9.9990
   chunk 151 optimal weight:    3.9990
   overall best weight:    2.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  96 GLN
I 102 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  24807  Z= 0.317
  Angle     :  0.577   7.781  33959  Z= 0.296
  Chirality :  0.041   0.288   3815
  Planarity :  0.004   0.047   4261
  Dihedral  : 14.970 178.758   4201
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.64 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.74 %
    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: -0.85 (0.15), residues: 2949
  helix:  1.25 (0.17), residues: 926
  sheet: -0.05 (0.23), residues: 510
  loop : -2.01 (0.15), residues: 1513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E  49 
 HIS   0.011   0.001   HIS A 203 
 PHE   0.018   0.001   PHE D 245 
 TYR   0.013   0.002   TYR G 290 
 ARG   0.008   0.000   ARG B 218 

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

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

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 235
  time to evaluate  : 2.971 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.5053 (OUTLIER) cc_final: 0.3631 (p-90)
REVERT: A  178 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8593 (mt)
REVERT: A  200 HIS cc_start: 0.8291 (t-90) cc_final: 0.7743 (t-90)
REVERT: A  228 TRP cc_start: 0.7734 (t-100) cc_final: 0.7438 (t-100)
REVERT: B  147 TRP cc_start: 0.8320 (t-100) cc_final: 0.8060 (t-100)
REVERT: B  170 ARG cc_start: 0.7696 (ttp80) cc_final: 0.7079 (mtm110)
REVERT: B  306 HIS cc_start: 0.7676 (m-70) cc_final: 0.7467 (m-70)
REVERT: C    1 MET cc_start: 0.6666 (mtt) cc_final: 0.5589 (ttp)
REVERT: C   56 GLU cc_start: 0.7968 (pm20) cc_final: 0.7283 (pm20)
REVERT: C  143 PHE cc_start: 0.7239 (p90) cc_final: 0.6223 (p90)
REVERT: D  146 ASN cc_start: 0.8370 (t0) cc_final: 0.8071 (t0)
REVERT: D  304 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8328 (m-80)
REVERT: F  258 LYS cc_start: 0.7320 (mmpt) cc_final: 0.6982 (mmpt)
REVERT: G   94 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.8135 (p0)
REVERT: H   94 ASN cc_start: 0.7968 (p0) cc_final: 0.7216 (t0)
REVERT: I   34 GLU cc_start: 0.8157 (tt0) cc_final: 0.7682 (tt0)
REVERT: I   96 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8361 (mt0)
REVERT: I  254 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7626 (mppt)
REVERT: I  302 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7972 (mt-10)
REVERT: I  348 ASN cc_start: 0.9147 (OUTLIER) cc_final: 0.8934 (t0)
REVERT: J   90 ASN cc_start: 0.8430 (t0) cc_final: 0.8038 (t0)
REVERT: J   99 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7797 (p-80)
REVERT: J  114 ASN cc_start: 0.8150 (m-40) cc_final: 0.7932 (m-40)
REVERT: K   82 LYS cc_start: 0.8876 (ttmt) cc_final: 0.8294 (ttmt)
REVERT: K   90 ASN cc_start: 0.8615 (t0) cc_final: 0.8321 (t0)
REVERT: K   99 HIS cc_start: 0.8326 (OUTLIER) cc_final: 0.6024 (p-80)
  outliers start: 60
  outliers final: 45
  residues processed: 275
  average time/residue: 0.4028
  time to fit residues: 168.3219
Evaluate side-chains
  284 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 230
  time to evaluate  : 2.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  159 ILE
Chi-restraints excluded: chain D residue   38 ASP
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  304 TYR
Chi-restraints excluded: chain E residue   82 ASP
Chi-restraints excluded: chain E residue  304 TYR
Chi-restraints excluded: chain E residue  308 THR
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue  250 LEU
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain F residue  304 TYR
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain F residue  310 GLN
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   68 VAL
Chi-restraints excluded: chain G residue   69 ARG
Chi-restraints excluded: chain G residue   78 THR
Chi-restraints excluded: chain G residue   94 ASN
Chi-restraints excluded: chain G residue  203 ARG
Chi-restraints excluded: chain G residue  237 ARG
Chi-restraints excluded: chain G residue  250 LEU
Chi-restraints excluded: chain G residue  251 ILE
Chi-restraints excluded: chain G residue  304 TYR
Chi-restraints excluded: chain G residue  307 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  106 ASP
Chi-restraints excluded: chain H residue  188 GLU
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain H residue  304 TYR
Chi-restraints excluded: chain I residue   44 MET
Chi-restraints excluded: chain I residue   53 ASP
Chi-restraints excluded: chain I residue   71 THR
Chi-restraints excluded: chain I residue   94 ASN
Chi-restraints excluded: chain I residue   96 GLN
Chi-restraints excluded: chain I residue  302 GLU
Chi-restraints excluded: chain I residue  348 ASN
Chi-restraints excluded: chain J residue   99 HIS
Chi-restraints excluded: chain K residue   99 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 298
   random chunks:
   chunk 277 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 164 optimal weight:    0.2980
   chunk 210 optimal weight:    0.7980
   chunk 163 optimal weight:    0.6980
   chunk 242 optimal weight:    0.5980
   chunk 161 optimal weight:    1.9990
   chunk 287 optimal weight:    0.8980
   chunk 179 optimal weight:    3.9990
   chunk 175 optimal weight:    0.0170
   chunk 132 optimal weight:    0.7980
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  96 GLN
I 102 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  24807  Z= 0.144
  Angle     :  0.509   8.661  33959  Z= 0.262
  Chirality :  0.039   0.323   3815
  Planarity :  0.003   0.045   4261
  Dihedral  : 14.783 179.490   4201
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 18.34 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.74 %
    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: 2949
  helix:  1.56 (0.17), residues: 926
  sheet:  0.09 (0.23), residues: 504
  loop : -1.88 (0.15), residues: 1519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 394 
 HIS   0.008   0.001   HIS C  29 
 PHE   0.021   0.001   PHE D 245 
 TYR   0.010   0.001   TYR D 304 
 ARG   0.005   0.000   ARG I  69 

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

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

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 260
  time to evaluate  : 2.835 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.4994 (OUTLIER) cc_final: 0.3770 (p-90)
REVERT: A   62 GLN cc_start: 0.7856 (mp10) cc_final: 0.7554 (mp10)
REVERT: A  200 HIS cc_start: 0.8187 (t-90) cc_final: 0.7726 (t-90)
REVERT: A  228 TRP cc_start: 0.7408 (t-100) cc_final: 0.7100 (t-100)
REVERT: B  170 ARG cc_start: 0.7608 (ttp80) cc_final: 0.7016 (mtm110)
REVERT: B  306 HIS cc_start: 0.7611 (m-70) cc_final: 0.7392 (m-70)
REVERT: C    1 MET cc_start: 0.6820 (mtt) cc_final: 0.5777 (ttp)
REVERT: C   56 GLU cc_start: 0.7945 (pm20) cc_final: 0.7294 (pm20)
REVERT: C  143 PHE cc_start: 0.7202 (p90) cc_final: 0.6182 (p90)
REVERT: D  146 ASN cc_start: 0.8345 (t0) cc_final: 0.8052 (t0)
REVERT: D  304 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.8337 (m-80)
REVERT: F  188 GLU cc_start: 0.7634 (pm20) cc_final: 0.6935 (pm20)
REVERT: H   94 ASN cc_start: 0.7986 (p0) cc_final: 0.7119 (t0)
REVERT: I   99 ASP cc_start: 0.8287 (m-30) cc_final: 0.7790 (m-30)
REVERT: I  261 LYS cc_start: 0.7844 (mttt) cc_final: 0.7510 (mttt)
REVERT: I  302 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7914 (mt-10)
REVERT: J   90 ASN cc_start: 0.8361 (t0) cc_final: 0.7941 (t0)
REVERT: J   99 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7548 (p-80)
REVERT: J  114 ASN cc_start: 0.8107 (m-40) cc_final: 0.7895 (m-40)
REVERT: K   82 LYS cc_start: 0.8844 (ttmt) cc_final: 0.8424 (ttmm)
REVERT: K   90 ASN cc_start: 0.8597 (t0) cc_final: 0.8335 (t0)
REVERT: K   99 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.6234 (p-80)
  outliers start: 47
  outliers final: 36
  residues processed: 288
  average time/residue: 0.3989
  time to fit residues: 174.3762
Evaluate side-chains
  289 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 248
  time to evaluate  : 2.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain C residue  159 ILE
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   38 ASP
Chi-restraints excluded: chain D residue  304 TYR
Chi-restraints excluded: chain E residue   53 ASP
Chi-restraints excluded: chain E residue  304 TYR
Chi-restraints excluded: chain E residue  308 THR
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue  146 ASN
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain F residue  304 TYR
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain F residue  308 THR
Chi-restraints excluded: chain G residue   68 VAL
Chi-restraints excluded: chain G residue   78 THR
Chi-restraints excluded: chain G residue  203 ARG
Chi-restraints excluded: chain G residue  237 ARG
Chi-restraints excluded: chain G residue  251 ILE
Chi-restraints excluded: chain G residue  304 TYR
Chi-restraints excluded: chain G residue  307 VAL
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  188 GLU
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain H residue  252 LEU
Chi-restraints excluded: chain H residue  304 TYR
Chi-restraints excluded: chain I residue   44 MET
Chi-restraints excluded: chain I residue  302 GLU
Chi-restraints excluded: chain I residue  333 ARG
Chi-restraints excluded: chain J residue   99 HIS
Chi-restraints excluded: chain K residue   99 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 298
   random chunks:
   chunk 177 optimal weight:    1.9990
   chunk 114 optimal weight:    4.9990
   chunk 171 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 182 optimal weight:    3.9990
   chunk 195 optimal weight:    0.9980
   chunk 142 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9980
   chunk 225 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  19 ASN
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 102 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  24807  Z= 0.172
  Angle     :  0.510   8.695  33959  Z= 0.262
  Chirality :  0.039   0.194   3815
  Planarity :  0.003   0.050   4261
  Dihedral  : 14.684 179.445   4201
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.64 %
    Favored  : 79.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.74 %
    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: -0.44 (0.15), residues: 2949
  helix:  1.70 (0.17), residues: 925
  sheet:  0.18 (0.23), residues: 496
  loop : -1.82 (0.15), residues: 1528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I  49 
 HIS   0.008   0.001   HIS A 203 
 PHE   0.020   0.001   PHE D 245 
 TYR   0.011   0.001   TYR D 304 
 ARG   0.005   0.000   ARG G 237 

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

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

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 253
  time to evaluate  : 2.666 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.5114 (OUTLIER) cc_final: 0.4019 (p-90)
REVERT: A   62 GLN cc_start: 0.7713 (mp10) cc_final: 0.7446 (mp10)
REVERT: A  200 HIS cc_start: 0.8200 (t-90) cc_final: 0.7727 (t-90)
REVERT: A  228 TRP cc_start: 0.7450 (t-100) cc_final: 0.7083 (t-100)
REVERT: B  147 TRP cc_start: 0.8190 (t-100) cc_final: 0.7917 (t-100)
REVERT: B  170 ARG cc_start: 0.7741 (ttp80) cc_final: 0.7133 (mtm110)
REVERT: B  306 HIS cc_start: 0.7653 (m-70) cc_final: 0.7434 (m-70)
REVERT: C    1 MET cc_start: 0.6726 (mtt) cc_final: 0.5585 (ttp)
REVERT: C   56 GLU cc_start: 0.7863 (pm20) cc_final: 0.7268 (pm20)
REVERT: C  143 PHE cc_start: 0.7214 (p90) cc_final: 0.6194 (p90)
REVERT: C  186 TRP cc_start: 0.7676 (t-100) cc_final: 0.7436 (t-100)
REVERT: D  146 ASN cc_start: 0.8343 (t0) cc_final: 0.8049 (t0)
REVERT: D  304 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.8335 (m-80)
REVERT: F  188 GLU cc_start: 0.7551 (pm20) cc_final: 0.7069 (pm20)
REVERT: H   94 ASN cc_start: 0.8084 (p0) cc_final: 0.7847 (p0)
REVERT: I  302 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7910 (mt-10)
REVERT: J   90 ASN cc_start: 0.8455 (t0) cc_final: 0.8062 (t0)
REVERT: J   99 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7608 (p-80)
REVERT: J  114 ASN cc_start: 0.8125 (m-40) cc_final: 0.7917 (m-40)
REVERT: K   82 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8421 (ttmm)
REVERT: K   90 ASN cc_start: 0.8579 (t0) cc_final: 0.8333 (t0)
REVERT: K   99 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.6206 (p-80)
  outliers start: 46
  outliers final: 37
  residues processed: 282
  average time/residue: 0.4067
  time to fit residues: 174.0504
Evaluate side-chains
  295 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 253
  time to evaluate  : 2.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  159 ILE
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   38 ASP
Chi-restraints excluded: chain D residue  304 TYR
Chi-restraints excluded: chain E residue   53 ASP
Chi-restraints excluded: chain E residue  304 TYR
Chi-restraints excluded: chain E residue  308 THR
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain F residue  304 TYR
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain G residue   68 VAL
Chi-restraints excluded: chain G residue   78 THR
Chi-restraints excluded: chain G residue  203 ARG
Chi-restraints excluded: chain G residue  237 ARG
Chi-restraints excluded: chain G residue  251 ILE
Chi-restraints excluded: chain G residue  304 TYR
Chi-restraints excluded: chain G residue  307 VAL
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  188 GLU
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain H residue  252 LEU
Chi-restraints excluded: chain H residue  304 TYR
Chi-restraints excluded: chain I residue   71 THR
Chi-restraints excluded: chain I residue   94 ASN
Chi-restraints excluded: chain I residue  302 GLU
Chi-restraints excluded: chain I residue  333 ARG
Chi-restraints excluded: chain J residue   99 HIS
Chi-restraints excluded: chain K residue   99 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 298
   random chunks:
   chunk 261 optimal weight:    8.9990
   chunk 275 optimal weight:    0.2980
   chunk 251 optimal weight:    0.9980
   chunk 267 optimal weight:    6.9990
   chunk 161 optimal weight:    1.9990
   chunk 116 optimal weight:    3.9990
   chunk 210 optimal weight:    0.9990
   chunk 82 optimal weight:    8.9990
   chunk 241 optimal weight:    2.9990
   chunk 253 optimal weight:    3.9990
   chunk 266 optimal weight:    0.9980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 121 HIS
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 329 ASN
** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 102 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  24807  Z= 0.193
  Angle     :  0.518   9.011  33959  Z= 0.265
  Chirality :  0.039   0.169   3815
  Planarity :  0.003   0.069   4261
  Dihedral  : 14.658 179.258   4201
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.21 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.74 %
    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: -0.39 (0.15), residues: 2949
  helix:  1.73 (0.17), residues: 926
  sheet:  0.21 (0.23), residues: 496
  loop : -1.78 (0.15), residues: 1527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 394 
 HIS   0.009   0.001   HIS A 203 
 PHE   0.021   0.001   PHE D 245 
 TYR   0.011   0.001   TYR D 304 
 ARG   0.005   0.000   ARG G 237 

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

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

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 253
  time to evaluate  : 2.729 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.5165 (OUTLIER) cc_final: 0.4109 (p-90)
REVERT: A   62 GLN cc_start: 0.7729 (mp10) cc_final: 0.7453 (mp10)
REVERT: A  200 HIS cc_start: 0.8194 (t-90) cc_final: 0.7709 (t-90)
REVERT: A  228 TRP cc_start: 0.7457 (t-100) cc_final: 0.7077 (t-100)
REVERT: B  147 TRP cc_start: 0.8256 (t-100) cc_final: 0.8010 (t-100)
REVERT: B  170 ARG cc_start: 0.7765 (ttp80) cc_final: 0.7147 (mtm110)
REVERT: B  306 HIS cc_start: 0.7681 (m-70) cc_final: 0.7468 (m-70)
REVERT: C    1 MET cc_start: 0.6721 (mtt) cc_final: 0.5560 (ttp)
REVERT: C  143 PHE cc_start: 0.7209 (p90) cc_final: 0.6199 (p90)
REVERT: C  186 TRP cc_start: 0.7649 (t-100) cc_final: 0.7405 (t-100)
REVERT: D  146 ASN cc_start: 0.8345 (t0) cc_final: 0.8053 (t0)
REVERT: D  304 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.8334 (m-80)
REVERT: F  188 GLU cc_start: 0.7536 (pm20) cc_final: 0.7067 (pm20)
REVERT: G   94 ASN cc_start: 0.8299 (p0) cc_final: 0.8090 (p0)
REVERT: G  185 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7741 (mmt-90)
REVERT: H   94 ASN cc_start: 0.7993 (p0) cc_final: 0.7107 (t0)
REVERT: I   34 GLU cc_start: 0.8118 (tt0) cc_final: 0.7663 (tt0)
REVERT: I   99 ASP cc_start: 0.8366 (m-30) cc_final: 0.7760 (m-30)
REVERT: I  261 LYS cc_start: 0.7766 (mttt) cc_final: 0.7558 (mttt)
REVERT: I  302 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7911 (mt-10)
REVERT: J   90 ASN cc_start: 0.8476 (t0) cc_final: 0.8079 (t0)
REVERT: J   99 HIS cc_start: 0.8182 (OUTLIER) cc_final: 0.7659 (p-80)
REVERT: J  114 ASN cc_start: 0.8131 (m-40) cc_final: 0.7915 (m-40)
REVERT: K   82 LYS cc_start: 0.8876 (ttmt) cc_final: 0.8242 (ttmt)
REVERT: K   90 ASN cc_start: 0.8588 (t0) cc_final: 0.8351 (t0)
REVERT: K   99 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.6263 (p-80)
  outliers start: 57
  outliers final: 43
  residues processed: 291
  average time/residue: 0.3920
  time to fit residues: 172.7767
Evaluate side-chains
  297 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 248
  time to evaluate  : 2.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain C residue   81 ASP
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  159 ILE
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   38 ASP
Chi-restraints excluded: chain D residue  304 TYR
Chi-restraints excluded: chain E residue   53 ASP
Chi-restraints excluded: chain E residue   82 ASP
Chi-restraints excluded: chain E residue  304 TYR
Chi-restraints excluded: chain E residue  308 THR
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain F residue  304 TYR
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain G residue   68 VAL
Chi-restraints excluded: chain G residue   78 THR
Chi-restraints excluded: chain G residue  185 ARG
Chi-restraints excluded: chain G residue  203 ARG
Chi-restraints excluded: chain G residue  237 ARG
Chi-restraints excluded: chain G residue  251 ILE
Chi-restraints excluded: chain G residue  304 TYR
Chi-restraints excluded: chain G residue  307 VAL
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  188 GLU
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain H residue  252 LEU
Chi-restraints excluded: chain H residue  304 TYR
Chi-restraints excluded: chain I residue   44 MET
Chi-restraints excluded: chain I residue   71 THR
Chi-restraints excluded: chain I residue   94 ASN
Chi-restraints excluded: chain I residue  118 VAL
Chi-restraints excluded: chain I residue  159 HIS
Chi-restraints excluded: chain I residue  302 GLU
Chi-restraints excluded: chain I residue  333 ARG
Chi-restraints excluded: chain I residue  339 VAL
Chi-restraints excluded: chain J residue   99 HIS
Chi-restraints excluded: chain K residue   99 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 298
   random chunks:
   chunk 175 optimal weight:    0.0970
   chunk 283 optimal weight:    2.9990
   chunk 172 optimal weight:    3.9990
   chunk 134 optimal weight:    3.9990
   chunk 196 optimal weight:    2.9990
   chunk 296 optimal weight:   20.0000
   chunk 273 optimal weight:    0.0970
   chunk 236 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 182 optimal weight:    0.8980
   chunk 144 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 329 ASN
** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 102 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  24807  Z= 0.151
  Angle     :  0.505   9.295  33959  Z= 0.258
  Chirality :  0.038   0.173   3815
  Planarity :  0.003   0.059   4261
  Dihedral  : 14.602 179.688   4201
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 19.08 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.74 %
    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: -0.27 (0.15), residues: 2949
  helix:  1.88 (0.17), residues: 925
  sheet:  0.35 (0.23), residues: 486
  loop : -1.75 (0.15), residues: 1538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 394 
 HIS   0.009   0.001   HIS A 203 
 PHE   0.021   0.001   PHE D 245 
 TYR   0.010   0.001   TYR D 304 
 ARG   0.004   0.000   ARG G 237 

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

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

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5898 Ramachandran restraints generated.
    2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 255
  time to evaluate  : 2.785 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 TRP cc_start: 0.5119 (OUTLIER) cc_final: 0.4156 (p-90)
REVERT: A   62 GLN cc_start: 0.7771 (mp10) cc_final: 0.7506 (mp10)
REVERT: A  200 HIS cc_start: 0.8145 (t-90) cc_final: 0.7582 (t-170)
REVERT: A  228 TRP cc_start: 0.7275 (t-100) cc_final: 0.6882 (t-100)
REVERT: B  170 ARG cc_start: 0.7720 (ttp80) cc_final: 0.7149 (mtm110)
REVERT: B  200 LEU cc_start: 0.8639 (tt) cc_final: 0.8206 (mm)
REVERT: C    1 MET cc_start: 0.6740 (mtt) cc_final: 0.5604 (ttp)
REVERT: C   56 GLU cc_start: 0.7838 (pm20) cc_final: 0.7231 (pm20)
REVERT: C  143 PHE cc_start: 0.7096 (p90) cc_final: 0.6177 (p90)
REVERT: D  146 ASN cc_start: 0.8296 (t0) cc_final: 0.7991 (t0)
REVERT: D  169 ARG cc_start: 0.8102 (ttt180) cc_final: 0.7793 (mtp85)
REVERT: D  304 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.8285 (m-80)
REVERT: F  188 GLU cc_start: 0.7394 (pm20) cc_final: 0.6900 (pm20)
REVERT: G  185 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7714 (mmt-90)
REVERT: H   94 ASN cc_start: 0.8027 (p0) cc_final: 0.7813 (p0)
REVERT: I   34 GLU cc_start: 0.8102 (tt0) cc_final: 0.7659 (tt0)
REVERT: I   99 ASP cc_start: 0.8303 (m-30) cc_final: 0.7674 (m-30)
REVERT: I  185 ARG cc_start: 0.7471 (tpp80) cc_final: 0.7062 (tpp80)
REVERT: I  302 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7887 (mt-10)
REVERT: J   90 ASN cc_start: 0.8399 (t0) cc_final: 0.8029 (t0)
REVERT: J   99 HIS cc_start: 0.8147 (OUTLIER) cc_final: 0.7550 (p-80)
REVERT: J  114 ASN cc_start: 0.8154 (m-40) cc_final: 0.7952 (m-40)
REVERT: K   82 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8235 (ttmt)
REVERT: K   90 ASN cc_start: 0.8580 (t0) cc_final: 0.8374 (t0)
REVERT: K   99 HIS cc_start: 0.8262 (OUTLIER) cc_final: 0.6304 (p-80)
  outliers start: 46
  outliers final: 37
  residues processed: 288
  average time/residue: 0.3970
  time to fit residues: 173.0657
Evaluate side-chains
  292 residues out of total 2408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 249
  time to evaluate  : 2.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TRP
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  159 ILE
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   38 ASP
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  304 TYR
Chi-restraints excluded: chain E residue   53 ASP
Chi-restraints excluded: chain E residue  304 TYR
Chi-restraints excluded: chain E residue  308 THR
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain F residue  304 TYR
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain G residue   68 VAL
Chi-restraints excluded: chain G residue   78 THR
Chi-restraints excluded: chain G residue  185 ARG
Chi-restraints excluded: chain G residue  203 ARG
Chi-restraints excluded: chain G residue  237 ARG
Chi-restraints excluded: chain G residue  251 ILE
Chi-restraints excluded: chain G residue  304 TYR
Chi-restraints excluded: chain G residue  307 VAL
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  188 GLU
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain H residue  252 LEU
Chi-restraints excluded: chain H residue  304 TYR
Chi-restraints excluded: chain I residue   71 THR
Chi-restraints excluded: chain I residue   94 ASN
Chi-restraints excluded: chain I residue  118 VAL
Chi-restraints excluded: chain I residue  302 GLU
Chi-restraints excluded: chain J residue   99 HIS
Chi-restraints excluded: chain K residue   99 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 298
   random chunks:
   chunk 187 optimal weight:    4.9990
   chunk 251 optimal weight:    8.9990
   chunk 72 optimal weight:    0.8980
   chunk 217 optimal weight:    2.9990
   chunk 34 optimal weight:   20.0000
   chunk 65 optimal weight:    0.6980
   chunk 236 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0970
   chunk 243 optimal weight:    0.3980
   chunk 29 optimal weight:    6.9990
   chunk 43 optimal weight:    0.1980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 173 GLN
** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 329 ASN
** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 102 ASN
K 114 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.141802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.098959 restraints weight = 42332.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 2.59
r_work: 0.2778 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2763
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2763
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  24807  Z= 0.140
  Angle     :  0.502   9.507  33959  Z= 0.255
  Chirality :  0.038   0.167   3815
  Planarity :  0.003   0.055   4261
  Dihedral  : 14.564 179.284   4201
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 19.51 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.74 %
    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: -0.15 (0.15), residues: 2949
  helix:  1.98 (0.17), residues: 926
  sheet:  0.41 (0.23), residues: 486
  loop : -1.69 (0.15), residues: 1537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 394 
 HIS   0.008   0.001   HIS A 203 
 PHE   0.022   0.001   PHE D 245 
 TYR   0.010   0.001   TYR D 304 
 ARG   0.004   0.000   ARG I 185 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5023.36 seconds
wall clock time: 92 minutes 41.24 seconds (5561.24 seconds total)