Starting phenix.real_space_refine
on Sun Mar 17 22:11:54 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njo_9390/03_2024/6njo_9390_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njo_9390/03_2024/6njo_9390.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njo_9390/03_2024/6njo_9390.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njo_9390/03_2024/6njo_9390.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njo_9390/03_2024/6njo_9390_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njo_9390/03_2024/6njo_9390_updated.pdb"
  }
  resolution = 3.34
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
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: 8
    Type Number    sf(0)   Gaussians
     Al      4      5.89       5
     P       8      5.49       5
     Mg      4      5.21       5
     S      78      5.16       5
     C   12092      2.51       5
     N    3282      2.21       5
     O    3610      1.98       5
     F      12      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   66": "NH1" <-> "NH2"
    Residue "A PHE   83": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  113": "NH1" <-> "NH2"
    Residue "A ARG  147": "NH1" <-> "NH2"
    Residue "A ARG  172": "NH1" <-> "NH2"
    Residue "A ARG  209": "NH1" <-> "NH2"
    Residue "A ARG  366": "NH1" <-> "NH2"
    Residue "A ARG  378": "NH1" <-> "NH2"
    Residue "A ARG  398": "NH1" <-> "NH2"
    Residue "B TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  113": "NH1" <-> "NH2"
    Residue "B ARG  147": "NH1" <-> "NH2"
    Residue "B ARG  207": "NH1" <-> "NH2"
    Residue "B ARG  366": "NH1" <-> "NH2"
    Residue "B ARG  378": "NH1" <-> "NH2"
    Residue "C ARG   49": "NH1" <-> "NH2"
    Residue "C ARG   54": "NH1" <-> "NH2"
    Residue "C TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG   66": "NH1" <-> "NH2"
    Residue "C ARG  147": "NH1" <-> "NH2"
    Residue "C ARG  288": "NH1" <-> "NH2"
    Residue "C ARG  305": "NH1" <-> "NH2"
    Residue "C ARG  366": "NH1" <-> "NH2"
    Residue "C ARG  378": "NH1" <-> "NH2"
    Residue "D TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG  120": "NH1" <-> "NH2"
    Residue "D ARG  147": "NH1" <-> "NH2"
    Residue "D ARG  159": "NH1" <-> "NH2"
    Residue "D PHE  176": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG  207": "NH1" <-> "NH2"
    Residue "D ARG  235": "NH1" <-> "NH2"
    Residue "D ARG  288": "NH1" <-> "NH2"
    Residue "D ARG  378": "NH1" <-> "NH2"
    Residue "D ARG  398": "NH1" <-> "NH2"
    Residue "E TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  113": "NH1" <-> "NH2"
    Residue "E ARG  120": "NH1" <-> "NH2"
    Residue "E ARG  135": "NH1" <-> "NH2"
    Residue "E ARG  147": "NH1" <-> "NH2"
    Residue "E ARG  209": "NH1" <-> "NH2"
    Residue "E ARG  255": "NH1" <-> "NH2"
    Residue "E ARG  270": "NH1" <-> "NH2"
    Residue "E ARG  288": "NH1" <-> "NH2"
    Residue "E ARG  305": "NH1" <-> "NH2"
    Residue "E ARG  336": "NH1" <-> "NH2"
    Residue "E ARG  378": "NH1" <-> "NH2"
    Residue "F ARG   54": "NH1" <-> "NH2"
    Residue "F TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG  105": "NH1" <-> "NH2"
    Residue "F ARG  147": "NH1" <-> "NH2"
    Residue "F ARG  172": "NH1" <-> "NH2"
    Residue "F ARG  207": "NH1" <-> "NH2"
    Residue "F ARG  209": "NH1" <-> "NH2"
    Residue "F ARG  255": "NH1" <-> "NH2"
    Residue "F ARG  347": "NH1" <-> "NH2"
    Residue "F ARG  378": "NH1" <-> "NH2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 19090
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 3164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 412, 3164
          Classifications: {'peptide': 412}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390}
    Chain: "B"
      Number of atoms: 3164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 412, 3164
          Classifications: {'peptide': 412}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390}
    Chain: "C"
      Number of atoms: 3164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 412, 3164
          Classifications: {'peptide': 412}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390}
    Chain: "D"
      Number of atoms: 3176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 413, 3176
          Classifications: {'peptide': 413}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 391}
    Chain: "E"
      Number of atoms: 3164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 412, 3164
          Classifications: {'peptide': 412}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390}
    Chain: "F"
      Number of atoms: 3110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 405, 3110
          Classifications: {'peptide': 405}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 383}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "E"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "D"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "E"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
  Residues with excluded nonbonded symmetry interactions: 24
    residue:
      pdb=" N   GLU A 140 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU A 140 " occ=0.50
    residue:
      pdb=" N   PRO A 141 " occ=0.75
      ... (5 atoms not shown)
      pdb=" CD  PRO A 141 " occ=0.75
    residue:
      pdb=" N   PRO A 142 " occ=0.50
      ... (5 atoms not shown)
      pdb=" CD  PRO A 142 " occ=0.50
    residue:
      pdb=" N   GLN A 148 " occ=0.75
      ... (7 atoms not shown)
      pdb=" NE2 GLN A 148 " occ=0.75
    residue:
      pdb=" N   GLU B 140 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU B 140 " occ=0.50
    residue:
      pdb=" N   PRO B 141 " occ=0.75
      ... (5 atoms not shown)
      pdb=" CD  PRO B 141 " occ=0.75
    residue:
      pdb=" N   PRO B 142 " occ=0.50
      ... (5 atoms not shown)
      pdb=" CD  PRO B 142 " occ=0.50
    residue:
      pdb=" N   GLN B 148 " occ=0.75
      ... (7 atoms not shown)
      pdb=" NE2 GLN B 148 " occ=0.75
    residue:
      pdb=" N   GLU C 140 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU C 140 " occ=0.50
    residue:
      pdb=" N   PRO C 141 " occ=0.75
      ... (5 atoms not shown)
      pdb=" CD  PRO C 141 " occ=0.75
    residue:
      pdb=" N   PRO C 142 " occ=0.50
      ... (5 atoms not shown)
      pdb=" CD  PRO C 142 " occ=0.50
    residue:
      pdb=" N   GLN C 148 " occ=0.75
      ... (7 atoms not shown)
      pdb=" NE2 GLN C 148 " occ=0.75
    ... (remaining 12 not shown)
  Time building chain proxies: 8.71, per 1000 atoms: 0.46
  Number of scatterers: 19090
  At special positions: 0
  Unit cell: (106.08, 118.32, 122.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      78     16.00
     P       8     15.00
     Al      4     13.00
     Mg      4     11.99
     F      12      9.00
     O    3610      8.00
     N    3282      7.00
     C   12092      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 6.42
  Conformation dependent library (CDL) restraints added in 3.8 seconds
  

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4512

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      88 helices and 18 sheets defined
      33.5% alpha, 14.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 25.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 159 through 163
    Processing helix  chain 'A' and resid 183 through 193
    Processing helix  chain 'A' and resid 208 through 215
    Processing helix  chain 'A' and resid 220 through 223
      No H-bonds generated for 'chain 'A' and resid 220 through 223'
    Processing helix  chain 'A' and resid 237 through 256
      removed outlier: 4.371A  pdb=" N   ALA A 244 " --> pdb=" O   ARG A 240 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   PHE A 245 " --> pdb=" O   MET A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 282
    Processing helix  chain 'A' and resid 293 through 303
      Proline residue:  A 300  - end of helix
    Processing helix  chain 'A' and resid 330 through 338
    Processing helix  chain 'A' and resid 348 through 351
      No H-bonds generated for 'chain 'A' and resid 348 through 351'
    Processing helix  chain 'A' and resid 374 through 397
      removed outlier: 3.862A  pdb=" N   CYS A 383 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LYS A 384 " --> pdb=" O   ALA A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 415
    Processing helix  chain 'A' and resid 417 through 424
    Processing helix  chain 'A' and resid 434 through 444
    Processing helix  chain 'B' and resid 108 through 110
      No H-bonds generated for 'chain 'B' and resid 108 through 110'
    Processing helix  chain 'B' and resid 159 through 163
    Processing helix  chain 'B' and resid 183 through 193
    Processing helix  chain 'B' and resid 208 through 216
      removed outlier: 3.551A  pdb=" N   VAL B 211 " --> pdb=" O   GLY B 208 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ASN B 212 " --> pdb=" O   ARG B 209 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   PHE B 214 " --> pdb=" O   VAL B 211 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ALA B 216 " --> pdb=" O   GLU B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 225
      removed outlier: 5.035A  pdb=" N   LYS B 225 " --> pdb=" O   SER B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 256
      removed outlier: 5.175A  pdb=" N   ALA B 244 " --> pdb=" O   ARG B 240 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   PHE B 245 " --> pdb=" O   MET B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 281
    Processing helix  chain 'B' and resid 293 through 304
      Proline residue:  B 300  - end of helix
    Processing helix  chain 'B' and resid 330 through 336
    Processing helix  chain 'B' and resid 347 through 350
      No H-bonds generated for 'chain 'B' and resid 347 through 350'
    Processing helix  chain 'B' and resid 368 through 371
      No H-bonds generated for 'chain 'B' and resid 368 through 371'
    Processing helix  chain 'B' and resid 374 through 391
    Processing helix  chain 'B' and resid 394 through 398
      removed outlier: 3.742A  pdb=" N   ARG B 398 " --> pdb=" O   LEU B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 422
      removed outlier: 5.186A  pdb=" N   LYS B 418 " --> pdb=" O   ILE B 414 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   LEU B 419 " --> pdb=" O   LYS B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 445
    Processing helix  chain 'C' and resid 108 through 110
      No H-bonds generated for 'chain 'C' and resid 108 through 110'
    Processing helix  chain 'C' and resid 144 through 146
      No H-bonds generated for 'chain 'C' and resid 144 through 146'
    Processing helix  chain 'C' and resid 160 through 163
      No H-bonds generated for 'chain 'C' and resid 160 through 163'
    Processing helix  chain 'C' and resid 183 through 189
    Processing helix  chain 'C' and resid 208 through 213
      removed outlier: 3.567A  pdb=" N   VAL C 211 " --> pdb=" O   GLY C 208 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ASN C 212 " --> pdb=" O   ARG C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 225
      removed outlier: 5.179A  pdb=" N   LYS C 225 " --> pdb=" O   SER C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 237 through 241
    Processing helix  chain 'C' and resid 244 through 256
    Processing helix  chain 'C' and resid 268 through 281
    Processing helix  chain 'C' and resid 293 through 296
      No H-bonds generated for 'chain 'C' and resid 293 through 296'
    Processing helix  chain 'C' and resid 300 through 305
      removed outlier: 5.546A  pdb=" N   ARG C 305 " --> pdb=" O   LYS C 301 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 336
    Processing helix  chain 'C' and resid 347 through 351
    Processing helix  chain 'C' and resid 368 through 371
      No H-bonds generated for 'chain 'C' and resid 368 through 371'
    Processing helix  chain 'C' and resid 374 through 399
      removed outlier: 5.826A  pdb=" N   LEU C 395 " --> pdb=" O   LYS C 391 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   LEU C 396 " --> pdb=" O   ASN C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 410 through 424
      removed outlier: 5.127A  pdb=" N   LYS C 418 " --> pdb=" O   ILE C 414 " (cutoff:3.500A)
      removed outlier: 5.532A  pdb=" N   LEU C 419 " --> pdb=" O   LYS C 415 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 434 through 445
    Processing helix  chain 'D' and resid 108 through 110
      No H-bonds generated for 'chain 'D' and resid 108 through 110'
    Processing helix  chain 'D' and resid 159 through 163
    Processing helix  chain 'D' and resid 183 through 193
    Processing helix  chain 'D' and resid 208 through 217
      removed outlier: 3.520A  pdb=" N   VAL D 211 " --> pdb=" O   GLY D 208 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ASN D 212 " --> pdb=" O   ARG D 209 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   PHE D 214 " --> pdb=" O   VAL D 211 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU D 217 " --> pdb=" O   PHE D 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 225
      removed outlier: 3.801A  pdb=" N   LYS D 225 " --> pdb=" O   SER D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 237 through 256
      removed outlier: 5.463A  pdb=" N   ALA D 244 " --> pdb=" O   ARG D 240 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   PHE D 245 " --> pdb=" O   MET D 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 268 through 281
    Processing helix  chain 'D' and resid 293 through 298
    Processing helix  chain 'D' and resid 300 through 305
      removed outlier: 5.233A  pdb=" N   ARG D 305 " --> pdb=" O   LYS D 301 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 330 through 338
    Processing helix  chain 'D' and resid 347 through 350
      No H-bonds generated for 'chain 'D' and resid 347 through 350'
    Processing helix  chain 'D' and resid 374 through 398
      removed outlier: 4.768A  pdb=" N   LEU D 395 " --> pdb=" O   LYS D 391 " (cutoff:3.500A)
      removed outlier: 5.132A  pdb=" N   LEU D 396 " --> pdb=" O   ASN D 392 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE D 397 " --> pdb=" O   VAL D 393 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 408 through 415
    Processing helix  chain 'D' and resid 417 through 424
      removed outlier: 3.861A  pdb=" N   ASN D 422 " --> pdb=" O   LYS D 418 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   PHE D 423 " --> pdb=" O   LEU D 419 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 434 through 445
      removed outlier: 3.505A  pdb=" N   ILE D 438 " --> pdb=" O   TYR D 434 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 163
      No H-bonds generated for 'chain 'E' and resid 160 through 163'
    Processing helix  chain 'E' and resid 183 through 192
    Processing helix  chain 'E' and resid 208 through 215
      removed outlier: 3.855A  pdb=" N   VAL E 211 " --> pdb=" O   GLY E 208 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   ASN E 212 " --> pdb=" O   ARG E 209 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU E 215 " --> pdb=" O   ASN E 212 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 223
      No H-bonds generated for 'chain 'E' and resid 220 through 223'
    Processing helix  chain 'E' and resid 237 through 256
      removed outlier: 5.259A  pdb=" N   ALA E 244 " --> pdb=" O   ARG E 240 " (cutoff:3.500A)
      removed outlier: 4.851A  pdb=" N   PHE E 245 " --> pdb=" O   MET E 241 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 268 through 282
      removed outlier: 3.687A  pdb=" N   ALA E 281 " --> pdb=" O   ASP E 277 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   SER E 282 " --> pdb=" O   VAL E 278 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 302
      Proline residue:  E 300  - end of helix
    Processing helix  chain 'E' and resid 333 through 337
    Processing helix  chain 'E' and resid 347 through 350
      No H-bonds generated for 'chain 'E' and resid 347 through 350'
    Processing helix  chain 'E' and resid 374 through 398
      removed outlier: 3.955A  pdb=" N   ASN E 392 " --> pdb=" O   ALA E 388 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU E 394 " --> pdb=" O   TYR E 390 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   LEU E 395 " --> pdb=" O   LYS E 391 " (cutoff:3.500A)
      removed outlier: 4.979A  pdb=" N   LEU E 396 " --> pdb=" O   ASN E 392 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 408 through 415
      removed outlier: 3.848A  pdb=" N   LYS E 415 " --> pdb=" O   ASP E 411 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 417 through 424
    Processing helix  chain 'E' and resid 434 through 445
    Processing helix  chain 'F' and resid 108 through 110
      No H-bonds generated for 'chain 'F' and resid 108 through 110'
    Processing helix  chain 'F' and resid 144 through 146
      No H-bonds generated for 'chain 'F' and resid 144 through 146'
    Processing helix  chain 'F' and resid 159 through 164
    Processing helix  chain 'F' and resid 183 through 191
    Processing helix  chain 'F' and resid 210 through 215
    Processing helix  chain 'F' and resid 220 through 223
      No H-bonds generated for 'chain 'F' and resid 220 through 223'
    Processing helix  chain 'F' and resid 237 through 256
      removed outlier: 5.292A  pdb=" N   ALA F 244 " --> pdb=" O   ARG F 240 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   PHE F 245 " --> pdb=" O   MET F 241 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 268 through 282
    Processing helix  chain 'F' and resid 293 through 303
      Proline residue:  F 300  - end of helix
    Processing helix  chain 'F' and resid 332 through 336
    Processing helix  chain 'F' and resid 374 through 387
    Processing helix  chain 'F' and resid 391 through 398
      removed outlier: 4.186A  pdb=" N   LEU F 395 " --> pdb=" O   LYS F 391 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   LEU F 396 " --> pdb=" O   ASN F 392 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 411 through 415
    Processing helix  chain 'F' and resid 418 through 423
    Processing helix  chain 'F' and resid 434 through 444
      removed outlier: 3.554A  pdb=" N   ILE F 438 " --> pdb=" O   TYR F 434 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLU F 439 " --> pdb=" O   GLU F 435 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 38 through 41
      removed outlier: 6.791A  pdb=" N   LYS A  47 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   ILE A  41 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   ILE A  45 " --> pdb=" O   ILE A  41 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ALA A  72 " --> pdb=" O   PHE A  79 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   LEU A  81 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   VAL A  70 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 103 through 106
    Processing sheet with id=  C, first strand: chain 'A' and resid 113 through 115
      removed outlier: 4.096A  pdb=" N   ARG A 113 " --> pdb=" O   CYS A 226 " (cutoff:3.500A)
      removed outlier: 7.474A  pdb=" N   ILE A 199 " --> pdb=" O   VAL A 227 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   VAL A 229 " --> pdb=" O   ILE A 199 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   LEU A 201 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE A 198 " --> pdb=" O   ASN A 260 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   SER A 313 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   LEU A 263 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   THR A 315 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   MET A 265 " --> pdb=" O   THR A 315 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ILE A 317 " --> pdb=" O   MET A 265 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 37 through 41
      removed outlier: 3.770A  pdb=" N   LYS B  37 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   LYS B  47 " --> pdb=" O   ILE B  39 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   ILE B  41 " --> pdb=" O   ILE B  45 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ILE B  45 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   LEU B  81 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   VAL B  70 " --> pdb=" O   LEU B  81 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 103 through 106
    Processing sheet with id=  F, first strand: chain 'B' and resid 172 through 177
      removed outlier: 8.039A  pdb=" N   ILE B 173 " --> pdb=" O   ILE B 314 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ALA B 316 " --> pdb=" O   ILE B 173 " (cutoff:3.500A)
      removed outlier: 7.766A  pdb=" N   ILE B 175 " --> pdb=" O   ALA B 316 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   TYR B 318 " --> pdb=" O   ILE B 175 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   ALA B 177 " --> pdb=" O   TYR B 318 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL B 320 " --> pdb=" O   ALA B 177 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ILE B 198 " --> pdb=" O   LEU B 262 " (cutoff:3.500A)
      removed outlier: 7.784A  pdb=" N   MET B 264 " --> pdb=" O   ILE B 198 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   VAL B 200 " --> pdb=" O   MET B 264 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   ASP B 266 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   ALA B 202 " --> pdb=" O   ASP B 266 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'C' and resid 37 through 41
      removed outlier: 3.754A  pdb=" N   LYS C  37 " --> pdb=" O   ARG C  49 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LYS C  47 " --> pdb=" O   ILE C  39 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ALA C  72 " --> pdb=" O   PHE C  79 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LEU C  81 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   VAL C  70 " --> pdb=" O   LEU C  81 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ARG C  66 " --> pdb=" O   ILE C  61 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   PHE C  58 " --> pdb=" O   GLN C  98 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'C' and resid 103 through 106
    Processing sheet with id=  I, first strand: chain 'C' and resid 342 through 344
      removed outlier: 8.532A  pdb=" N   ILE C 343 " --> pdb=" O   ARG C 172 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   GLY C 174 " --> pdb=" O   ILE C 343 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   ILE C 173 " --> pdb=" O   ILE C 314 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ALA C 316 " --> pdb=" O   ILE C 173 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   ILE C 175 " --> pdb=" O   ALA C 316 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   TYR C 318 " --> pdb=" O   ILE C 175 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   ALA C 177 " --> pdb=" O   TYR C 318 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   VAL C 320 " --> pdb=" O   ALA C 177 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ILE C 198 " --> pdb=" O   LEU C 262 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   MET C 264 " --> pdb=" O   ILE C 198 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   VAL C 200 " --> pdb=" O   MET C 264 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'D' and resid 93 through 95
      removed outlier: 4.118A  pdb=" N   GLN D  93 " --> pdb=" O   ILE D  38 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLY D  36 " --> pdb=" O   LEU D  95 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   LYS D  47 " --> pdb=" O   ILE D  39 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   ILE D  41 " --> pdb=" O   ILE D  45 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   ILE D  45 " --> pdb=" O   ILE D  41 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   LEU D  81 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   VAL D  70 " --> pdb=" O   LEU D  81 " (cutoff:3.500A)
      removed outlier: 5.410A  pdb=" N   LYS D  60 " --> pdb=" O   TYR D  97 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   TYR D  97 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'D' and resid 103 through 106
    Processing sheet with id=  L, first strand: chain 'D' and resid 113 through 115
      removed outlier: 3.566A  pdb=" N   LEU D 228 " --> pdb=" O   ARG D 113 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE D 198 " --> pdb=" O   ASN D 260 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE D 204 " --> pdb=" O   ASP D 266 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   SER D 313 " --> pdb=" O   VAL D 261 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   LEU D 263 " --> pdb=" O   SER D 313 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   THR D 315 " --> pdb=" O   LEU D 263 " (cutoff:3.500A)
      removed outlier: 7.525A  pdb=" N   MET D 265 " --> pdb=" O   THR D 315 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ILE D 317 " --> pdb=" O   MET D 265 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'E' and resid 36 through 38
      removed outlier: 3.805A  pdb=" N   GLY E  36 " --> pdb=" O   LEU E  95 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   GLN E  93 " --> pdb=" O   ILE E  38 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   PHE E  79 " --> pdb=" O   ILE E  71 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ARG E  49 " --> pdb=" O   ILE E  38 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   ILE E  38 " --> pdb=" O   ARG E  49 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'E' and resid 103 through 106
    Processing sheet with id=  O, first strand: chain 'E' and resid 342 through 344
      removed outlier: 8.253A  pdb=" N   ILE E 343 " --> pdb=" O   ARG E 172 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   GLY E 174 " --> pdb=" O   ILE E 343 " (cutoff:3.500A)
      removed outlier: 8.382A  pdb=" N   ILE E 173 " --> pdb=" O   ILE E 314 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   ALA E 316 " --> pdb=" O   ILE E 173 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   ILE E 175 " --> pdb=" O   ALA E 316 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   TYR E 318 " --> pdb=" O   ILE E 175 " (cutoff:3.500A)
      removed outlier: 7.879A  pdb=" N   ALA E 177 " --> pdb=" O   TYR E 318 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   VAL E 320 " --> pdb=" O   ALA E 177 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL E 261 " --> pdb=" O   THR E 315 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   ILE E 317 " --> pdb=" O   VAL E 261 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU E 263 " --> pdb=" O   ILE E 317 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   THR E 319 " --> pdb=" O   LEU E 263 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   MET E 265 " --> pdb=" O   THR E 319 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   LEU E 321 " --> pdb=" O   MET E 265 " (cutoff:3.500A)
    Processing sheet with id=  P, first strand: chain 'F' and resid 37 through 41
      removed outlier: 4.000A  pdb=" N   LYS F  37 " --> pdb=" O   ARG F  49 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   LYS F  47 " --> pdb=" O   ILE F  39 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   ILE F  41 " --> pdb=" O   ILE F  45 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ILE F  45 " --> pdb=" O   ILE F  41 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   LEU F  81 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
      removed outlier: 5.309A  pdb=" N   VAL F  70 " --> pdb=" O   LEU F  81 " (cutoff:3.500A)
    Processing sheet with id=  Q, first strand: chain 'F' and resid 103 through 106
      removed outlier: 3.760A  pdb=" N   PHE F 133 " --> pdb=" O   VAL F 106 " (cutoff:3.500A)
    Processing sheet with id=  R, first strand: chain 'F' and resid 113 through 115
      removed outlier: 4.112A  pdb=" N   ARG F 113 " --> pdb=" O   CYS F 226 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   LEU F 228 " --> pdb=" O   ARG F 113 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE F 115 " --> pdb=" O   LEU F 228 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ILE F 199 " --> pdb=" O   VAL F 227 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   VAL F 229 " --> pdb=" O   ILE F 199 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   LEU F 201 " --> pdb=" O   VAL F 229 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ILE F 173 " --> pdb=" O   TYR F 318 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   VAL F 320 " --> pdb=" O   ILE F 173 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ILE F 175 " --> pdb=" O   VAL F 320 " (cutoff:3.500A)

    592 hydrogen bonds defined for protein.
    1713 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.66

  Time building geometry restraints manager: 7.10 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 5278
        1.33 -     1.45: 3114
        1.45 -     1.57: 10846
        1.57 -     1.69: 20
        1.69 -     1.82: 130
  Bond restraints: 19388
  Sorted by residual:
  bond pdb=" F3  AF3 C 602 "
       pdb="AL   AF3 C 602 "
    ideal  model  delta    sigma   weight residual
    1.637  1.733 -0.096 2.00e-02 2.50e+03 2.30e+01
  bond pdb=" F3  AF3 B 602 "
       pdb="AL   AF3 B 602 "
    ideal  model  delta    sigma   weight residual
    1.637  1.732 -0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" F3  AF3 D 602 "
       pdb="AL   AF3 D 602 "
    ideal  model  delta    sigma   weight residual
    1.637  1.731 -0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" F3  AF3 E 602 "
       pdb="AL   AF3 E 602 "
    ideal  model  delta    sigma   weight residual
    1.637  1.730 -0.093 2.00e-02 2.50e+03 2.15e+01
  bond pdb=" CB  THR C 269 "
       pdb=" CG2 THR C 269 "
    ideal  model  delta    sigma   weight residual
    1.521  1.439  0.082 3.30e-02 9.18e+02 6.18e+00
  ... (remaining 19383 not shown)

  Histogram of bond angle deviations from ideal:
       96.57 -   104.60: 391
      104.60 -   112.63: 9957
      112.63 -   120.66: 9503
      120.66 -   128.69: 6317
      128.69 -   136.72: 88
  Bond angle restraints: 26256
  Sorted by residual:
  angle pdb=" N   ARG E 207 "
        pdb=" CA  ARG E 207 "
        pdb=" C   ARG E 207 "
      ideal   model   delta    sigma   weight residual
     110.10  117.79   -7.69 1.49e+00 4.50e-01 2.67e+01
  angle pdb=" C   ASP E  74 "
        pdb=" N   GLU E  75 "
        pdb=" CA  GLU E  75 "
      ideal   model   delta    sigma   weight residual
     121.54  131.19   -9.65 1.91e+00 2.74e-01 2.55e+01
  angle pdb=" C   ASP C  74 "
        pdb=" N   GLU C  75 "
        pdb=" CA  GLU C  75 "
      ideal   model   delta    sigma   weight residual
     121.54  130.95   -9.41 1.91e+00 2.74e-01 2.43e+01
  angle pdb=" C2' ADP C 600 "
        pdb=" C3' ADP C 600 "
        pdb=" C4' ADP C 600 "
      ideal   model   delta    sigma   weight residual
     111.00   97.09   13.91 3.00e+00 1.11e-01 2.15e+01
  angle pdb=" CA  LEU E 339 "
        pdb=" CB  LEU E 339 "
        pdb=" CG  LEU E 339 "
      ideal   model   delta    sigma   weight residual
     116.30  132.52  -16.22 3.50e+00 8.16e-02 2.15e+01
  ... (remaining 26251 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.27: 11640
       30.27 -    60.53: 173
       60.53 -    90.80: 18
       90.80 -   121.06: 2
      121.06 -   151.33: 2
  Dihedral angle restraints: 11835
    sinusoidal: 4797
      harmonic: 7038
  Sorted by residual:
  dihedral pdb=" O1B ADP B 600 "
           pdb=" O3A ADP B 600 "
           pdb=" PB  ADP B 600 "
           pdb=" PA  ADP B 600 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  148.67  151.33     1      2.00e+01 2.50e-03 4.51e+01
  dihedral pdb=" C5' ADP B 600 "
           pdb=" O5' ADP B 600 "
           pdb=" PA  ADP B 600 "
           pdb=" O2A ADP B 600 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  175.76  124.25     1      2.00e+01 2.50e-03 3.75e+01
  dihedral pdb=" CA  TYR A  90 "
           pdb=" C   TYR A  90 "
           pdb=" N   CYS A  91 "
           pdb=" CA  CYS A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.35   29.65     0      5.00e+00 4.00e-02 3.52e+01
  ... (remaining 11832 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 2743
       0.111 -    0.222: 277
       0.222 -    0.332: 14
       0.332 -    0.443: 4
       0.443 -    0.554: 1
  Chirality restraints: 3039
  Sorted by residual:
  chirality pdb=" CB  ILE F 199 "
            pdb=" CA  ILE F 199 "
            pdb=" CG1 ILE F 199 "
            pdb=" CG2 ILE F 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.09    0.55 2.00e-01 2.50e+01 7.67e+00
  chirality pdb=" CB  ILE B 314 "
            pdb=" CA  ILE B 314 "
            pdb=" CG1 ILE B 314 "
            pdb=" CG2 ILE B 314 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.21    0.44 2.00e-01 2.50e+01 4.83e+00
  chirality pdb=" CB  ILE F 314 "
            pdb=" CA  ILE F 314 "
            pdb=" CG1 ILE F 314 "
            pdb=" CG2 ILE F 314 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.24    0.40 2.00e-01 2.50e+01 4.05e+00
  ... (remaining 3036 not shown)

  Planarity restraints: 3388
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 131 "    0.048 5.00e-02 4.00e+02   7.23e-02 8.36e+00
        pdb=" N   PRO C 132 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO C 132 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO C 132 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 329 "   -0.041 5.00e-02 4.00e+02   6.20e-02 6.15e+00
        pdb=" N   PRO D 330 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO D 330 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D 330 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 425 "    0.012 2.00e-02 2.50e+03   2.40e-02 5.74e+00
        pdb=" CD  GLN B 425 "   -0.041 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 425 "    0.016 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 425 "    0.014 2.00e-02 2.50e+03
  ... (remaining 3385 not shown)

  Histogram of nonbonded interaction distances:
        1.36 -     2.07: 7
        2.07 -     2.78: 3975
        2.78 -     3.48: 24942
        3.48 -     4.19: 44760
        4.19 -     4.90: 80434
  Nonbonded interactions: 154118
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 161 "
            pdb=" O   LEU B 165 "
     model   vdw
     1.361 3.040
  nonbonded pdb=" OG  SER B 184 "
            pdb="MG    MG B 601 "
     model   vdw
     1.720 2.170
  nonbonded pdb=" OG  SER C 184 "
            pdb="MG    MG C 601 "
     model   vdw
     1.921 2.170
  nonbonded pdb=" NH1 ARG D 366 "
            pdb=" NH2 ARG E 207 "
     model   vdw
     1.929 3.200
  nonbonded pdb=" OD1 ASP D 266 "
            pdb=" O   HOH D1002 "
     model   vdw
     1.956 2.440
  ... (remaining 154113 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 35 through 322 or resid 330 through 446))
  selection = (chain 'B' and (resid 35 through 322 or resid 330 through 446))
  selection = (chain 'C' and (resid 35 through 322 or resid 330 through 446))
  selection = (chain 'D' and (resid 35 through 322 or resid 330 through 446))
  selection = (chain 'E' and (resid 35 through 322 or resid 330 through 446))
  selection = chain 'F'
}

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=0.30 max=1.00 mean=0.99
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:             2.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          2.830
  Check model and map are aligned:         0.300
  Set scattering table:                    0.180
  Process input model:                     45.710
  Find NCS groups from input model:        1.670
  Set up NCS constraints:                  0.090
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
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   0.096  19388  Z= 0.643
  Angle     :  1.199  16.220  26256  Z= 0.609
  Chirality :  0.069   0.554   3039
  Planarity :  0.008   0.072   3388
  Dihedral  : 11.616 151.327   7323
  Min Nonbonded Distance : 1.361

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  5.54 %
    Favored  : 93.97 %
  Cbeta Deviations :  0.04 %
  Peptide Plane:
    Cis-proline     : 4.80 %
    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: -4.27 (0.13), residues: 2452
  helix: -3.09 (0.12), residues: 919
  sheet: -2.26 (0.22), residues: 440
  loop : -2.72 (0.15), residues: 1093

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  94 
 HIS   0.010   0.003   HIS D 376 
 PHE   0.038   0.004   PHE C  58 
 TYR   0.030   0.004   TYR B 434 
 ARG   0.015   0.002   ARG E 209 

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

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

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 315
  time to evaluate  : 2.288 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.7225 (mtp-110) cc_final: 0.6622 (ttm-80)
REVERT: A   69 GLU cc_start: 0.4942 (tt0) cc_final: 0.4647 (tp30)
REVERT: A  113 ARG cc_start: 0.6918 (mmt-90) cc_final: 0.6529 (mmt90)
REVERT: A  267 SER cc_start: 0.8294 (t) cc_final: 0.8039 (p)
REVERT: A  436 LYS cc_start: 0.7768 (tmtt) cc_final: 0.7305 (ttpt)
REVERT: A  441 LEU cc_start: 0.7067 (tp) cc_final: 0.6813 (tp)
REVERT: B   98 GLN cc_start: 0.7839 (mm110) cc_final: 0.7524 (mm110)
REVERT: B  368 MET cc_start: 0.8904 (tpt) cc_final: 0.8615 (tpt)
REVERT: B  414 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6537 (mp)
REVERT: C   41 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8074 (mp)
REVERT: C   54 ARG cc_start: 0.7692 (mmt90) cc_final: 0.7473 (mpp80)
REVERT: C   84 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7568 (mm-30)
REVERT: C  220 GLN cc_start: 0.6746 (tp40) cc_final: 0.6159 (tp-100)
REVERT: C  398 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.6825 (ttm170)
REVERT: C  402 TYR cc_start: 0.6403 (t80) cc_final: 0.6120 (t80)
REVERT: D  311 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8159 (mtmm)
REVERT: D  436 LYS cc_start: 0.7277 (tmtt) cc_final: 0.6780 (ttpt)
REVERT: E   75 GLU cc_start: 0.4953 (tm-30) cc_final: 0.4226 (pp20)
REVERT: E  113 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7460 (mmp80)
REVERT: E  149 VAL cc_start: 0.7794 (t) cc_final: 0.7489 (p)
REVERT: E  271 TYR cc_start: 0.9015 (t80) cc_final: 0.8665 (t80)
REVERT: E  311 LYS cc_start: 0.7553 (tptm) cc_final: 0.7230 (ptmt)
REVERT: E  431 ILE cc_start: 0.8247 (pt) cc_final: 0.7788 (mm)
REVERT: F   52 LYS cc_start: 0.6594 (pttp) cc_final: 0.6297 (tptt)
REVERT: F  116 ASP cc_start: 0.7924 (t70) cc_final: 0.7554 (t0)
REVERT: F  265 MET cc_start: 0.7606 (ttm) cc_final: 0.7380 (ttm)
REVERT: F  394 GLU cc_start: 0.5836 (tp30) cc_final: 0.5570 (tp30)
REVERT: F  443 LYS cc_start: 0.6856 (pmtt) cc_final: 0.6532 (mppt)
  outliers start: 10
  outliers final: 3
  residues processed: 325
  average time/residue: 0.3848
  time to fit residues: 176.7322
Evaluate side-chains
  225 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 220
  time to evaluate  : 2.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain E residue  261 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 245
   random chunks:
   chunk 206 optimal weight:    1.9990
   chunk 185 optimal weight:    0.9990
   chunk 103 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 125 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 192 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 116 optimal weight:    0.9980
   chunk 142 optimal weight:    3.9990
   chunk 222 optimal weight:    7.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** D  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 260 ASN
E 220 GLN
F 212 ASN
F 257 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  19388  Z= 0.161
  Angle     :  0.620   7.088  26256  Z= 0.301
  Chirality :  0.045   0.220   3039
  Planarity :  0.005   0.063   3388
  Dihedral  :  7.595 126.070   2740
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  :  9.46 %
    Favored  : 88.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.80 %
    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: -2.93 (0.15), residues: 2452
  helix: -1.48 (0.16), residues: 934
  sheet: -1.94 (0.22), residues: 445
  loop : -2.26 (0.17), residues: 1073

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  94 
 HIS   0.002   0.001   HIS F  85 
 PHE   0.017   0.001   PHE F  58 
 TYR   0.022   0.002   TYR B 390 
 ARG   0.005   0.000   ARG F 270 

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

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

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 259
  time to evaluate  : 2.347 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.7015 (mtp-110) cc_final: 0.6527 (ttm-80)
REVERT: A   74 ASP cc_start: 0.5918 (OUTLIER) cc_final: 0.5429 (m-30)
REVERT: A  113 ARG cc_start: 0.6860 (mmt-90) cc_final: 0.6466 (mmt90)
REVERT: A  191 CYS cc_start: 0.7483 (m) cc_final: 0.6972 (m)
REVERT: A  418 LYS cc_start: 0.7193 (tptp) cc_final: 0.6933 (tptp)
REVERT: A  429 LYS cc_start: 0.8264 (mtmm) cc_final: 0.7958 (mmtt)
REVERT: B   47 LYS cc_start: 0.8281 (mttm) cc_final: 0.8077 (mttm)
REVERT: B  120 ARG cc_start: 0.7366 (mtm180) cc_final: 0.7083 (mtm-85)
REVERT: C   41 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7690 (mp)
REVERT: C  105 ARG cc_start: 0.8431 (tpp-160) cc_final: 0.8117 (tpp-160)
REVERT: C  220 GLN cc_start: 0.6471 (tp40) cc_final: 0.5956 (tp-100)
REVERT: C  368 MET cc_start: 0.8651 (ttp) cc_final: 0.8441 (ttt)
REVERT: C  398 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.6888 (ttm170)
REVERT: C  406 GLN cc_start: 0.5900 (tt0) cc_final: 0.5252 (mt0)
REVERT: C  436 LYS cc_start: 0.7185 (tttt) cc_final: 0.6751 (tmtt)
REVERT: D   59 TYR cc_start: 0.8522 (m-80) cc_final: 0.8311 (m-80)
REVERT: D  311 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8152 (mtpp)
REVERT: D  436 LYS cc_start: 0.7132 (tmtt) cc_final: 0.6598 (ttpt)
REVERT: E   75 GLU cc_start: 0.4803 (tm-30) cc_final: 0.4500 (tm-30)
REVERT: E  113 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7505 (mmp80)
REVERT: E  145 LEU cc_start: 0.8355 (mt) cc_final: 0.7944 (mt)
REVERT: E  238 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7472 (pt)
REVERT: E  271 TYR cc_start: 0.8902 (t80) cc_final: 0.8646 (t80)
REVERT: E  311 LYS cc_start: 0.7338 (tptm) cc_final: 0.7032 (ptmm)
REVERT: E  370 ASN cc_start: 0.8455 (m110) cc_final: 0.8129 (m110)
REVERT: E  431 ILE cc_start: 0.8179 (pt) cc_final: 0.7804 (mm)
REVERT: F  116 ASP cc_start: 0.7857 (t70) cc_final: 0.7523 (t0)
REVERT: F  189 MET cc_start: 0.6992 (ptm) cc_final: 0.6769 (ptm)
REVERT: F  311 LYS cc_start: 0.4764 (pmmt) cc_final: 0.3908 (ttpp)
REVERT: F  360 ILE cc_start: 0.8985 (mm) cc_final: 0.8761 (mm)
  outliers start: 47
  outliers final: 20
  residues processed: 297
  average time/residue: 0.3741
  time to fit residues: 160.5204
Evaluate side-chains
  225 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 202
  time to evaluate  : 2.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  108 ASP
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  191 CYS
Chi-restraints excluded: chain C residue  315 THR
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain E residue  238 LEU
Chi-restraints excluded: chain E residue  261 VAL
Chi-restraints excluded: chain E residue  377 LEU
Chi-restraints excluded: chain E residue  444 VAL
Chi-restraints excluded: chain F residue  227 VAL
Chi-restraints excluded: chain F residue  303 LEU
Chi-restraints excluded: chain F residue  321 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 245
   random chunks:
   chunk 123 optimal weight:    0.0870
   chunk 69 optimal weight:    6.9990
   chunk 185 optimal weight:    7.9990
   chunk 151 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 222 optimal weight:    6.9990
   chunk 240 optimal weight:    9.9990
   chunk 198 optimal weight:   20.0000
   chunk 221 optimal weight:   20.0000
   chunk 75 optimal weight:    6.9990
   chunk 178 optimal weight:    4.9990
   overall best weight:    3.0164

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

Flipped N/Q/H residues before XYZ refinement:
B  85 HIS
D  93 GLN
E  98 GLN
E 376 HIS
F  85 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  19388  Z= 0.327
  Angle     :  0.700  11.197  26256  Z= 0.335
  Chirality :  0.048   0.217   3039
  Planarity :  0.005   0.066   3388
  Dihedral  :  7.672 128.036   2738
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 11.13 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.80 %
    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: -2.40 (0.16), residues: 2452
  helix: -0.89 (0.17), residues: 929
  sheet: -1.74 (0.23), residues: 450
  loop : -2.06 (0.17), residues: 1073

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  94 
 HIS   0.005   0.001   HIS C 342 
 PHE   0.020   0.002   PHE C  58 
 TYR   0.019   0.002   TYR C  97 
 ARG   0.005   0.001   ARG B 417 

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

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

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 78
    poor density    : 208
  time to evaluate  : 2.158 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.6961 (mtp-110) cc_final: 0.6510 (ttm-80)
REVERT: A   74 ASP cc_start: 0.6204 (OUTLIER) cc_final: 0.5960 (m-30)
REVERT: A  375 GLU cc_start: 0.6393 (pm20) cc_final: 0.6013 (pm20)
REVERT: B  120 ARG cc_start: 0.7422 (mtm180) cc_final: 0.7105 (mtm-85)
REVERT: C   41 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7911 (mp)
REVERT: C  113 ARG cc_start: 0.8664 (ptp-110) cc_final: 0.8398 (ptp-110)
REVERT: C  220 GLN cc_start: 0.6727 (tp40) cc_final: 0.6153 (tp-100)
REVERT: C  398 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.6891 (ttm170)
REVERT: C  436 LYS cc_start: 0.7349 (tttt) cc_final: 0.6863 (tmtt)
REVERT: D  311 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8214 (mtpp)
REVERT: D  396 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6319 (pp)
REVERT: D  436 LYS cc_start: 0.7418 (tmtt) cc_final: 0.6756 (ttpt)
REVERT: E   75 GLU cc_start: 0.4748 (tm-30) cc_final: 0.4197 (tm-30)
REVERT: E  113 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7427 (mmp80)
REVERT: E  238 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7635 (pt)
REVERT: E  311 LYS cc_start: 0.7426 (tptm) cc_final: 0.7136 (ptmt)
REVERT: E  431 ILE cc_start: 0.8133 (pt) cc_final: 0.7669 (mm)
REVERT: F  116 ASP cc_start: 0.7957 (t70) cc_final: 0.7488 (t0)
REVERT: F  252 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7599 (mt-10)
REVERT: F  311 LYS cc_start: 0.5030 (pmmt) cc_final: 0.4123 (ttpp)
  outliers start: 78
  outliers final: 40
  residues processed: 274
  average time/residue: 0.3614
  time to fit residues: 143.5316
Evaluate side-chains
  232 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 188
  time to evaluate  : 2.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  392 ASN
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  108 ASP
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  191 CYS
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  224 SER
Chi-restraints excluded: chain C residue  315 THR
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain D residue  372 VAL
Chi-restraints excluded: chain D residue  396 LEU
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  238 LEU
Chi-restraints excluded: chain E residue  261 VAL
Chi-restraints excluded: chain E residue  377 LEU
Chi-restraints excluded: chain E residue  444 VAL
Chi-restraints excluded: chain F residue   80 LEU
Chi-restraints excluded: chain F residue  227 VAL
Chi-restraints excluded: chain F residue  277 ASP
Chi-restraints excluded: chain F residue  282 SER
Chi-restraints excluded: chain F residue  303 LEU
Chi-restraints excluded: chain F residue  321 LEU
Chi-restraints excluded: chain F residue  349 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 245
   random chunks:
   chunk 220 optimal weight:    9.9990
   chunk 167 optimal weight:    6.9990
   chunk 115 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 106 optimal weight:    0.6980
   chunk 149 optimal weight:    4.9990
   chunk 223 optimal weight:    2.9990
   chunk 236 optimal weight:    6.9990
   chunk 116 optimal weight:   10.0000
   chunk 212 optimal weight:    9.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    4.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  85 HIS
B  85 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067  19388  Z= 0.455
  Angle     :  0.781  11.155  26256  Z= 0.375
  Chirality :  0.051   0.426   3039
  Planarity :  0.006   0.071   3388
  Dihedral  :  7.968 128.566   2736
  Min Nonbonded Distance : 1.767

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 12.11 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.80 %
    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: -2.29 (0.16), residues: 2452
  helix: -0.80 (0.17), residues: 920
  sheet: -1.75 (0.24), residues: 457
  loop : -1.96 (0.17), residues: 1075

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  94 
 HIS   0.007   0.002   HIS C 342 
 PHE   0.027   0.002   PHE A  58 
 TYR   0.021   0.002   TYR C  97 
 ARG   0.006   0.001   ARG E 288 

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

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

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 87
    poor density    : 204
  time to evaluate  : 1.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.7128 (mtp-110) cc_final: 0.6675 (ttm-80)
REVERT: A   79 PHE cc_start: 0.7211 (m-80) cc_final: 0.6995 (m-80)
REVERT: A  162 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7578 (t0)
REVERT: A  333 ASP cc_start: 0.7987 (t70) cc_final: 0.7578 (t0)
REVERT: B  101 GLU cc_start: 0.7424 (pt0) cc_final: 0.7196 (mt-10)
REVERT: B  120 ARG cc_start: 0.7480 (mtm180) cc_final: 0.7153 (mtm-85)
REVERT: C   41 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.7949 (mp)
REVERT: C  113 ARG cc_start: 0.8773 (ptp-110) cc_final: 0.8563 (ptp-110)
REVERT: C  220 GLN cc_start: 0.6630 (tp40) cc_final: 0.6053 (tp40)
REVERT: C  398 ARG cc_start: 0.7811 (ttm-80) cc_final: 0.6843 (ttm170)
REVERT: C  436 LYS cc_start: 0.7323 (tttt) cc_final: 0.6842 (tmtt)
REVERT: D  311 LYS cc_start: 0.8494 (mtmt) cc_final: 0.8224 (mtpp)
REVERT: D  396 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6427 (pp)
REVERT: E   75 GLU cc_start: 0.4718 (tm-30) cc_final: 0.3412 (tt0)
REVERT: E  113 ARG cc_start: 0.7906 (mmm-85) cc_final: 0.7532 (mmp80)
REVERT: E  198 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8040 (mt)
REVERT: E  238 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7762 (pt)
REVERT: E  311 LYS cc_start: 0.7500 (tptm) cc_final: 0.7169 (ptmt)
REVERT: E  385 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7386 (tppt)
REVERT: E  394 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.4615 (pm20)
REVERT: F   69 GLU cc_start: 0.7561 (tm-30) cc_final: 0.6824 (tm-30)
REVERT: F  116 ASP cc_start: 0.7919 (t70) cc_final: 0.7433 (t0)
REVERT: F  311 LYS cc_start: 0.4667 (pmmt) cc_final: 0.3915 (ttpp)
  outliers start: 87
  outliers final: 51
  residues processed: 278
  average time/residue: 0.3550
  time to fit residues: 147.4019
Evaluate side-chains
  242 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 185
  time to evaluate  : 2.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  392 ASN
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  108 ASP
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  191 CYS
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  315 THR
Chi-restraints excluded: chain C residue  368 MET
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  372 VAL
Chi-restraints excluded: chain D residue  396 LEU
Chi-restraints excluded: chain D residue  420 ILE
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  238 LEU
Chi-restraints excluded: chain E residue  261 VAL
Chi-restraints excluded: chain E residue  334 GLU
Chi-restraints excluded: chain E residue  394 GLU
Chi-restraints excluded: chain E residue  444 VAL
Chi-restraints excluded: chain F residue   80 LEU
Chi-restraints excluded: chain F residue  227 VAL
Chi-restraints excluded: chain F residue  277 ASP
Chi-restraints excluded: chain F residue  282 SER
Chi-restraints excluded: chain F residue  304 GLU
Chi-restraints excluded: chain F residue  321 LEU
Chi-restraints excluded: chain F residue  349 LEU
Chi-restraints excluded: chain F residue  372 VAL
Chi-restraints excluded: chain F residue  393 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 245
   random chunks:
   chunk 197 optimal weight:    5.9990
   chunk 134 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 176 optimal weight:    7.9990
   chunk 97 optimal weight:    0.7980
   chunk 202 optimal weight:    6.9990
   chunk 163 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 120 optimal weight:    4.9990
   chunk 212 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   overall best weight:    2.4784

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

Flipped N/Q/H residues before XYZ refinement:
B  85 HIS
F 392 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  19388  Z= 0.274
  Angle     :  0.663  10.078  26256  Z= 0.315
  Chirality :  0.046   0.291   3039
  Planarity :  0.005   0.069   3388
  Dihedral  :  7.453 115.022   2736
  Min Nonbonded Distance : 1.806

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 13.28 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.80 %
    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: -1.84 (0.17), residues: 2452
  helix: -0.31 (0.18), residues: 891
  sheet: -1.63 (0.24), residues: 453
  loop : -1.72 (0.18), residues: 1108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  94 
 HIS   0.005   0.001   HIS C 342 
 PHE   0.018   0.001   PHE C  58 
 TYR   0.021   0.002   TYR B 390 
 ARG   0.004   0.000   ARG E 288 

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

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

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 85
    poor density    : 200
  time to evaluate  : 2.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.7085 (mtp-110) cc_final: 0.6646 (ttm-80)
REVERT: A  333 ASP cc_start: 0.7978 (t70) cc_final: 0.7595 (t0)
REVERT: A  375 GLU cc_start: 0.6548 (pm20) cc_final: 0.6172 (pm20)
REVERT: B  120 ARG cc_start: 0.7283 (mtm180) cc_final: 0.6961 (mtm-85)
REVERT: C   41 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7691 (mp)
REVERT: C  220 GLN cc_start: 0.6619 (tp40) cc_final: 0.6005 (tp40)
REVERT: C  398 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.6808 (ttm170)
REVERT: C  436 LYS cc_start: 0.7233 (tttt) cc_final: 0.6756 (tmtt)
REVERT: D  311 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8191 (mtpp)
REVERT: D  396 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6413 (pp)
REVERT: E   75 GLU cc_start: 0.4810 (tm-30) cc_final: 0.4115 (tm-30)
REVERT: E  113 ARG cc_start: 0.7942 (mmm-85) cc_final: 0.7578 (mmp80)
REVERT: E  238 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7659 (pt)
REVERT: E  311 LYS cc_start: 0.7450 (tptm) cc_final: 0.7186 (ptmt)
REVERT: E  385 LYS cc_start: 0.8083 (ttmt) cc_final: 0.7371 (tppt)
REVERT: E  394 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.4545 (pm20)
REVERT: F  116 ASP cc_start: 0.7859 (t70) cc_final: 0.7245 (t0)
REVERT: F  120 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6148 (mtm-85)
REVERT: F  443 LYS cc_start: 0.6729 (mppt) cc_final: 0.6422 (mmtt)
  outliers start: 85
  outliers final: 52
  residues processed: 272
  average time/residue: 0.3373
  time to fit residues: 135.6526
Evaluate side-chains
  247 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 190
  time to evaluate  : 2.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  108 ASP
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  191 CYS
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain C residue  234 ASP
Chi-restraints excluded: chain C residue  315 THR
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  368 MET
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain D residue   55 ILE
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  241 MET
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain D residue  372 VAL
Chi-restraints excluded: chain D residue  396 LEU
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  238 LEU
Chi-restraints excluded: chain E residue  261 VAL
Chi-restraints excluded: chain E residue  377 LEU
Chi-restraints excluded: chain E residue  394 GLU
Chi-restraints excluded: chain E residue  431 ILE
Chi-restraints excluded: chain F residue   80 LEU
Chi-restraints excluded: chain F residue  120 ARG
Chi-restraints excluded: chain F residue  227 VAL
Chi-restraints excluded: chain F residue  282 SER
Chi-restraints excluded: chain F residue  295 VAL
Chi-restraints excluded: chain F residue  302 LEU
Chi-restraints excluded: chain F residue  304 GLU
Chi-restraints excluded: chain F residue  321 LEU
Chi-restraints excluded: chain F residue  349 LEU
Chi-restraints excluded: chain F residue  372 VAL
Chi-restraints excluded: chain F residue  382 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 245
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 213 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 139 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 237 optimal weight:   20.0000
   chunk 196 optimal weight:    0.9990
   chunk 109 optimal weight:    0.7980
   chunk 19 optimal weight:   10.0000
   chunk 78 optimal weight:    6.9990
   chunk 124 optimal weight:    6.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
B  85 HIS
E 422 ASN
F 392 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  19388  Z= 0.267
  Angle     :  0.652  10.495  26256  Z= 0.309
  Chirality :  0.046   0.316   3039
  Planarity :  0.004   0.070   3388
  Dihedral  :  7.270 109.718   2736
  Min Nonbonded Distance : 1.815

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 13.43 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.80 %
    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: -1.67 (0.17), residues: 2452
  helix: -0.10 (0.18), residues: 885
  sheet: -1.55 (0.24), residues: 443
  loop : -1.69 (0.18), residues: 1124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  94 
 HIS   0.004   0.001   HIS C 342 
 PHE   0.018   0.002   PHE C  58 
 TYR   0.018   0.002   TYR C  97 
 ARG   0.007   0.000   ARG C 113 

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

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

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 94
    poor density    : 203
  time to evaluate  : 2.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.7188 (mtp-110) cc_final: 0.6621 (ttm-80)
REVERT: A  333 ASP cc_start: 0.8032 (t70) cc_final: 0.7636 (t0)
REVERT: B  120 ARG cc_start: 0.7271 (mtm180) cc_final: 0.6947 (mtm-85)
REVERT: B  421 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.6299 (mp10)
REVERT: B  425 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.6160 (mp10)
REVERT: C   41 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7746 (mp)
REVERT: C  220 GLN cc_start: 0.6539 (tp40) cc_final: 0.5958 (tp40)
REVERT: C  398 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.6805 (ttm170)
REVERT: C  406 GLN cc_start: 0.5816 (tt0) cc_final: 0.5198 (mt0)
REVERT: C  436 LYS cc_start: 0.7238 (tttt) cc_final: 0.6777 (tmtt)
REVERT: D  311 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8242 (mtpp)
REVERT: D  396 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6490 (pp)
REVERT: E   75 GLU cc_start: 0.4897 (tm-30) cc_final: 0.4160 (tm-30)
REVERT: E  110 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7463 (tt)
REVERT: E  113 ARG cc_start: 0.7924 (mmm-85) cc_final: 0.7593 (mmp80)
REVERT: E  238 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7638 (pt)
REVERT: E  311 LYS cc_start: 0.7463 (tptm) cc_final: 0.7205 (ptmt)
REVERT: E  385 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7376 (tppt)
REVERT: E  394 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.4505 (pm20)
REVERT: F   69 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6776 (tm-30)
REVERT: F  116 ASP cc_start: 0.7819 (t70) cc_final: 0.7241 (t0)
REVERT: F  120 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6174 (mtm-85)
REVERT: F  443 LYS cc_start: 0.6738 (mppt) cc_final: 0.6422 (mmtt)
  outliers start: 94
  outliers final: 62
  residues processed: 286
  average time/residue: 0.3332
  time to fit residues: 141.0295
Evaluate side-chains
  261 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 70
    poor density    : 191
  time to evaluate  : 2.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  392 ASN
Chi-restraints excluded: chain A residue  418 LYS
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  108 ASP
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  421 GLN
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  191 CYS
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain C residue  234 ASP
Chi-restraints excluded: chain C residue  315 THR
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  368 MET
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain D residue   55 ILE
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  241 MET
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain D residue  372 VAL
Chi-restraints excluded: chain D residue  396 LEU
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  238 LEU
Chi-restraints excluded: chain E residue  261 VAL
Chi-restraints excluded: chain E residue  334 GLU
Chi-restraints excluded: chain E residue  377 LEU
Chi-restraints excluded: chain E residue  394 GLU
Chi-restraints excluded: chain E residue  399 ILE
Chi-restraints excluded: chain E residue  431 ILE
Chi-restraints excluded: chain F residue   80 LEU
Chi-restraints excluded: chain F residue  120 ARG
Chi-restraints excluded: chain F residue  227 VAL
Chi-restraints excluded: chain F residue  282 SER
Chi-restraints excluded: chain F residue  295 VAL
Chi-restraints excluded: chain F residue  302 LEU
Chi-restraints excluded: chain F residue  304 GLU
Chi-restraints excluded: chain F residue  321 LEU
Chi-restraints excluded: chain F residue  349 LEU
Chi-restraints excluded: chain F residue  372 VAL
Chi-restraints excluded: chain F residue  382 GLU
Chi-restraints excluded: chain F residue  393 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 245
   random chunks:
   chunk 228 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 135 optimal weight:    0.8980
   chunk 173 optimal weight:    8.9990
   chunk 134 optimal weight:    7.9990
   chunk 199 optimal weight:   10.0000
   chunk 132 optimal weight:    9.9990
   chunk 236 optimal weight:    2.9990
   chunk 147 optimal weight:    2.9990
   chunk 143 optimal weight:    0.9990
   chunk 109 optimal weight:    8.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
B  85 HIS
** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 392 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  19388  Z= 0.251
  Angle     :  0.647  10.278  26256  Z= 0.306
  Chirality :  0.046   0.369   3039
  Planarity :  0.004   0.068   3388
  Dihedral  :  7.103 106.271   2736
  Min Nonbonded Distance : 1.825

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 13.48 %
    Favored  : 82.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.80 %
    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: -1.54 (0.17), residues: 2452
  helix:  0.04 (0.18), residues: 885
  sheet: -1.45 (0.25), residues: 443
  loop : -1.66 (0.18), residues: 1124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  94 
 HIS   0.004   0.001   HIS C 342 
 PHE   0.018   0.001   PHE C  58 
 TYR   0.017   0.002   TYR C  97 
 ARG   0.005   0.000   ARG C 113 

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

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

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 91
    poor density    : 203
  time to evaluate  : 1.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.7192 (mtp-110) cc_final: 0.6620 (ttm-80)
REVERT: A  333 ASP cc_start: 0.8008 (t70) cc_final: 0.7638 (t0)
REVERT: A  375 GLU cc_start: 0.6501 (pm20) cc_final: 0.6120 (pm20)
REVERT: B  120 ARG cc_start: 0.7189 (mtm180) cc_final: 0.6874 (mtm-85)
REVERT: B  362 LEU cc_start: 0.8599 (mm) cc_final: 0.8147 (mt)
REVERT: B  421 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.6232 (mp10)
REVERT: B  425 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.6049 (mp10)
REVERT: B  427 SER cc_start: 0.8526 (m) cc_final: 0.8235 (m)
REVERT: C   41 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7686 (mp)
REVERT: C  220 GLN cc_start: 0.6535 (tp40) cc_final: 0.5957 (tp40)
REVERT: C  398 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.6808 (ttm170)
REVERT: C  436 LYS cc_start: 0.7213 (tttt) cc_final: 0.6746 (tmtt)
REVERT: D  192 ASN cc_start: 0.7888 (t0) cc_final: 0.7649 (t0)
REVERT: D  311 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8234 (mtpp)
REVERT: D  396 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6552 (pp)
REVERT: E   75 GLU cc_start: 0.4880 (tm-30) cc_final: 0.4142 (tm-30)
REVERT: E  110 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7467 (tt)
REVERT: E  113 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7567 (mmp80)
REVERT: E  198 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7978 (mt)
REVERT: E  238 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7592 (pt)
REVERT: E  311 LYS cc_start: 0.7460 (tptm) cc_final: 0.7203 (ptmt)
REVERT: E  385 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7382 (tppt)
REVERT: E  394 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.4534 (pm20)
REVERT: F   69 GLU cc_start: 0.7529 (tm-30) cc_final: 0.6782 (tm-30)
REVERT: F  116 ASP cc_start: 0.7792 (t70) cc_final: 0.7218 (t0)
REVERT: F  120 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6173 (mtm-85)
REVERT: F  164 LEU cc_start: 0.7475 (mp) cc_final: 0.7232 (mm)
REVERT: F  443 LYS cc_start: 0.6758 (mppt) cc_final: 0.6437 (mmtt)
  outliers start: 91
  outliers final: 60
  residues processed: 284
  average time/residue: 0.3457
  time to fit residues: 144.4182
Evaluate side-chains
  267 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 69
    poor density    : 198
  time to evaluate  : 2.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  392 ASN
Chi-restraints excluded: chain A residue  418 LYS
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  108 ASP
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  421 GLN
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  191 CYS
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain C residue  234 ASP
Chi-restraints excluded: chain C residue  315 THR
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  368 MET
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain D residue   55 ILE
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  241 MET
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain D residue  372 VAL
Chi-restraints excluded: chain D residue  396 LEU
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  238 LEU
Chi-restraints excluded: chain E residue  261 VAL
Chi-restraints excluded: chain E residue  334 GLU
Chi-restraints excluded: chain E residue  377 LEU
Chi-restraints excluded: chain E residue  394 GLU
Chi-restraints excluded: chain E residue  399 ILE
Chi-restraints excluded: chain E residue  431 ILE
Chi-restraints excluded: chain F residue   80 LEU
Chi-restraints excluded: chain F residue  120 ARG
Chi-restraints excluded: chain F residue  227 VAL
Chi-restraints excluded: chain F residue  282 SER
Chi-restraints excluded: chain F residue  295 VAL
Chi-restraints excluded: chain F residue  302 LEU
Chi-restraints excluded: chain F residue  321 LEU
Chi-restraints excluded: chain F residue  349 LEU
Chi-restraints excluded: chain F residue  372 VAL
Chi-restraints excluded: chain F residue  382 GLU
Chi-restraints excluded: chain F residue  389 THR
Chi-restraints excluded: chain F residue  393 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 245
   random chunks:
   chunk 146 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 141 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 150 optimal weight:    6.9990
   chunk 160 optimal weight:    9.9990
   chunk 116 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 185 optimal weight:    5.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
B  85 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  19388  Z= 0.285
  Angle     :  0.670  11.723  26256  Z= 0.316
  Chirality :  0.047   0.427   3039
  Planarity :  0.004   0.071   3388
  Dihedral  :  7.066 103.377   2736
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 14.02 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.80 %
    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: -1.49 (0.17), residues: 2452
  helix:  0.09 (0.18), residues: 879
  sheet: -1.35 (0.25), residues: 432
  loop : -1.67 (0.17), residues: 1141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  94 
 HIS   0.005   0.001   HIS C 342 
 PHE   0.018   0.002   PHE C  58 
 TYR   0.018   0.002   TYR C  97 
 ARG   0.006   0.000   ARG D 113 

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

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

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 84
    poor density    : 198
  time to evaluate  : 2.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.7219 (mtp-110) cc_final: 0.6633 (ttm-80)
REVERT: A  333 ASP cc_start: 0.8019 (t70) cc_final: 0.7630 (t0)
REVERT: A  375 GLU cc_start: 0.6482 (pm20) cc_final: 0.6080 (pm20)
REVERT: B   66 ARG cc_start: 0.7803 (ptt180) cc_final: 0.7472 (ptt180)
REVERT: B  120 ARG cc_start: 0.7204 (mtm180) cc_final: 0.6886 (mtm-85)
REVERT: B  421 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.6222 (mp10)
REVERT: B  425 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.6102 (mp10)
REVERT: B  427 SER cc_start: 0.8558 (m) cc_final: 0.8265 (m)
REVERT: C   41 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7803 (mp)
REVERT: C  220 GLN cc_start: 0.6530 (tp40) cc_final: 0.5952 (tp40)
REVERT: C  398 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.6791 (ttm170)
REVERT: C  406 GLN cc_start: 0.5959 (tt0) cc_final: 0.5231 (mt0)
REVERT: C  436 LYS cc_start: 0.7233 (tttt) cc_final: 0.6772 (tmtt)
REVERT: D  165 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6923 (mt)
REVERT: D  311 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8268 (mtpp)
REVERT: D  396 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6605 (pp)
REVERT: E   54 ARG cc_start: 0.7611 (mpt180) cc_final: 0.7342 (mpt180)
REVERT: E   75 GLU cc_start: 0.4881 (tm-30) cc_final: 0.4110 (tm-30)
REVERT: E  110 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7464 (tt)
REVERT: E  113 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7612 (mmp80)
REVERT: E  198 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8029 (mt)
REVERT: E  238 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7641 (pt)
REVERT: E  311 LYS cc_start: 0.7472 (tptm) cc_final: 0.7211 (ptmt)
REVERT: E  385 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7452 (tppt)
REVERT: E  394 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.4558 (pm20)
REVERT: F   69 GLU cc_start: 0.7538 (tm-30) cc_final: 0.6786 (tm-30)
REVERT: F  116 ASP cc_start: 0.7820 (t70) cc_final: 0.7216 (t0)
REVERT: F  120 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6115 (mtm-85)
REVERT: F  164 LEU cc_start: 0.7519 (mp) cc_final: 0.7316 (mm)
  outliers start: 84
  outliers final: 62
  residues processed: 269
  average time/residue: 0.3037
  time to fit residues: 121.0320
Evaluate side-chains
  267 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 72
    poor density    : 195
  time to evaluate  : 1.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  392 ASN
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  108 ASP
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  421 GLN
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  191 CYS
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain C residue  234 ASP
Chi-restraints excluded: chain C residue  264 MET
Chi-restraints excluded: chain C residue  315 THR
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  368 MET
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain D residue   55 ILE
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  241 MET
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain D residue  372 VAL
Chi-restraints excluded: chain D residue  396 LEU
Chi-restraints excluded: chain D residue  420 ILE
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  238 LEU
Chi-restraints excluded: chain E residue  261 VAL
Chi-restraints excluded: chain E residue  334 GLU
Chi-restraints excluded: chain E residue  377 LEU
Chi-restraints excluded: chain E residue  394 GLU
Chi-restraints excluded: chain E residue  399 ILE
Chi-restraints excluded: chain E residue  431 ILE
Chi-restraints excluded: chain F residue   80 LEU
Chi-restraints excluded: chain F residue  120 ARG
Chi-restraints excluded: chain F residue  227 VAL
Chi-restraints excluded: chain F residue  228 LEU
Chi-restraints excluded: chain F residue  282 SER
Chi-restraints excluded: chain F residue  295 VAL
Chi-restraints excluded: chain F residue  302 LEU
Chi-restraints excluded: chain F residue  321 LEU
Chi-restraints excluded: chain F residue  349 LEU
Chi-restraints excluded: chain F residue  372 VAL
Chi-restraints excluded: chain F residue  382 GLU
Chi-restraints excluded: chain F residue  389 THR
Chi-restraints excluded: chain F residue  393 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 245
   random chunks:
   chunk 214 optimal weight:    0.9980
   chunk 226 optimal weight:    7.9990
   chunk 206 optimal weight:    9.9990
   chunk 220 optimal weight:    0.9990
   chunk 132 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 172 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 198 optimal weight:    9.9990
   chunk 208 optimal weight:    3.9990
   chunk 219 optimal weight:    0.0470
   overall best weight:    1.8084

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

Flipped N/Q/H residues before XYZ refinement:
B  85 HIS
** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  19388  Z= 0.219
  Angle     :  0.628  11.154  26256  Z= 0.295
  Chirality :  0.045   0.408   3039
  Planarity :  0.004   0.072   3388
  Dihedral  :  6.686  93.317   2736
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 14.61 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.80 %
    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: -1.31 (0.17), residues: 2452
  helix:  0.30 (0.19), residues: 876
  sheet: -1.36 (0.26), residues: 406
  loop : -1.56 (0.17), residues: 1170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  94 
 HIS   0.003   0.001   HIS D 376 
 PHE   0.017   0.001   PHE C  58 
 TYR   0.017   0.002   TYR C  97 
 ARG   0.005   0.000   ARG D 113 

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

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

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 76
    poor density    : 202
  time to evaluate  : 2.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.7181 (mtp-110) cc_final: 0.6600 (ttm-80)
REVERT: A  333 ASP cc_start: 0.7996 (t70) cc_final: 0.7620 (t0)
REVERT: A  351 GLU cc_start: 0.6235 (mm-30) cc_final: 0.5237 (mt-10)
REVERT: B   66 ARG cc_start: 0.7748 (ptt180) cc_final: 0.7409 (ptt180)
REVERT: B  120 ARG cc_start: 0.7168 (mtm180) cc_final: 0.6851 (mtm-85)
REVERT: B  362 LEU cc_start: 0.8579 (mm) cc_final: 0.8313 (mt)
REVERT: B  421 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.6224 (mp10)
REVERT: B  425 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.6154 (mp10)
REVERT: C  220 GLN cc_start: 0.6551 (tp40) cc_final: 0.6179 (tp40)
REVERT: C  368 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8484 (ttt)
REVERT: C  378 ARG cc_start: 0.7718 (ttp-110) cc_final: 0.7242 (ttp-110)
REVERT: C  398 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.6807 (ttm170)
REVERT: C  436 LYS cc_start: 0.7230 (tttt) cc_final: 0.6782 (tmtt)
REVERT: D   59 TYR cc_start: 0.8550 (m-80) cc_final: 0.8246 (m-80)
REVERT: D  165 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6888 (mt)
REVERT: D  192 ASN cc_start: 0.7877 (t0) cc_final: 0.7658 (t0)
REVERT: D  311 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8207 (mtpp)
REVERT: D  396 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6641 (pp)
REVERT: E   54 ARG cc_start: 0.7557 (mpt180) cc_final: 0.7290 (mpt180)
REVERT: E   75 GLU cc_start: 0.4800 (tm-30) cc_final: 0.4062 (tm-30)
REVERT: E  113 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.7566 (mmp80)
REVERT: E  198 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7971 (mt)
REVERT: E  238 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7569 (pt)
REVERT: E  311 LYS cc_start: 0.7456 (tptm) cc_final: 0.7145 (ptmt)
REVERT: E  385 LYS cc_start: 0.8018 (ttmt) cc_final: 0.7288 (tppt)
REVERT: E  394 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.4484 (pm20)
REVERT: F   69 GLU cc_start: 0.7532 (tm-30) cc_final: 0.6849 (tm-30)
REVERT: F  116 ASP cc_start: 0.7709 (t70) cc_final: 0.7204 (t0)
REVERT: F  120 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6171 (mtm-85)
  outliers start: 76
  outliers final: 55
  residues processed: 264
  average time/residue: 0.3467
  time to fit residues: 135.0943
Evaluate side-chains
  263 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 199
  time to evaluate  : 2.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  392 ASN
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  108 ASP
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  421 GLN
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  191 CYS
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain C residue  234 ASP
Chi-restraints excluded: chain C residue  315 THR
Chi-restraints excluded: chain C residue  368 MET
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain D residue   55 ILE
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  241 MET
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain D residue  372 VAL
Chi-restraints excluded: chain D residue  396 LEU
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  238 LEU
Chi-restraints excluded: chain E residue  261 VAL
Chi-restraints excluded: chain E residue  334 GLU
Chi-restraints excluded: chain E residue  377 LEU
Chi-restraints excluded: chain E residue  394 GLU
Chi-restraints excluded: chain E residue  431 ILE
Chi-restraints excluded: chain F residue   80 LEU
Chi-restraints excluded: chain F residue  120 ARG
Chi-restraints excluded: chain F residue  227 VAL
Chi-restraints excluded: chain F residue  228 LEU
Chi-restraints excluded: chain F residue  282 SER
Chi-restraints excluded: chain F residue  295 VAL
Chi-restraints excluded: chain F residue  302 LEU
Chi-restraints excluded: chain F residue  321 LEU
Chi-restraints excluded: chain F residue  349 LEU
Chi-restraints excluded: chain F residue  372 VAL
Chi-restraints excluded: chain F residue  382 GLU
Chi-restraints excluded: chain F residue  389 THR
Chi-restraints excluded: chain F residue  393 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 245
   random chunks:
   chunk 144 optimal weight:    6.9990
   chunk 232 optimal weight:    3.9990
   chunk 142 optimal weight:    6.9990
   chunk 110 optimal weight:    1.9990
   chunk 161 optimal weight:    8.9990
   chunk 244 optimal weight:    7.9990
   chunk 224 optimal weight:    3.9990
   chunk 194 optimal weight:    7.9990
   chunk 20 optimal weight:    0.2980
   chunk 150 optimal weight:    0.0170
   chunk 119 optimal weight:    0.0870
   overall best weight:    1.2800

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

Flipped N/Q/H residues before XYZ refinement:
B  85 HIS
** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  19388  Z= 0.178
  Angle     :  0.606  10.508  26256  Z= 0.283
  Chirality :  0.045   0.409   3039
  Planarity :  0.004   0.065   3388
  Dihedral  :  6.287  83.358   2734
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.20 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.80 %
    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: -1.12 (0.17), residues: 2452
  helix:  0.45 (0.19), residues: 873
  sheet: -1.17 (0.27), residues: 392
  loop : -1.49 (0.17), residues: 1187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  94 
 HIS   0.003   0.001   HIS D 376 
 PHE   0.016   0.001   PHE C  58 
 TYR   0.019   0.001   TYR F 318 
 ARG   0.004   0.000   ARG D 113 

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

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

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4904 Ramachandran restraints generated.
    2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 213
  time to evaluate  : 2.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.7076 (mtp-110) cc_final: 0.6632 (ttm-80)
REVERT: A  351 GLU cc_start: 0.6123 (mm-30) cc_final: 0.5206 (mt-10)
REVERT: A  375 GLU cc_start: 0.6231 (pm20) cc_final: 0.5790 (pm20)
REVERT: B   66 ARG cc_start: 0.7657 (ptt180) cc_final: 0.7337 (ptt180)
REVERT: B  120 ARG cc_start: 0.7127 (mtm180) cc_final: 0.6817 (mtm-85)
REVERT: B  362 LEU cc_start: 0.8485 (mm) cc_final: 0.8209 (mt)
REVERT: B  421 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6923 (mm-40)
REVERT: B  425 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.5921 (mp10)
REVERT: C  220 GLN cc_start: 0.6546 (tp40) cc_final: 0.6252 (tp40)
REVERT: C  368 MET cc_start: 0.8714 (ttp) cc_final: 0.8497 (ttt)
REVERT: C  378 ARG cc_start: 0.7672 (ttp-110) cc_final: 0.7226 (ttp-110)
REVERT: C  398 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.6766 (ttm170)
REVERT: C  436 LYS cc_start: 0.7154 (tttt) cc_final: 0.6768 (tmtt)
REVERT: D  165 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6863 (mt)
REVERT: D  311 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8204 (mtpp)
REVERT: D  396 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6620 (pp)
REVERT: D  436 LYS cc_start: 0.7190 (tptp) cc_final: 0.6931 (tptp)
REVERT: E   75 GLU cc_start: 0.4769 (tm-30) cc_final: 0.4097 (tm-30)
REVERT: E  113 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7518 (mmp80)
REVERT: E  198 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7939 (mt)
REVERT: E  311 LYS cc_start: 0.7430 (tptm) cc_final: 0.7077 (ptmm)
REVERT: E  385 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7288 (tppt)
REVERT: F   69 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6780 (tm-30)
REVERT: F  116 ASP cc_start: 0.7665 (t70) cc_final: 0.7225 (t0)
REVERT: F  120 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6211 (mtm-85)
  outliers start: 60
  outliers final: 47
  residues processed: 262
  average time/residue: 0.3494
  time to fit residues: 132.7444
Evaluate side-chains
  257 residues out of total 2040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 204
  time to evaluate  : 2.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  392 ASN
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  108 ASP
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  421 GLN
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  191 CYS
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain C residue  234 ASP
Chi-restraints excluded: chain C residue  315 THR
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain D residue   55 ILE
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  241 MET
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain D residue  372 VAL
Chi-restraints excluded: chain D residue  396 LEU
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain E residue  261 VAL
Chi-restraints excluded: chain E residue  334 GLU
Chi-restraints excluded: chain E residue  377 LEU
Chi-restraints excluded: chain F residue   80 LEU
Chi-restraints excluded: chain F residue  120 ARG
Chi-restraints excluded: chain F residue  227 VAL
Chi-restraints excluded: chain F residue  228 LEU
Chi-restraints excluded: chain F residue  282 SER
Chi-restraints excluded: chain F residue  295 VAL
Chi-restraints excluded: chain F residue  349 LEU
Chi-restraints excluded: chain F residue  372 VAL
Chi-restraints excluded: chain F residue  382 GLU
Chi-restraints excluded: chain F residue  389 THR
Chi-restraints excluded: chain F residue  393 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 245
   random chunks:
   chunk 154 optimal weight:    5.9990
   chunk 207 optimal weight:    0.9980
   chunk 59 optimal weight:   10.0000
   chunk 179 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 54 optimal weight:    7.9990
   chunk 194 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 199 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   chunk 35 optimal weight:   10.0000
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
B  85 HIS
F 212 ASN
F 392 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.137771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.110971 restraints weight = 34478.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 2.55
r_work: 0.2984 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2903
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2885 r_free = 0.2885    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2885
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073  19388  Z= 0.427
  Angle     :  0.757  16.211  26256  Z= 0.358
  Chirality :  0.050   0.562   3039
  Planarity :  0.005   0.074   3388
  Dihedral  :  7.100  98.730   2734
  Min Nonbonded Distance : 1.769

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.25 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.80 %
    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: -1.49 (0.17), residues: 2452
  helix:  0.08 (0.18), residues: 879
  sheet: -1.40 (0.25), residues: 450
  loop : -1.63 (0.18), residues: 1123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C  94 
 HIS   0.008   0.002   HIS C 342 
 PHE   0.024   0.002   PHE A  58 
 TYR   0.023   0.002   TYR A 390 
 ARG   0.006   0.001   ARG D 113 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3688.58 seconds
wall clock time: 69 minutes 35.85 seconds (4175.85 seconds total)