Starting phenix.real_space_refine
on Thu Sep 18 10:05:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9byw_45046/09_2025/9byw_45046_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9byw_45046/09_2025/9byw_45046.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9byw_45046/09_2025/9byw_45046_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9byw_45046/09_2025/9byw_45046_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9byw_45046/09_2025/9byw_45046.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9byw_45046/09_2025/9byw_45046.map"
  }
  resolution = 4.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Mn      4      7.51       5
     P      16      5.49       5
     Mg      2      5.21       5
     S      82      5.16       5
     C   10228      2.51       5
     N    2614      2.21       5
     O    3092      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16038
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 5554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 683, 5554
          Classifications: {'peptide': 683}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665}
    Chain: "B"
      Number of atoms: 5554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 683, 5554
          Classifications: {'peptide': 683}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665}
    Chain: "C"
      Number of atoms: 2374
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2374
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 7, 'TRANS': 281}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2374
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2374
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 7, 'TRANS': 281}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 89
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 89
          Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 89
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 89
          Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   SER D 187 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER D 187 " occ=0.50
    residue:
      pdb=" N   SER D 253 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER D 253 " occ=0.50
    residue:
      pdb="MN    MN C 401 " occ=0.85
    residue:
      pdb="MN    MN C 402 " occ=0.85
  Time building chain proxies: 3.94, per 1000 atoms: 0.25
  Number of scatterers: 16038
  At special positions: 0
  Unit cell: (96.615, 125.091, 132.21, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Mn      4     24.99
     S      82     16.00
     P      16     15.00
     Mg      2     11.99
     O    3092      8.00
     N    2614      7.00
     C   10228      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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.49
  Conformation dependent library (CDL) restraints added in 712.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3696

  Finding SS restraints...
    Secondary structure from input PDB file:
      98 helices and 11 sheets defined
      64.0% alpha, 6.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 15
    Processing helix  chain 'A' and resid 25 through 39
      removed outlier: 4.103A  pdb=" N   ASP A  29 " --> pdb=" O   GLN A  25 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   LYS A  30 " --> pdb=" O   PHE A  26 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLU A  31 " --> pdb=" O   ASP A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 61
    Processing helix  chain 'A' and resid 65 through 71
      removed outlier: 3.985A  pdb=" N   LEU A  69 " --> pdb=" O   GLU A  65 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A  71 " --> pdb=" O   GLU A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 87
      removed outlier: 3.954A  pdb=" N   LYS A  87 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 104
      removed outlier: 3.665A  pdb=" N   ALA A  97 " --> pdb=" O   SER A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 133 through 146
    Processing helix  chain 'A' and resid 152 through 159
    Processing helix  chain 'A' and resid 178 through 195
    Processing helix  chain 'A' and resid 221 through 237
      removed outlier: 4.127A  pdb=" N   GLY A 225 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   VAL A 226 " --> pdb=" O   GLY A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 264
    Processing helix  chain 'A' and resid 285 through 294
      removed outlier: 3.574A  pdb=" N   VAL A 289 " --> pdb=" O   PRO A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 311
    Processing helix  chain 'A' and resid 313 through 317
      removed outlier: 3.694A  pdb=" N   MET A 317 " --> pdb=" O   MET A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 329
      removed outlier: 5.394A  pdb=" N   ASP A 324 " --> pdb=" O   ASN A 320 " (cutoff:3.500A)
      removed outlier: 4.851A  pdb=" N   LYS A 325 " --> pdb=" O   GLU A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 354
    Processing helix  chain 'A' and resid 361 through 366
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 424 through 442
    Processing helix  chain 'A' and resid 448 through 459
    Processing helix  chain 'A' and resid 467 through 475
    Processing helix  chain 'A' and resid 481 through 511
    Processing helix  chain 'A' and resid 520 through 525
    Processing helix  chain 'A' and resid 528 through 534
    Processing helix  chain 'A' and resid 540 through 547
    Processing helix  chain 'A' and resid 554 through 569
    Processing helix  chain 'A' and resid 583 through 588
      removed outlier: 3.628A  pdb=" N   VAL A 587 " --> pdb=" O   SER A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 633 through 646
    Processing helix  chain 'A' and resid 663 through 678
    Processing helix  chain 'B' and resid 7 through 15
    Processing helix  chain 'B' and resid 25 through 40
      removed outlier: 4.119A  pdb=" N   ASP B  29 " --> pdb=" O   GLN B  25 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LYS B  30 " --> pdb=" O   PHE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 45
    Processing helix  chain 'B' and resid 50 through 61
    Processing helix  chain 'B' and resid 65 through 71
      removed outlier: 4.074A  pdb=" N   LEU B  69 " --> pdb=" O   GLU B  65 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU B  71 " --> pdb=" O   GLU B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 87
      removed outlier: 3.959A  pdb=" N   LYS B  87 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 104
      removed outlier: 3.676A  pdb=" N   ALA B  97 " --> pdb=" O   SER B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 131
    Processing helix  chain 'B' and resid 133 through 146
    Processing helix  chain 'B' and resid 152 through 159
    Processing helix  chain 'B' and resid 178 through 195
    Processing helix  chain 'B' and resid 221 through 237
      removed outlier: 3.879A  pdb=" N   GLY B 225 " --> pdb=" O   LYS B 221 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL B 226 " --> pdb=" O   GLY B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 242
    Processing helix  chain 'B' and resid 257 through 264
    Processing helix  chain 'B' and resid 285 through 295
      removed outlier: 3.645A  pdb=" N   VAL B 289 " --> pdb=" O   PRO B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 311
    Processing helix  chain 'B' and resid 313 through 317
      removed outlier: 3.730A  pdb=" N   MET B 317 " --> pdb=" O   MET B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 329
      removed outlier: 6.027A  pdb=" N   ASP B 324 " --> pdb=" O   ASN B 320 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   LYS B 325 " --> pdb=" O   GLU B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 354
    Processing helix  chain 'B' and resid 361 through 366
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 424 through 442
    Processing helix  chain 'B' and resid 448 through 459
    Processing helix  chain 'B' and resid 467 through 475
    Processing helix  chain 'B' and resid 481 through 511
    Processing helix  chain 'B' and resid 516 through 519
      removed outlier: 3.633A  pdb=" N   GLY B 519 " --> pdb=" O   GLN B 516 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 516 through 519'
    Processing helix  chain 'B' and resid 520 through 525
    Processing helix  chain 'B' and resid 528 through 534
    Processing helix  chain 'B' and resid 540 through 547
    Processing helix  chain 'B' and resid 554 through 569
    Processing helix  chain 'B' and resid 583 through 588
      removed outlier: 4.067A  pdb=" N   VAL B 587 " --> pdb=" O   SER B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 633 through 646
    Processing helix  chain 'B' and resid 663 through 678
    Processing helix  chain 'C' and resid 17 through 28
    Processing helix  chain 'C' and resid 31 through 35
    Processing helix  chain 'C' and resid 37 through 39
      No H-bonds generated for 'chain 'C' and resid 37 through 39'
    Processing helix  chain 'C' and resid 40 through 46
    Processing helix  chain 'C' and resid 48 through 72
    Processing helix  chain 'C' and resid 72 through 81
    Processing helix  chain 'C' and resid 83 through 100
    Processing helix  chain 'C' and resid 100 through 113
      removed outlier: 3.545A  pdb=" N   TYR C 105 " --> pdb=" O   HIS C 101 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   SER C 106 " --> pdb=" O   ALA C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 128
      removed outlier: 3.515A  pdb=" N   LYS C 126 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 144
    Processing helix  chain 'C' and resid 149 through 166
    Processing helix  chain 'C' and resid 168 through 180
      removed outlier: 4.935A  pdb=" N   TYR C 174 " --> pdb=" O   SER C 170 " (cutoff:3.500A)
      Proline residue:  C 175  - end of helix
    Processing helix  chain 'C' and resid 184 through 214
      removed outlier: 3.566A  pdb=" N   ILE C 200 " --> pdb=" O   ARG C 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 248
    Processing helix  chain 'C' and resid 249 through 251
      No H-bonds generated for 'chain 'C' and resid 249 through 251'
    Processing helix  chain 'C' and resid 252 through 271
    Processing helix  chain 'C' and resid 283 through 289
    Processing helix  chain 'C' and resid 316 through 321
      removed outlier: 3.669A  pdb=" N   PHE C 320 " --> pdb=" O   ASP C 317 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   TYR C 321 " --> pdb=" O   ASP C 318 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 28
    Processing helix  chain 'D' and resid 31 through 35
    Processing helix  chain 'D' and resid 37 through 39
      No H-bonds generated for 'chain 'D' and resid 37 through 39'
    Processing helix  chain 'D' and resid 40 through 45
    Processing helix  chain 'D' and resid 48 through 72
    Processing helix  chain 'D' and resid 72 through 81
    Processing helix  chain 'D' and resid 83 through 100
    Processing helix  chain 'D' and resid 100 through 113
    Processing helix  chain 'D' and resid 114 through 128
    Processing helix  chain 'D' and resid 128 through 144
    Processing helix  chain 'D' and resid 149 through 166
    Processing helix  chain 'D' and resid 168 through 180
      removed outlier: 4.875A  pdb=" N   TYR D 174 " --> pdb=" O   SER D 170 " (cutoff:3.500A)
      Proline residue:  D 175  - end of helix
    Processing helix  chain 'D' and resid 184 through 214
    Processing helix  chain 'D' and resid 217 through 248
    Processing helix  chain 'D' and resid 249 through 251
      No H-bonds generated for 'chain 'D' and resid 249 through 251'
    Processing helix  chain 'D' and resid 252 through 271
    Processing helix  chain 'D' and resid 283 through 290
    Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20
    Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151
      removed outlier: 6.360A  pdb=" N   GLY A 412 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   MET A 466 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   LEU A 414 " --> pdb=" O   MET A 466 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174
      removed outlier: 6.478A  pdb=" N   VAL A 199 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   TYR A 250 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LEU A 201 " --> pdb=" O   TYR A 250 " (cutoff:3.500A)
      removed outlier: 8.394A  pdb=" N   ASN A 252 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   GLY A 247 " --> pdb=" O   SER A 279 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   GLY A 281 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   ALA A 249 " --> pdb=" O   GLY A 281 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   VAL A 283 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   LEU A 251 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301
    Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606
    Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658
      removed outlier: 6.478A  pdb=" N   LEU A 656 " --> pdb=" O   ARG A 686 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151
      removed outlier: 7.185A  pdb=" N   GLY B 462 " --> pdb=" O   SER B 408 " (cutoff:3.500A)
      removed outlier: 5.660A  pdb=" N   ASN B 410 " --> pdb=" O   GLY B 462 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   GLY B 464 " --> pdb=" O   ASN B 410 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   GLY B 412 " --> pdb=" O   GLY B 464 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   MET B 466 " --> pdb=" O   GLY B 412 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   LEU B 414 " --> pdb=" O   MET B 466 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151
      removed outlier: 4.049A  pdb=" N   CYS B 409 " --> pdb=" O   CYS B 170 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   CYS B 170 " --> pdb=" O   CYS B 409 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL B 199 " --> pdb=" O   ALA B 248 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   TYR B 250 " --> pdb=" O   VAL B 199 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   LEU B 201 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
      removed outlier: 8.344A  pdb=" N   ASN B 252 " --> pdb=" O   LEU B 201 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLY B 247 " --> pdb=" O   SER B 279 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   GLY B 281 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ALA B 249 " --> pdb=" O   GLY B 281 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   VAL B 283 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   LEU B 251 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301
    Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606
    Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659

    873 hydrogen bonds defined for protein.
    2571 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: 3.22

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 4896
        1.34 -     1.46: 2984
        1.46 -     1.58: 8324
        1.58 -     1.70: 26
        1.70 -     1.82: 156
  Bond restraints: 16386
  Sorted by residual:
  bond pdb=" CA  VAL C 125 "
       pdb=" CB  VAL C 125 "
    ideal  model  delta    sigma   weight residual
    1.540  1.600 -0.060 1.25e-02 6.40e+03 2.31e+01
  bond pdb=" CA  ILE D 138 "
       pdb=" CB  ILE D 138 "
    ideal  model  delta    sigma   weight residual
    1.539  1.578 -0.038 1.20e-02 6.94e+03 1.01e+01
  bond pdb=" CA  VAL C 250 "
       pdb=" CB  VAL C 250 "
    ideal  model  delta    sigma   weight residual
    1.542  1.575 -0.033 1.08e-02 8.57e+03 9.33e+00
  bond pdb=" CA  ILE D  35 "
       pdb=" CB  ILE D  35 "
    ideal  model  delta    sigma   weight residual
    1.537  1.568 -0.031 1.17e-02 7.31e+03 7.16e+00
  bond pdb=" CA  ILE C  35 "
       pdb=" CB  ILE C  35 "
    ideal  model  delta    sigma   weight residual
    1.537  1.569 -0.032 1.21e-02 6.83e+03 7.12e+00
  ... (remaining 16381 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 21575
        2.09 -     4.19: 517
        4.19 -     6.28: 37
        6.28 -     8.37: 1
        8.37 -    10.47: 4
  Bond angle restraints: 22134
  Sorted by residual:
  angle pdb=" N   VAL C 125 "
        pdb=" CA  VAL C 125 "
        pdb=" CB  VAL C 125 "
      ideal   model   delta    sigma   weight residual
     110.54  116.65   -6.11 1.36e+00 5.41e-01 2.02e+01
  angle pdb=" N   LEU C 167 "
        pdb=" CA  LEU C 167 "
        pdb=" C   LEU C 167 "
      ideal   model   delta    sigma   weight residual
     111.71  116.11   -4.40 1.15e+00 7.56e-01 1.46e+01
  angle pdb=" N   TYR C 247 "
        pdb=" CA  TYR C 247 "
        pdb=" C   TYR C 247 "
      ideal   model   delta    sigma   weight residual
     113.50  117.83   -4.33 1.23e+00 6.61e-01 1.24e+01
  angle pdb=" N   ASN D  38 "
        pdb=" CA  ASN D  38 "
        pdb=" C   ASN D  38 "
      ideal   model   delta    sigma   weight residual
     111.71  115.70   -3.99 1.15e+00 7.56e-01 1.21e+01
  angle pdb=" C   MET D  74 "
        pdb=" N   PRO D  75 "
        pdb=" CA  PRO D  75 "
      ideal   model   delta    sigma   weight residual
     119.19  115.58    3.61 1.06e+00 8.90e-01 1.16e+01
  ... (remaining 22129 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.79: 9469
       35.79 -    71.59: 338
       71.59 -   107.38: 37
      107.38 -   143.17: 3
      143.17 -   178.97: 3
  Dihedral angle restraints: 9850
    sinusoidal: 4092
      harmonic: 5758
  Sorted by residual:
  dihedral pdb=" C2  TTP A 803 "
           pdb=" C1' TTP A 803 "
           pdb=" N1  TTP A 803 "
           pdb=" O4' TTP A 803 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -58.32  120.65 -178.97     1      2.00e+01 2.50e-03 4.80e+01
  dihedral pdb=" C2  TTP B 801 "
           pdb=" C1' TTP B 801 "
           pdb=" N1  TTP B 801 "
           pdb=" O4' TTP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.68  151.18  150.51     1      2.00e+01 2.50e-03 4.49e+01
  dihedral pdb=" C5' TTP A 803 "
           pdb=" O5' TTP A 803 "
           pdb=" PA  TTP A 803 "
           pdb=" O3A TTP A 803 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.97   31.86  148.12     1      2.00e+01 2.50e-03 4.44e+01
  ... (remaining 9847 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 2144
       0.093 -    0.186: 182
       0.186 -    0.279: 29
       0.279 -    0.372: 3
       0.372 -    0.465: 2
  Chirality restraints: 2360
  Sorted by residual:
  chirality pdb=" CA  ASN C  98 "
            pdb=" N   ASN C  98 "
            pdb=" C   ASN C  98 "
            pdb=" CB  ASN C  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.40e+00
  chirality pdb=" CA  TYR C 169 "
            pdb=" N   TYR C 169 "
            pdb=" C   TYR C 169 "
            pdb=" CB  TYR C 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.61e+00
  chirality pdb=" CA  TYR D 169 "
            pdb=" N   TYR D 169 "
            pdb=" C   TYR D 169 "
            pdb=" CB  TYR D 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.95e+00
  ... (remaining 2357 not shown)

  Planarity restraints: 2818
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D  74 "   -0.027 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO D  75 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO D  75 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D  75 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  92 "    0.017 2.00e-02 2.50e+03   1.12e-02 2.20e+00
        pdb=" CG  PHE D  92 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  92 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  92 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  92 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  92 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  92 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 169 "    0.017 2.00e-02 2.50e+03   9.90e-03 1.96e+00
        pdb=" CG  TYR C 169 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 169 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 169 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 169 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 169 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 169 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 169 "    0.008 2.00e-02 2.50e+03
  ... (remaining 2815 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 129
        2.51 -     3.11: 11553
        3.11 -     3.70: 27038
        3.70 -     4.30: 41546
        4.30 -     4.90: 65401
  Nonbonded interactions: 145667
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D  97 "
            pdb="MN    MN D 401 "
     model   vdw
     1.912 2.320
  nonbonded pdb=" OE2 GLU C  97 "
            pdb="MN    MN C 401 "
     model   vdw
     1.961 2.320
  nonbonded pdb=" OE2 GLU C 164 "
            pdb="MN    MN C 401 "
     model   vdw
     1.964 2.320
  nonbonded pdb=" OE1 GLU D  97 "
            pdb="MN    MN D 402 "
     model   vdw
     1.991 2.320
  nonbonded pdb=" OG1 THR A 108 "
            pdb=" OD1 ASP A 110 "
     model   vdw
     2.013 3.040
  ... (remaining 145662 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 6 through 688)
  selection = (chain 'B' and resid 6 through 688)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     15.940
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5821
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  16386  Z= 0.315
  Angle     :  0.740  10.466  22134  Z= 0.463
  Chirality :  0.057   0.465   2360
  Planarity :  0.003   0.041   2818
  Dihedral  : 17.953 178.965   6154
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 15.38 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.18), residues: 1932
  helix:  0.58 (0.14), residues: 1151
  sheet:  0.46 (0.42), residues: 124
  loop :  0.23 (0.23), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 196 
 TYR   0.020   0.002   TYR D 179 
 PHE   0.021   0.002   PHE D  92 
 TRP   0.008   0.002   TRP D  44 
 HIS   0.006   0.001   HIS C 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 (16386)
  covalent geometry    : angle       0.74048 (22134)
  hydrogen bonds       : bond        0.15421 (  871)
  hydrogen bonds       : angle       6.51765 ( 2571)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  802 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 779
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LEU cc_start: 0.9137 (mt) cc_final: 0.6543 (mt)
REVERT: A   95 MET cc_start: 0.8221 (tpp) cc_final: 0.7892 (mmm)
REVERT: A  136 LYS cc_start: 0.8134 (tptt) cc_final: 0.7433 (tttt)
REVERT: A  143 LEU cc_start: 0.9004 (tp) cc_final: 0.8637 (tp)
REVERT: A  147 GLN cc_start: 0.8415 (mt0) cc_final: 0.7912 (mt0)
REVERT: A  155 THR cc_start: 0.9063 (m) cc_final: 0.8749 (m)
REVERT: A  166 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8431 (mm-30)
REVERT: A  172 LEU cc_start: 0.8583 (mp) cc_final: 0.8353 (mp)
REVERT: A  173 LEU cc_start: 0.7045 (mt) cc_final: 0.6673 (mt)
REVERT: A  181 ASP cc_start: 0.7470 (m-30) cc_final: 0.6966 (m-30)
REVERT: A  190 MET cc_start: 0.7882 (mtt) cc_final: 0.7606 (mtt)
REVERT: A  205 LYS cc_start: 0.7012 (mttp) cc_final: 0.6718 (mttt)
REVERT: A  288 PHE cc_start: 0.7716 (t80) cc_final: 0.7511 (t80)
REVERT: A  367 VAL cc_start: 0.8759 (m) cc_final: 0.8356 (m)
REVERT: A  550 MET cc_start: 0.6875 (mtm) cc_final: 0.6163 (mtp)
REVERT: A  597 ILE cc_start: 0.8618 (pt) cc_final: 0.8410 (pt)
REVERT: A  634 MET cc_start: 0.8480 (mmp) cc_final: 0.8021 (mmm)
REVERT: A  637 VAL cc_start: 0.8973 (t) cc_final: 0.8597 (p)
REVERT: A  645 GLN cc_start: 0.6999 (tp40) cc_final: 0.6707 (tp-100)
REVERT: A  650 GLN cc_start: 0.6815 (mt0) cc_final: 0.6450 (mt0)
REVERT: A  655 THR cc_start: 0.7160 (m) cc_final: 0.6489 (m)
REVERT: A  658 LEU cc_start: 0.8182 (mt) cc_final: 0.7626 (mt)
REVERT: A  667 LEU cc_start: 0.8626 (tt) cc_final: 0.8219 (tp)
REVERT: B   62 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8324 (mp10)
REVERT: B   89 PHE cc_start: 0.7137 (t80) cc_final: 0.6792 (t80)
REVERT: B   96 SER cc_start: 0.9284 (m) cc_final: 0.8885 (p)
REVERT: B  125 VAL cc_start: 0.9206 (t) cc_final: 0.8977 (t)
REVERT: B  143 LEU cc_start: 0.9058 (tp) cc_final: 0.8853 (tp)
REVERT: B  179 LEU cc_start: 0.8385 (tp) cc_final: 0.8121 (tp)
REVERT: B  191 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8216 (mm-40)
REVERT: B  193 SER cc_start: 0.8165 (m) cc_final: 0.7935 (p)
REVERT: B  200 SER cc_start: 0.8143 (t) cc_final: 0.7857 (m)
REVERT: B  213 ILE cc_start: 0.8627 (mt) cc_final: 0.8239 (mp)
REVERT: B  216 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.7796 (m)
REVERT: B  232 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.7132 (t0)
REVERT: B  265 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7548 (mmmm)
REVERT: B  282 VAL cc_start: 0.8804 (t) cc_final: 0.8491 (m)
REVERT: B  288 PHE cc_start: 0.7210 (t80) cc_final: 0.6414 (t80)
REVERT: B  319 MET cc_start: 0.7580 (tpp) cc_final: 0.6762 (tpp)
REVERT: B  358 ILE cc_start: 0.8730 (mm) cc_final: 0.8283 (mm)
REVERT: B  362 ASP cc_start: 0.5782 (m-30) cc_final: 0.4557 (m-30)
REVERT: B  373 ILE cc_start: 0.9091 (mt) cc_final: 0.8001 (mt)
REVERT: B  384 GLU cc_start: 0.6657 (pm20) cc_final: 0.6285 (pm20)
REVERT: B  391 VAL cc_start: 0.9072 (p) cc_final: 0.8869 (p)
REVERT: B  410 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8107 (m-40)
REVERT: B  411 LEU cc_start: 0.7568 (mp) cc_final: 0.7153 (mp)
REVERT: B  417 LEU cc_start: 0.8670 (tp) cc_final: 0.7411 (tt)
REVERT: B  445 ILE cc_start: 0.8671 (mt) cc_final: 0.8447 (mm)
REVERT: B  471 TYR cc_start: 0.6004 (t80) cc_final: 0.5307 (t80)
REVERT: B  474 GLN cc_start: 0.8332 (mt0) cc_final: 0.8121 (mt0)
REVERT: B  565 VAL cc_start: 0.9400 (t) cc_final: 0.9122 (p)
REVERT: B  585 SER cc_start: 0.9134 (p) cc_final: 0.8444 (t)
REVERT: B  589 SER cc_start: 0.8091 (m) cc_final: 0.7538 (t)
REVERT: B  613 TYR cc_start: 0.7322 (t80) cc_final: 0.6638 (t80)
REVERT: B  634 MET cc_start: 0.8149 (mmp) cc_final: 0.7805 (mmm)
REVERT: B  656 LEU cc_start: 0.8616 (mt) cc_final: 0.8200 (mt)
REVERT: C   90 LEU cc_start: 0.5687 (mt) cc_final: 0.4386 (mt)
REVERT: C  151 ILE cc_start: 0.6601 (mm) cc_final: 0.6135 (mm)
REVERT: C  208 LEU cc_start: 0.6294 (mt) cc_final: 0.5703 (mt)
REVERT: D  126 LYS cc_start: 0.2375 (OUTLIER) cc_final: 0.2032 (tptp)
REVERT: D  174 TYR cc_start: 0.1481 (t80) cc_final: 0.0316 (t80)
REVERT: D  195 LEU cc_start: 0.8036 (tt) cc_final: 0.7760 (tt)
REVERT: D  229 ILE cc_start: 0.5863 (mm) cc_final: 0.5618 (mm)
REVERT: D  282 ILE cc_start: -0.1245 (OUTLIER) cc_final: -0.1508 (tp)
  outliers start: 23
  outliers final: 5
  residues processed: 799
  average time/residue: 0.1338
  time to fit residues: 154.7844
Evaluate side-chains
  523 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 513
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    9.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 232 ASN
A 239 GLN
A 320 ASN
A 365 ASN
** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 ASN
B  11 GLN
** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 232 ASN
B 304 HIS
** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 645 GLN
C  24 GLN
C  28 GLN
C  38 ASN
C 119 ASN
D  80 HIS
D 127 GLN
D 136 GLN
** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.132596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.090745 restraints weight = 48780.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.094281 restraints weight = 30579.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.096535 restraints weight = 21427.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.098141 restraints weight = 16333.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.099368 restraints weight = 13345.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3404
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3404 r_free = 0.3404    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3400
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.4174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  16386  Z= 0.218
  Angle     :  0.661   7.129  22134  Z= 0.353
  Chirality :  0.044   0.239   2360
  Planarity :  0.004   0.058   2818
  Dihedral  : 11.643 175.689   2242
  Min Nonbonded Distance : 1.770

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.67 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.19), residues: 1932
  helix:  1.38 (0.15), residues: 1117
  sheet: -0.17 (0.40), residues: 152
  loop :  0.70 (0.25), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 453 
 TYR   0.026   0.002   TYR A 140 
 PHE   0.035   0.002   PHE D 178 
 TRP   0.026   0.003   TRP B 558 
 HIS   0.008   0.002   HIS A 304 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (16386)
  covalent geometry    : angle       0.66149 (22134)
  hydrogen bonds       : bond        0.04746 (  871)
  hydrogen bonds       : angle       5.15693 ( 2571)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  576 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 571
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LEU cc_start: 0.9198 (mt) cc_final: 0.8963 (mt)
REVERT: A  123 SER cc_start: 0.9270 (m) cc_final: 0.9051 (p)
REVERT: A  128 PHE cc_start: 0.9175 (t80) cc_final: 0.8711 (t80)
REVERT: A  143 LEU cc_start: 0.9118 (tp) cc_final: 0.8916 (tp)
REVERT: A  147 GLN cc_start: 0.9091 (mt0) cc_final: 0.8593 (mt0)
REVERT: A  168 VAL cc_start: 0.8577 (t) cc_final: 0.8301 (t)
REVERT: A  172 LEU cc_start: 0.8916 (mp) cc_final: 0.8420 (mp)
REVERT: A  173 LEU cc_start: 0.9122 (mt) cc_final: 0.8835 (mt)
REVERT: A  214 LYS cc_start: 0.9249 (mmmt) cc_final: 0.8801 (mmtt)
REVERT: A  259 ASN cc_start: 0.8256 (p0) cc_final: 0.8046 (p0)
REVERT: A  270 ASP cc_start: 0.8757 (m-30) cc_final: 0.8082 (t70)
REVERT: A  286 ASP cc_start: 0.8783 (m-30) cc_final: 0.8493 (m-30)
REVERT: A  319 MET cc_start: 0.8998 (tpp) cc_final: 0.8736 (tpp)
REVERT: A  322 MET cc_start: 0.8695 (mmm) cc_final: 0.7924 (mmm)
REVERT: A  344 GLU cc_start: 0.9058 (pp20) cc_final: 0.8846 (pt0)
REVERT: A  348 MET cc_start: 0.9435 (ttp) cc_final: 0.9112 (ptp)
REVERT: A  349 LEU cc_start: 0.8465 (tp) cc_final: 0.8219 (tp)
REVERT: A  359 MET cc_start: 0.7981 (ttt) cc_final: 0.7741 (ttt)
REVERT: A  375 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8602 (mmtm)
REVERT: A  406 ASP cc_start: 0.8262 (m-30) cc_final: 0.8001 (m-30)
REVERT: A  407 ILE cc_start: 0.8910 (mt) cc_final: 0.8599 (mt)
REVERT: A  425 ILE cc_start: 0.9415 (mt) cc_final: 0.9189 (mt)
REVERT: A  498 TYR cc_start: 0.8795 (m-80) cc_final: 0.8362 (m-80)
REVERT: A  512 GLU cc_start: 0.8442 (pm20) cc_final: 0.7905 (pm20)
REVERT: A  546 LEU cc_start: 0.9411 (mt) cc_final: 0.9202 (mt)
REVERT: A  550 MET cc_start: 0.7361 (mtm) cc_final: 0.6309 (mtp)
REVERT: A  598 MET cc_start: 0.8913 (mtm) cc_final: 0.8507 (mtt)
REVERT: A  599 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7179 (mm-30)
REVERT: A  601 ILE cc_start: 0.8847 (tt) cc_final: 0.8572 (tt)
REVERT: A  602 GLU cc_start: 0.8198 (pm20) cc_final: 0.6470 (mp0)
REVERT: A  645 GLN cc_start: 0.8428 (tp40) cc_final: 0.8030 (tp-100)
REVERT: A  650 GLN cc_start: 0.7786 (mt0) cc_final: 0.7132 (mt0)
REVERT: A  655 THR cc_start: 0.7741 (m) cc_final: 0.6934 (m)
REVERT: A  659 LYS cc_start: 0.8680 (mttt) cc_final: 0.8446 (mmmt)
REVERT: A  672 LEU cc_start: 0.8929 (mt) cc_final: 0.8686 (mt)
REVERT: B    8 LYS cc_start: 0.9451 (tttm) cc_final: 0.9201 (tppt)
REVERT: B   12 LEU cc_start: 0.9575 (mt) cc_final: 0.9353 (mt)
REVERT: B   95 MET cc_start: 0.8965 (tpp) cc_final: 0.7869 (tpp)
REVERT: B   99 LYS cc_start: 0.9589 (mmmt) cc_final: 0.8832 (mmmt)
REVERT: B  115 LEU cc_start: 0.8618 (mp) cc_final: 0.8339 (mp)
REVERT: B  229 LEU cc_start: 0.8073 (mp) cc_final: 0.7868 (mp)
REVERT: B  260 ASP cc_start: 0.9214 (m-30) cc_final: 0.8806 (m-30)
REVERT: B  288 PHE cc_start: 0.9355 (t80) cc_final: 0.8867 (t80)
REVERT: B  326 PHE cc_start: 0.9221 (m-80) cc_final: 0.8437 (m-80)
REVERT: B  350 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7592 (mtm110)
REVERT: B  358 ILE cc_start: 0.8487 (mm) cc_final: 0.8253 (mm)
REVERT: B  394 TYR cc_start: 0.8770 (m-80) cc_final: 0.7854 (m-80)
REVERT: B  413 SER cc_start: 0.9168 (m) cc_final: 0.8455 (t)
REVERT: B  417 LEU cc_start: 0.9381 (tt) cc_final: 0.8949 (tt)
REVERT: B  425 ILE cc_start: 0.9053 (mt) cc_final: 0.8681 (mt)
REVERT: B  458 MET cc_start: 0.9270 (mmm) cc_final: 0.8870 (mmm)
REVERT: B  459 LYS cc_start: 0.8781 (mttm) cc_final: 0.8263 (mtmm)
REVERT: B  479 TYR cc_start: 0.8372 (t80) cc_final: 0.7970 (t80)
REVERT: B  493 MET cc_start: 0.9199 (tmm) cc_final: 0.8965 (tmm)
REVERT: B  494 MET cc_start: 0.9474 (mtp) cc_final: 0.9091 (mtp)
REVERT: B  506 ILE cc_start: 0.9578 (mm) cc_final: 0.9373 (mm)
REVERT: B  512 GLU cc_start: 0.8579 (pm20) cc_final: 0.8322 (pm20)
REVERT: B  584 ILE cc_start: 0.8730 (tp) cc_final: 0.8273 (mt)
REVERT: B  588 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8764 (mm-40)
REVERT: B  645 GLN cc_start: 0.8950 (tp40) cc_final: 0.8671 (tp-100)
REVERT: B  683 TYR cc_start: 0.8449 (t80) cc_final: 0.7790 (t80)
REVERT: C   38 ASN cc_start: 0.7128 (m-40) cc_final: 0.6257 (p0)
REVERT: C   95 MET cc_start: 0.8228 (tmm) cc_final: 0.7859 (tmm)
REVERT: C   96 MET cc_start: 0.8574 (mmm) cc_final: 0.8055 (mmm)
REVERT: C  151 ILE cc_start: 0.8247 (mm) cc_final: 0.7985 (mm)
REVERT: C  227 PHE cc_start: 0.7932 (t80) cc_final: 0.7621 (t80)
REVERT: C  259 PHE cc_start: 0.6611 (t80) cc_final: 0.5862 (t80)
REVERT: D   55 TYR cc_start: 0.8276 (t80) cc_final: 0.8072 (t80)
REVERT: D  154 PHE cc_start: 0.8159 (t80) cc_final: 0.7851 (t80)
REVERT: D  169 TYR cc_start: 0.7700 (m-80) cc_final: 0.6891 (m-80)
REVERT: D  174 TYR cc_start: 0.1960 (t80) cc_final: 0.1294 (t80)
REVERT: D  178 PHE cc_start: 0.7938 (m-80) cc_final: 0.7655 (m-80)
REVERT: D  249 GLN cc_start: 0.7303 (pt0) cc_final: 0.6926 (pm20)
  outliers start: 5
  outliers final: 0
  residues processed: 573
  average time/residue: 0.1224
  time to fit residues: 104.4241
Evaluate side-chains
  460 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 460
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 167 optimal weight:    7.9990
   chunk 131 optimal weight:    1.9990
   chunk 164 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 182 optimal weight:   10.0000
   chunk 159 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9980
   chunk 150 optimal weight:   20.0000
   chunk 63 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 158 optimal weight:   10.0000
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 180 ASN
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 ASN
** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 455 ASN
B  61 ASN
B 218 ASN
B 232 ASN
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 475 ASN
** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 676 HIS
C 132 GLN
D  71 ASN
D 265 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.128187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.087857 restraints weight = 48862.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.091128 restraints weight = 30852.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.093414 restraints weight = 21386.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.094914 restraints weight = 16611.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.096088 restraints weight = 13481.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3381
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3381
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.4895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  16386  Z= 0.180
  Angle     :  0.598   7.292  22134  Z= 0.318
  Chirality :  0.042   0.177   2360
  Planarity :  0.004   0.043   2818
  Dihedral  : 11.489 172.280   2242
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.68 %
    Favored  : 97.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.19), residues: 1932
  helix:  1.30 (0.15), residues: 1130
  sheet: -0.46 (0.40), residues: 160
  loop :  0.58 (0.25), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 161 
 TYR   0.019   0.002   TYR B 626 
 PHE   0.032   0.002   PHE D 166 
 TRP   0.032   0.002   TRP B 558 
 HIS   0.006   0.001   HIS B 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (16386)
  covalent geometry    : angle       0.59808 (22134)
  hydrogen bonds       : bond        0.04348 (  871)
  hydrogen bonds       : angle       4.93943 ( 2571)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  558 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 554
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 GLU cc_start: 0.9280 (tp30) cc_final: 0.8756 (tp30)
REVERT: A   71 LEU cc_start: 0.9409 (mt) cc_final: 0.8914 (mt)
REVERT: A   81 PHE cc_start: 0.9442 (m-80) cc_final: 0.9111 (m-80)
REVERT: A   99 LYS cc_start: 0.9249 (mmtp) cc_final: 0.8631 (mttt)
REVERT: A  108 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8671 (p)
REVERT: A  117 ARG cc_start: 0.9059 (mmt90) cc_final: 0.8639 (mtp85)
REVERT: A  119 GLU cc_start: 0.8659 (mp0) cc_final: 0.8380 (tm-30)
REVERT: A  128 PHE cc_start: 0.9160 (t80) cc_final: 0.8754 (t80)
REVERT: A  147 GLN cc_start: 0.9093 (mt0) cc_final: 0.8616 (mt0)
REVERT: A  168 VAL cc_start: 0.8271 (t) cc_final: 0.7941 (p)
REVERT: A  172 LEU cc_start: 0.8794 (mp) cc_final: 0.8207 (mp)
REVERT: A  173 LEU cc_start: 0.9094 (mt) cc_final: 0.8836 (mt)
REVERT: A  205 LYS cc_start: 0.7339 (mttt) cc_final: 0.7034 (mttt)
REVERT: A  214 LYS cc_start: 0.9313 (mmmt) cc_final: 0.9023 (mmtt)
REVERT: A  270 ASP cc_start: 0.8765 (m-30) cc_final: 0.8124 (t70)
REVERT: A  348 MET cc_start: 0.9394 (ttp) cc_final: 0.9164 (ptp)
REVERT: A  349 LEU cc_start: 0.8519 (tp) cc_final: 0.8271 (tp)
REVERT: A  375 LYS cc_start: 0.9117 (mmtm) cc_final: 0.8656 (mmtm)
REVERT: A  385 VAL cc_start: 0.8773 (t) cc_final: 0.8358 (p)
REVERT: A  402 GLU cc_start: 0.8801 (mp0) cc_final: 0.8546 (mp0)
REVERT: A  406 ASP cc_start: 0.8208 (m-30) cc_final: 0.7953 (m-30)
REVERT: A  407 ILE cc_start: 0.8867 (mt) cc_final: 0.8473 (mt)
REVERT: A  427 LYS cc_start: 0.9409 (mmpt) cc_final: 0.9120 (mtmm)
REVERT: A  441 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8523 (mt-10)
REVERT: A  458 MET cc_start: 0.9146 (mmp) cc_final: 0.8803 (mmp)
REVERT: A  466 MET cc_start: 0.9296 (ptt) cc_final: 0.9021 (ptp)
REVERT: A  468 LEU cc_start: 0.9467 (tp) cc_final: 0.9254 (tp)
REVERT: A  479 TYR cc_start: 0.8742 (t80) cc_final: 0.8532 (t80)
REVERT: A  498 TYR cc_start: 0.8860 (m-80) cc_final: 0.8393 (m-80)
REVERT: A  550 MET cc_start: 0.7317 (mtm) cc_final: 0.6221 (mtm)
REVERT: A  598 MET cc_start: 0.8869 (mtm) cc_final: 0.8476 (mtm)
REVERT: A  599 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7399 (mm-30)
REVERT: A  602 GLU cc_start: 0.8937 (pm20) cc_final: 0.7794 (pm20)
REVERT: A  615 MET cc_start: 0.8305 (mmp) cc_final: 0.8053 (mmm)
REVERT: A  659 LYS cc_start: 0.8587 (mttt) cc_final: 0.8381 (mmmt)
REVERT: A  672 LEU cc_start: 0.9042 (mt) cc_final: 0.8821 (mt)
REVERT: B    8 LYS cc_start: 0.9479 (tttm) cc_final: 0.9211 (tppt)
REVERT: B   12 LEU cc_start: 0.9544 (mt) cc_final: 0.9318 (mt)
REVERT: B   24 PHE cc_start: 0.8633 (m-80) cc_final: 0.8189 (m-80)
REVERT: B   67 GLU cc_start: 0.8681 (mp0) cc_final: 0.8430 (mp0)
REVERT: B   95 MET cc_start: 0.9101 (tpp) cc_final: 0.7859 (tpp)
REVERT: B   98 PHE cc_start: 0.9610 (t80) cc_final: 0.8960 (t80)
REVERT: B   99 LYS cc_start: 0.9611 (mmmt) cc_final: 0.8925 (mmmt)
REVERT: B  107 LYS cc_start: 0.8808 (mppt) cc_final: 0.8564 (mptt)
REVERT: B  115 LEU cc_start: 0.8734 (mp) cc_final: 0.8446 (mp)
REVERT: B  200 SER cc_start: 0.7111 (m) cc_final: 0.6832 (p)
REVERT: B  228 LYS cc_start: 0.8114 (mmmm) cc_final: 0.7909 (tppt)
REVERT: B  235 ARG cc_start: 0.8057 (mmt90) cc_final: 0.7691 (mmt90)
REVERT: B  288 PHE cc_start: 0.9401 (t80) cc_final: 0.8886 (t80)
REVERT: B  307 TYR cc_start: 0.9273 (t80) cc_final: 0.8836 (t80)
REVERT: B  326 PHE cc_start: 0.9147 (m-80) cc_final: 0.8556 (m-80)
REVERT: B  379 SER cc_start: 0.8227 (t) cc_final: 0.7936 (t)
REVERT: B  386 LEU cc_start: 0.8816 (mt) cc_final: 0.8394 (mt)
REVERT: B  394 TYR cc_start: 0.8839 (m-80) cc_final: 0.8601 (m-80)
REVERT: B  403 ILE cc_start: 0.8913 (mp) cc_final: 0.8593 (mp)
REVERT: B  407 ILE cc_start: 0.8341 (mt) cc_final: 0.8141 (mt)
REVERT: B  413 SER cc_start: 0.9245 (m) cc_final: 0.8571 (t)
REVERT: B  441 GLU cc_start: 0.9380 (pt0) cc_final: 0.9098 (pt0)
REVERT: B  453 ARG cc_start: 0.8992 (ttt-90) cc_final: 0.8513 (ttt-90)
REVERT: B  458 MET cc_start: 0.9250 (mmm) cc_final: 0.9032 (mmm)
REVERT: B  459 LYS cc_start: 0.8736 (mttm) cc_final: 0.8021 (mtmm)
REVERT: B  472 LEU cc_start: 0.9167 (mm) cc_final: 0.8844 (mt)
REVERT: B  492 PHE cc_start: 0.9193 (m-80) cc_final: 0.8520 (m-80)
REVERT: B  493 MET cc_start: 0.9306 (tmm) cc_final: 0.8805 (tmm)
REVERT: B  494 MET cc_start: 0.9450 (mtp) cc_final: 0.9035 (mtp)
REVERT: B  506 ILE cc_start: 0.9621 (mm) cc_final: 0.9287 (mm)
REVERT: B  509 GLU cc_start: 0.8936 (pt0) cc_final: 0.8613 (pp20)
REVERT: B  510 LYS cc_start: 0.9483 (mmtp) cc_final: 0.9209 (mmmm)
REVERT: B  558 TRP cc_start: 0.8242 (m100) cc_final: 0.8038 (m100)
REVERT: B  585 SER cc_start: 0.8801 (p) cc_final: 0.8460 (t)
REVERT: B  597 ILE cc_start: 0.9042 (pt) cc_final: 0.8735 (pt)
REVERT: B  615 MET cc_start: 0.8915 (mmp) cc_final: 0.8687 (mmm)
REVERT: B  645 GLN cc_start: 0.9126 (tp40) cc_final: 0.8863 (tp-100)
REVERT: B  648 ILE cc_start: 0.9125 (mm) cc_final: 0.8887 (mm)
REVERT: B  657 PHE cc_start: 0.8406 (m-80) cc_final: 0.7959 (m-80)
REVERT: C   95 MET cc_start: 0.7921 (tmm) cc_final: 0.7187 (tmm)
REVERT: C   96 MET cc_start: 0.8355 (mmm) cc_final: 0.8007 (mmm)
REVERT: C  137 MET cc_start: 0.6755 (mpp) cc_final: 0.6030 (tpt)
REVERT: C  149 ASP cc_start: 0.7999 (t0) cc_final: 0.7715 (t0)
REVERT: C  151 ILE cc_start: 0.8305 (mm) cc_final: 0.8012 (mm)
REVERT: C  227 PHE cc_start: 0.8004 (t80) cc_final: 0.7565 (t80)
REVERT: C  259 PHE cc_start: 0.6497 (t80) cc_final: 0.5742 (t80)
REVERT: C  269 MET cc_start: 0.5304 (ptt) cc_final: 0.4963 (ppp)
REVERT: C  276 TYR cc_start: 0.8134 (t80) cc_final: 0.7821 (t80)
REVERT: D   40 ASP cc_start: 0.7367 (p0) cc_final: 0.6709 (p0)
REVERT: D  178 PHE cc_start: 0.8239 (m-80) cc_final: 0.7803 (m-80)
REVERT: D  249 GLN cc_start: 0.7356 (pt0) cc_final: 0.6983 (pm20)
  outliers start: 4
  outliers final: 1
  residues processed: 557
  average time/residue: 0.1167
  time to fit residues: 97.9824
Evaluate side-chains
  463 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 461
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 157 optimal weight:   10.0000
   chunk 168 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 127 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 185 optimal weight:    7.9990
   chunk 191 optimal weight:   30.0000
   chunk 159 optimal weight:    0.9990
   chunk 182 optimal weight:   20.0000
   chunk 93 optimal weight:    0.8980
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 191 GLN
** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 ASN
** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  24 GLN
** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.126600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.085937 restraints weight = 49400.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.088948 restraints weight = 31271.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.091184 restraints weight = 22142.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.092343 restraints weight = 16951.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.093584 restraints weight = 14459.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.5455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  16386  Z= 0.180
  Angle     :  0.601   9.703  22134  Z= 0.318
  Chirality :  0.043   0.206   2360
  Planarity :  0.004   0.043   2818
  Dihedral  : 11.262 169.201   2242
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.74 %
    Favored  : 97.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.19), residues: 1932
  helix:  1.26 (0.15), residues: 1127
  sheet: -0.48 (0.40), residues: 154
  loop :  0.59 (0.25), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 161 
 TYR   0.019   0.002   TYR D 242 
 PHE   0.032   0.002   PHE B  81 
 TRP   0.019   0.001   TRP B 558 
 HIS   0.005   0.001   HIS D 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (16386)
  covalent geometry    : angle       0.60056 (22134)
  hydrogen bonds       : bond        0.04083 (  871)
  hydrogen bonds       : angle       4.93323 ( 2571)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  534 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 533
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 GLU cc_start: 0.9271 (tp30) cc_final: 0.8817 (tp30)
REVERT: A   71 LEU cc_start: 0.9417 (mt) cc_final: 0.9079 (mt)
REVERT: A   99 LYS cc_start: 0.9267 (mmtp) cc_final: 0.8704 (mttt)
REVERT: A  117 ARG cc_start: 0.9142 (mmt90) cc_final: 0.8764 (mtp85)
REVERT: A  128 PHE cc_start: 0.9218 (t80) cc_final: 0.8795 (t80)
REVERT: A  129 PHE cc_start: 0.9541 (m-10) cc_final: 0.9281 (m-10)
REVERT: A  147 GLN cc_start: 0.9154 (mt0) cc_final: 0.8676 (mt0)
REVERT: A  168 VAL cc_start: 0.8226 (t) cc_final: 0.7897 (p)
REVERT: A  172 LEU cc_start: 0.8826 (mp) cc_final: 0.8357 (mp)
REVERT: A  173 LEU cc_start: 0.9154 (mt) cc_final: 0.8944 (mt)
REVERT: A  205 LYS cc_start: 0.7497 (mttt) cc_final: 0.7208 (mttt)
REVERT: A  214 LYS cc_start: 0.9314 (mmmt) cc_final: 0.9024 (mmtt)
REVERT: A  349 LEU cc_start: 0.8545 (tp) cc_final: 0.8291 (tp)
REVERT: A  373 ILE cc_start: 0.9542 (mt) cc_final: 0.9022 (mt)
REVERT: A  375 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8681 (mmtm)
REVERT: A  385 VAL cc_start: 0.8754 (t) cc_final: 0.8528 (p)
REVERT: A  386 LEU cc_start: 0.9277 (mt) cc_final: 0.8978 (mt)
REVERT: A  402 GLU cc_start: 0.8804 (mp0) cc_final: 0.8545 (mp0)
REVERT: A  406 ASP cc_start: 0.8201 (m-30) cc_final: 0.7991 (m-30)
REVERT: A  407 ILE cc_start: 0.8943 (mt) cc_final: 0.8497 (mt)
REVERT: A  425 ILE cc_start: 0.9420 (mt) cc_final: 0.9043 (mm)
REVERT: A  444 ASP cc_start: 0.8061 (t0) cc_final: 0.7142 (t0)
REVERT: A  447 ASN cc_start: 0.8213 (m-40) cc_final: 0.7789 (m-40)
REVERT: A  466 MET cc_start: 0.9299 (ptt) cc_final: 0.9043 (ptp)
REVERT: A  498 TYR cc_start: 0.8931 (m-80) cc_final: 0.8613 (m-80)
REVERT: A  516 GLN cc_start: 0.9531 (mt0) cc_final: 0.9194 (tt0)
REVERT: A  546 LEU cc_start: 0.9419 (mt) cc_final: 0.9192 (mt)
REVERT: A  550 MET cc_start: 0.7262 (mtm) cc_final: 0.6666 (mtm)
REVERT: A  598 MET cc_start: 0.8884 (mtm) cc_final: 0.8457 (mtm)
REVERT: A  599 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7344 (mm-30)
REVERT: A  602 GLU cc_start: 0.8667 (pm20) cc_final: 0.8289 (pm20)
REVERT: A  640 MET cc_start: 0.9332 (tpt) cc_final: 0.9030 (tpp)
REVERT: A  659 LYS cc_start: 0.8829 (mttt) cc_final: 0.8432 (mmmt)
REVERT: B    8 LYS cc_start: 0.9469 (tttm) cc_final: 0.9189 (tppt)
REVERT: B   12 LEU cc_start: 0.9556 (mt) cc_final: 0.9312 (mt)
REVERT: B   17 MET cc_start: 0.9077 (mmm) cc_final: 0.8377 (mmt)
REVERT: B   24 PHE cc_start: 0.8714 (m-80) cc_final: 0.7805 (m-80)
REVERT: B   95 MET cc_start: 0.9120 (tpp) cc_final: 0.7973 (tpp)
REVERT: B   98 PHE cc_start: 0.9592 (t80) cc_final: 0.8838 (t80)
REVERT: B   99 LYS cc_start: 0.9641 (mmmt) cc_final: 0.8940 (mmmt)
REVERT: B  107 LYS cc_start: 0.8919 (mppt) cc_final: 0.8521 (mptt)
REVERT: B  184 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8035 (mmm160)
REVERT: B  187 ASP cc_start: 0.9061 (t0) cc_final: 0.8539 (t0)
REVERT: B  235 ARG cc_start: 0.8239 (mmt90) cc_final: 0.7939 (mmt90)
REVERT: B  288 PHE cc_start: 0.9395 (t80) cc_final: 0.8951 (t80)
REVERT: B  307 TYR cc_start: 0.9283 (t80) cc_final: 0.8801 (t80)
REVERT: B  319 MET cc_start: 0.8941 (tpp) cc_final: 0.8732 (tpp)
REVERT: B  326 PHE cc_start: 0.9350 (m-10) cc_final: 0.8511 (m-80)
REVERT: B  333 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8144 (ttmt)
REVERT: B  359 MET cc_start: 0.7696 (tmm) cc_final: 0.7191 (tmm)
REVERT: B  413 SER cc_start: 0.9175 (m) cc_final: 0.8651 (t)
REVERT: B  414 LEU cc_start: 0.9278 (mt) cc_final: 0.9063 (mt)
REVERT: B  417 LEU cc_start: 0.9314 (tt) cc_final: 0.8710 (tt)
REVERT: B  441 GLU cc_start: 0.9413 (pt0) cc_final: 0.9112 (pt0)
REVERT: B  459 LYS cc_start: 0.8695 (mttm) cc_final: 0.8011 (mtmm)
REVERT: B  466 MET cc_start: 0.8718 (ptp) cc_final: 0.8515 (ptp)
REVERT: B  472 LEU cc_start: 0.9239 (mm) cc_final: 0.8937 (mm)
REVERT: B  492 PHE cc_start: 0.9177 (m-80) cc_final: 0.8565 (m-80)
REVERT: B  493 MET cc_start: 0.9233 (tmm) cc_final: 0.8699 (tmm)
REVERT: B  494 MET cc_start: 0.9451 (mtp) cc_final: 0.8806 (mtp)
REVERT: B  506 ILE cc_start: 0.9628 (mm) cc_final: 0.9205 (mm)
REVERT: B  509 GLU cc_start: 0.9044 (pt0) cc_final: 0.8801 (pp20)
REVERT: B  510 LYS cc_start: 0.9524 (mmtp) cc_final: 0.9226 (mmmm)
REVERT: B  522 TYR cc_start: 0.8405 (m-80) cc_final: 0.7987 (m-10)
REVERT: B  558 TRP cc_start: 0.8267 (m100) cc_final: 0.7981 (m100)
REVERT: B  597 ILE cc_start: 0.8934 (pt) cc_final: 0.8706 (pt)
REVERT: B  615 MET cc_start: 0.8909 (mmp) cc_final: 0.8627 (mmm)
REVERT: B  640 MET cc_start: 0.9032 (mmt) cc_final: 0.8738 (mmt)
REVERT: B  645 GLN cc_start: 0.9192 (tp40) cc_final: 0.8984 (tp-100)
REVERT: B  675 HIS cc_start: 0.8907 (t-90) cc_final: 0.8541 (t-90)
REVERT: C   95 MET cc_start: 0.7963 (tmm) cc_final: 0.7061 (tmm)
REVERT: C   96 MET cc_start: 0.8406 (mmm) cc_final: 0.7958 (mmm)
REVERT: C  149 ASP cc_start: 0.8053 (t0) cc_final: 0.7801 (t0)
REVERT: C  151 ILE cc_start: 0.8251 (mm) cc_final: 0.7984 (mm)
REVERT: C  227 PHE cc_start: 0.7920 (t80) cc_final: 0.7529 (t80)
REVERT: C  259 PHE cc_start: 0.6296 (t80) cc_final: 0.5561 (t80)
REVERT: C  276 TYR cc_start: 0.8249 (t80) cc_final: 0.7966 (t80)
REVERT: D  169 TYR cc_start: 0.7931 (m-80) cc_final: 0.7005 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 533
  average time/residue: 0.1221
  time to fit residues: 97.2059
Evaluate side-chains
  460 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 460
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 99 optimal weight:    9.9990
   chunk 46 optimal weight:    7.9990
   chunk 120 optimal weight:    0.0870
   chunk 37 optimal weight:    2.9990
   chunk 126 optimal weight:    1.9990
   chunk 129 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 122 optimal weight:    5.9990
   chunk 115 optimal weight:    8.9990
   chunk 168 optimal weight:    7.9990
   chunk 157 optimal weight:    9.9990
   overall best weight:    3.8166

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 150 GLN
B 218 ASN
** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.122814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.082698 restraints weight = 51555.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.085921 restraints weight = 31798.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.088030 restraints weight = 22041.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.089576 restraints weight = 16855.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.090633 restraints weight = 13599.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3274
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3274 r_free = 0.3274    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3274 r_free = 0.3274    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3274
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.5968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  16386  Z= 0.238
  Angle     :  0.657   8.634  22134  Z= 0.347
  Chirality :  0.044   0.183   2360
  Planarity :  0.004   0.039   2818
  Dihedral  : 11.350 169.600   2242
  Min Nonbonded Distance : 1.810

Molprobity Statistics.
  All-atom Clashscore : 17.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.16 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.19), residues: 1932
  helix:  1.08 (0.15), residues: 1127
  sheet: -0.68 (0.39), residues: 156
  loop :  0.45 (0.25), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 161 
 TYR   0.024   0.002   TYR D 174 
 PHE   0.028   0.002   PHE B  81 
 TRP   0.019   0.002   TRP B 558 
 HIS   0.006   0.001   HIS B 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (16386)
  covalent geometry    : angle       0.65696 (22134)
  hydrogen bonds       : bond        0.04212 (  871)
  hydrogen bonds       : angle       5.12510 ( 2571)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  517 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 515
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 GLU cc_start: 0.9284 (tp30) cc_final: 0.8946 (tp30)
REVERT: A  117 ARG cc_start: 0.9132 (mmt90) cc_final: 0.8808 (mtp85)
REVERT: A  147 GLN cc_start: 0.9210 (mt0) cc_final: 0.8798 (mt0)
REVERT: A  172 LEU cc_start: 0.8885 (mp) cc_final: 0.8429 (mp)
REVERT: A  173 LEU cc_start: 0.9172 (mt) cc_final: 0.8970 (mt)
REVERT: A  214 LYS cc_start: 0.9330 (mmmt) cc_final: 0.8984 (mmtt)
REVERT: A  252 ASN cc_start: 0.8502 (t0) cc_final: 0.8125 (t0)
REVERT: A  314 MET cc_start: 0.8513 (ppp) cc_final: 0.8158 (ppp)
REVERT: A  345 LYS cc_start: 0.9255 (mttp) cc_final: 0.9030 (mttm)
REVERT: A  361 GLN cc_start: 0.9023 (tp40) cc_final: 0.8786 (tp-100)
REVERT: A  375 LYS cc_start: 0.9076 (mmtm) cc_final: 0.8668 (mmtm)
REVERT: A  402 GLU cc_start: 0.8803 (mp0) cc_final: 0.8536 (mp0)
REVERT: A  406 ASP cc_start: 0.8375 (m-30) cc_final: 0.8070 (m-30)
REVERT: A  407 ILE cc_start: 0.8998 (mt) cc_final: 0.8511 (mt)
REVERT: A  498 TYR cc_start: 0.8983 (m-80) cc_final: 0.8617 (m-80)
REVERT: A  550 MET cc_start: 0.7882 (mtm) cc_final: 0.7102 (mtm)
REVERT: A  598 MET cc_start: 0.8743 (mtm) cc_final: 0.8360 (ttm)
REVERT: A  615 MET cc_start: 0.8076 (mmp) cc_final: 0.7568 (mmp)
REVERT: A  640 MET cc_start: 0.9441 (tpt) cc_final: 0.9112 (tpp)
REVERT: A  650 GLN cc_start: 0.7070 (mm-40) cc_final: 0.6772 (mm110)
REVERT: A  659 LYS cc_start: 0.8843 (mttt) cc_final: 0.8504 (mmmt)
REVERT: B    8 LYS cc_start: 0.9481 (tttm) cc_final: 0.9181 (tppt)
REVERT: B   12 LEU cc_start: 0.9565 (mt) cc_final: 0.9337 (mt)
REVERT: B   24 PHE cc_start: 0.8888 (m-80) cc_final: 0.8325 (m-80)
REVERT: B   95 MET cc_start: 0.9274 (tpp) cc_final: 0.7715 (tpp)
REVERT: B   98 PHE cc_start: 0.9630 (t80) cc_final: 0.8155 (t80)
REVERT: B   99 LYS cc_start: 0.9651 (mmmt) cc_final: 0.8863 (mmmt)
REVERT: B  122 ILE cc_start: 0.9227 (mt) cc_final: 0.8878 (mt)
REVERT: B  124 ILE cc_start: 0.9210 (tp) cc_final: 0.8898 (tp)
REVERT: B  184 ARG cc_start: 0.8761 (mmm160) cc_final: 0.7974 (mmm160)
REVERT: B  187 ASP cc_start: 0.9096 (t0) cc_final: 0.8580 (t0)
REVERT: B  235 ARG cc_start: 0.8316 (mmt90) cc_final: 0.7924 (mmt90)
REVERT: B  288 PHE cc_start: 0.9431 (t80) cc_final: 0.9039 (t80)
REVERT: B  307 TYR cc_start: 0.9326 (t80) cc_final: 0.8883 (t80)
REVERT: B  326 PHE cc_start: 0.9184 (m-10) cc_final: 0.8541 (m-80)
REVERT: B  333 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8008 (ttpt)
REVERT: B  379 SER cc_start: 0.8150 (t) cc_final: 0.7854 (t)
REVERT: B  441 GLU cc_start: 0.9399 (pt0) cc_final: 0.9038 (pt0)
REVERT: B  444 ASP cc_start: 0.9113 (t0) cc_final: 0.8909 (t70)
REVERT: B  459 LYS cc_start: 0.8786 (mttm) cc_final: 0.8058 (mtmm)
REVERT: B  472 LEU cc_start: 0.9220 (mm) cc_final: 0.8768 (mt)
REVERT: B  492 PHE cc_start: 0.9322 (m-80) cc_final: 0.8817 (m-80)
REVERT: B  493 MET cc_start: 0.9235 (tmm) cc_final: 0.8647 (tmm)
REVERT: B  494 MET cc_start: 0.9316 (mtp) cc_final: 0.8861 (mtp)
REVERT: B  506 ILE cc_start: 0.9647 (mm) cc_final: 0.9444 (mm)
REVERT: B  522 TYR cc_start: 0.8749 (m-80) cc_final: 0.8466 (m-10)
REVERT: B  558 TRP cc_start: 0.8264 (m100) cc_final: 0.7937 (m100)
REVERT: B  615 MET cc_start: 0.8860 (mmp) cc_final: 0.8642 (mmm)
REVERT: B  640 MET cc_start: 0.9082 (mmt) cc_final: 0.8624 (mmt)
REVERT: B  645 GLN cc_start: 0.9152 (tp40) cc_final: 0.8779 (tp-100)
REVERT: B  648 ILE cc_start: 0.9034 (mm) cc_final: 0.8828 (mm)
REVERT: C   95 MET cc_start: 0.8124 (tmm) cc_final: 0.7356 (tmm)
REVERT: C   96 MET cc_start: 0.8385 (mmm) cc_final: 0.7985 (mmm)
REVERT: C  137 MET cc_start: 0.7468 (mpp) cc_final: 0.6558 (tpt)
REVERT: C  149 ASP cc_start: 0.8085 (t0) cc_final: 0.7764 (t0)
REVERT: C  151 ILE cc_start: 0.8266 (mm) cc_final: 0.7859 (tp)
REVERT: C  227 PHE cc_start: 0.8010 (t80) cc_final: 0.7733 (t80)
REVERT: C  259 PHE cc_start: 0.6480 (t80) cc_final: 0.5738 (t80)
REVERT: C  276 TYR cc_start: 0.8316 (t80) cc_final: 0.7858 (t80)
REVERT: D   82 ASP cc_start: 0.8532 (p0) cc_final: 0.8117 (m-30)
REVERT: D  169 TYR cc_start: 0.8021 (m-80) cc_final: 0.7090 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 517
  average time/residue: 0.1238
  time to fit residues: 95.3664
Evaluate side-chains
  417 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 417
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 183 optimal weight:    9.9990
   chunk 72 optimal weight:    3.9990
   chunk 172 optimal weight:    9.9990
   chunk 52 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 77 optimal weight:    0.1980
   chunk 27 optimal weight:    2.9990
   chunk 136 optimal weight:   10.0000
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 447 ASN
A 646 GLN
B 180 ASN
B 218 ASN
** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 447 ASN
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 201 HIS
** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.127198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.088570 restraints weight = 51779.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.091579 restraints weight = 33006.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.093567 restraints weight = 23095.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.094614 restraints weight = 17844.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.095991 restraints weight = 14849.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3317
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3317 r_free = 0.3317    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3317 r_free = 0.3317    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3317
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
moved from start:          0.6193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  16386  Z= 0.159
  Angle     :  0.607   7.839  22134  Z= 0.320
  Chirality :  0.043   0.181   2360
  Planarity :  0.003   0.040   2818
  Dihedral  : 10.979 160.136   2242
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  1.46 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.19), residues: 1932
  helix:  1.18 (0.15), residues: 1110
  sheet: -0.55 (0.39), residues: 158
  loop :  0.42 (0.25), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 196 
 TYR   0.020   0.002   TYR D 174 
 PHE   0.031   0.002   PHE D 178 
 TRP   0.010   0.001   TRP B 558 
 HIS   0.006   0.001   HIS D 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (16386)
  covalent geometry    : angle       0.60707 (22134)
  hydrogen bonds       : bond        0.03987 (  871)
  hydrogen bonds       : angle       4.98382 ( 2571)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  525 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 522
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 GLU cc_start: 0.9216 (tp30) cc_final: 0.8803 (tp30)
REVERT: A   71 LEU cc_start: 0.9381 (mt) cc_final: 0.9092 (mt)
REVERT: A  117 ARG cc_start: 0.9180 (mmt90) cc_final: 0.8874 (mtp85)
REVERT: A  147 GLN cc_start: 0.9088 (mt0) cc_final: 0.8663 (mt0)
REVERT: A  172 LEU cc_start: 0.8841 (mp) cc_final: 0.8285 (mp)
REVERT: A  202 ASN cc_start: 0.8574 (t0) cc_final: 0.8363 (t0)
REVERT: A  270 ASP cc_start: 0.8698 (m-30) cc_final: 0.8058 (t70)
REVERT: A  314 MET cc_start: 0.8486 (ppp) cc_final: 0.8158 (ppp)
REVERT: A  345 LYS cc_start: 0.9268 (mttp) cc_final: 0.8947 (mttt)
REVERT: A  359 MET cc_start: 0.8209 (ttp) cc_final: 0.7993 (ttp)
REVERT: A  361 GLN cc_start: 0.9099 (tp40) cc_final: 0.8835 (tp-100)
REVERT: A  375 LYS cc_start: 0.9062 (mmtm) cc_final: 0.8612 (mmtm)
REVERT: A  402 GLU cc_start: 0.8860 (mp0) cc_final: 0.8580 (mp0)
REVERT: A  407 ILE cc_start: 0.8855 (mt) cc_final: 0.8551 (mt)
REVERT: A  425 ILE cc_start: 0.9341 (mm) cc_final: 0.8862 (mm)
REVERT: A  456 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8345 (mmtm)
REVERT: A  498 TYR cc_start: 0.9110 (m-80) cc_final: 0.8794 (m-80)
REVERT: A  501 GLN cc_start: 0.9098 (tp-100) cc_final: 0.8794 (tp-100)
REVERT: A  550 MET cc_start: 0.7442 (mtm) cc_final: 0.6674 (mtm)
REVERT: A  615 MET cc_start: 0.8173 (mmp) cc_final: 0.7886 (mmp)
REVERT: A  640 MET cc_start: 0.9438 (tpt) cc_final: 0.9126 (tpp)
REVERT: A  650 GLN cc_start: 0.7127 (mm-40) cc_final: 0.6788 (mm-40)
REVERT: A  659 LYS cc_start: 0.8922 (mttt) cc_final: 0.8566 (mmmt)
REVERT: B    8 LYS cc_start: 0.9473 (tttm) cc_final: 0.9154 (tppt)
REVERT: B   12 LEU cc_start: 0.9569 (mt) cc_final: 0.9320 (mt)
REVERT: B   17 MET cc_start: 0.8854 (mmm) cc_final: 0.8461 (mmt)
REVERT: B   24 PHE cc_start: 0.8688 (m-80) cc_final: 0.8257 (m-80)
REVERT: B   41 ILE cc_start: 0.9512 (mm) cc_final: 0.9275 (mm)
REVERT: B   95 MET cc_start: 0.9186 (tpp) cc_final: 0.8058 (tpp)
REVERT: B   98 PHE cc_start: 0.9594 (t80) cc_final: 0.8785 (t80)
REVERT: B   99 LYS cc_start: 0.9667 (mmmt) cc_final: 0.8998 (mmmt)
REVERT: B  122 ILE cc_start: 0.9259 (mt) cc_final: 0.8883 (mt)
REVERT: B  124 ILE cc_start: 0.9279 (tp) cc_final: 0.8785 (tp)
REVERT: B  184 ARG cc_start: 0.8747 (mmm160) cc_final: 0.7954 (mmm160)
REVERT: B  187 ASP cc_start: 0.9058 (t0) cc_final: 0.8593 (t0)
REVERT: B  235 ARG cc_start: 0.8317 (mmt90) cc_final: 0.7956 (mmt90)
REVERT: B  288 PHE cc_start: 0.9423 (t80) cc_final: 0.9063 (t80)
REVERT: B  307 TYR cc_start: 0.9288 (t80) cc_final: 0.8795 (t80)
REVERT: B  317 MET cc_start: 0.8588 (mtm) cc_final: 0.8110 (mpp)
REVERT: B  326 PHE cc_start: 0.9311 (m-10) cc_final: 0.8577 (m-80)
REVERT: B  333 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8095 (ttpt)
REVERT: B  379 SER cc_start: 0.8016 (t) cc_final: 0.7652 (t)
REVERT: B  417 LEU cc_start: 0.9321 (tt) cc_final: 0.8885 (tt)
REVERT: B  459 LYS cc_start: 0.8696 (mttm) cc_final: 0.7972 (mtmm)
REVERT: B  472 LEU cc_start: 0.9230 (mm) cc_final: 0.8792 (mt)
REVERT: B  492 PHE cc_start: 0.9322 (m-80) cc_final: 0.8785 (m-80)
REVERT: B  493 MET cc_start: 0.9164 (tmm) cc_final: 0.8572 (tmm)
REVERT: B  494 MET cc_start: 0.9412 (mtp) cc_final: 0.8776 (mtp)
REVERT: B  522 TYR cc_start: 0.8668 (m-80) cc_final: 0.8360 (m-10)
REVERT: B  558 TRP cc_start: 0.8253 (m100) cc_final: 0.7952 (m100)
REVERT: B  585 SER cc_start: 0.8754 (p) cc_final: 0.8418 (t)
REVERT: B  615 MET cc_start: 0.8775 (mmp) cc_final: 0.8547 (mmm)
REVERT: B  632 MET cc_start: 0.8492 (mtt) cc_final: 0.8218 (mtt)
REVERT: B  640 MET cc_start: 0.9253 (mmt) cc_final: 0.8929 (mmt)
REVERT: B  645 GLN cc_start: 0.9135 (tp40) cc_final: 0.8899 (tp-100)
REVERT: B  667 LEU cc_start: 0.8230 (tt) cc_final: 0.7922 (tt)
REVERT: C   95 MET cc_start: 0.7962 (tmm) cc_final: 0.7073 (tmm)
REVERT: C   96 MET cc_start: 0.8336 (mmm) cc_final: 0.7911 (mmm)
REVERT: C  137 MET cc_start: 0.7539 (mpp) cc_final: 0.6889 (tpt)
REVERT: C  149 ASP cc_start: 0.8085 (t0) cc_final: 0.7870 (t0)
REVERT: C  151 ILE cc_start: 0.8275 (mm) cc_final: 0.8003 (mm)
REVERT: C  259 PHE cc_start: 0.6473 (t80) cc_final: 0.5720 (t80)
REVERT: C  276 TYR cc_start: 0.8333 (t80) cc_final: 0.7896 (t80)
REVERT: D   96 MET cc_start: 0.4350 (tpt) cc_final: 0.3929 (mmt)
REVERT: D  169 TYR cc_start: 0.8155 (m-80) cc_final: 0.7296 (m-80)
REVERT: D  179 TYR cc_start: 0.8578 (t80) cc_final: 0.8327 (t80)
  outliers start: 3
  outliers final: 1
  residues processed: 525
  average time/residue: 0.1254
  time to fit residues: 99.3554
Evaluate side-chains
  416 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 415
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 186 optimal weight:    6.9990
   chunk 140 optimal weight:    5.9990
   chunk 115 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9990
   chunk 68 optimal weight:   10.0000
   chunk 156 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 180 ASN
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 418 ASN
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 238 ASN
D  24 GLN
** D  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.128561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.088485 restraints weight = 50212.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.091660 restraints weight = 31388.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.093709 restraints weight = 21921.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.095313 restraints weight = 16949.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.096455 restraints weight = 13824.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3416
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3416 r_free = 0.3416    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.6457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  16386  Z= 0.128
  Angle     :  0.606   8.278  22134  Z= 0.319
  Chirality :  0.042   0.176   2360
  Planarity :  0.003   0.041   2818
  Dihedral  : 10.554 152.952   2242
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  1.75 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.19), residues: 1932
  helix:  1.10 (0.15), residues: 1125
  sheet: -0.48 (0.40), residues: 148
  loop :  0.45 (0.25), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 161 
 TYR   0.027   0.001   TYR A 571 
 PHE   0.017   0.002   PHE C 322 
 TRP   0.008   0.001   TRP B 558 
 HIS   0.023   0.001   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (16386)
  covalent geometry    : angle       0.60607 (22134)
  hydrogen bonds       : bond        0.03884 (  871)
  hydrogen bonds       : angle       5.00778 ( 2571)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  504 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 503
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 GLU cc_start: 0.9209 (tp30) cc_final: 0.8808 (tp30)
REVERT: A   71 LEU cc_start: 0.9404 (mt) cc_final: 0.9123 (mt)
REVERT: A   99 LYS cc_start: 0.9486 (mmtp) cc_final: 0.9020 (mttt)
REVERT: A  117 ARG cc_start: 0.9153 (mmt90) cc_final: 0.8737 (mtp85)
REVERT: A  136 LYS cc_start: 0.8997 (ttpp) cc_final: 0.8737 (tttt)
REVERT: A  147 GLN cc_start: 0.9002 (mt0) cc_final: 0.8511 (mt0)
REVERT: A  202 ASN cc_start: 0.8582 (t0) cc_final: 0.8240 (t0)
REVERT: A  236 TYR cc_start: 0.7348 (t80) cc_final: 0.7116 (t80)
REVERT: A  259 ASN cc_start: 0.8144 (p0) cc_final: 0.7889 (p0)
REVERT: A  270 ASP cc_start: 0.8701 (m-30) cc_final: 0.8084 (t70)
REVERT: A  314 MET cc_start: 0.8540 (ppp) cc_final: 0.8167 (ppp)
REVERT: A  361 GLN cc_start: 0.9064 (tp40) cc_final: 0.8765 (tp-100)
REVERT: A  402 GLU cc_start: 0.8838 (mp0) cc_final: 0.8537 (mp0)
REVERT: A  407 ILE cc_start: 0.8947 (mt) cc_final: 0.8640 (mt)
REVERT: A  444 ASP cc_start: 0.8325 (t0) cc_final: 0.7394 (t0)
REVERT: A  456 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8286 (mmtm)
REVERT: A  466 MET cc_start: 0.8159 (ptp) cc_final: 0.7437 (pmm)
REVERT: A  479 TYR cc_start: 0.8509 (t80) cc_final: 0.8231 (t80)
REVERT: A  498 TYR cc_start: 0.9124 (m-80) cc_final: 0.8808 (m-80)
REVERT: A  501 GLN cc_start: 0.9159 (tp-100) cc_final: 0.8815 (tp-100)
REVERT: A  550 MET cc_start: 0.7721 (mtm) cc_final: 0.7032 (mtm)
REVERT: A  571 TYR cc_start: 0.8791 (t80) cc_final: 0.8497 (t80)
REVERT: A  595 MET cc_start: 0.8802 (tpp) cc_final: 0.8574 (mmm)
REVERT: A  611 THR cc_start: 0.8921 (t) cc_final: 0.8693 (t)
REVERT: A  615 MET cc_start: 0.8246 (mmp) cc_final: 0.7848 (mmp)
REVERT: A  640 MET cc_start: 0.9402 (tpt) cc_final: 0.9136 (tpp)
REVERT: A  650 GLN cc_start: 0.7015 (mm-40) cc_final: 0.6603 (mm-40)
REVERT: A  659 LYS cc_start: 0.8960 (mttt) cc_final: 0.8682 (mmmm)
REVERT: B    8 LYS cc_start: 0.9439 (tttm) cc_final: 0.9141 (tppt)
REVERT: B   12 LEU cc_start: 0.9603 (mt) cc_final: 0.9329 (mt)
REVERT: B   17 MET cc_start: 0.8691 (mmm) cc_final: 0.8294 (mmt)
REVERT: B   24 PHE cc_start: 0.8772 (m-80) cc_final: 0.8133 (m-80)
REVERT: B   41 ILE cc_start: 0.9409 (mm) cc_final: 0.8989 (mm)
REVERT: B   95 MET cc_start: 0.9088 (tpp) cc_final: 0.7964 (tpp)
REVERT: B   98 PHE cc_start: 0.9573 (t80) cc_final: 0.9080 (t80)
REVERT: B   99 LYS cc_start: 0.9662 (mmmt) cc_final: 0.8998 (mmmt)
REVERT: B  124 ILE cc_start: 0.9283 (tp) cc_final: 0.8882 (tp)
REVERT: B  235 ARG cc_start: 0.8353 (mmt90) cc_final: 0.7968 (mmt90)
REVERT: B  288 PHE cc_start: 0.9328 (t80) cc_final: 0.9091 (t80)
REVERT: B  307 TYR cc_start: 0.9279 (t80) cc_final: 0.8759 (t80)
REVERT: B  317 MET cc_start: 0.8308 (mtm) cc_final: 0.7883 (mpp)
REVERT: B  326 PHE cc_start: 0.9336 (m-10) cc_final: 0.8607 (m-80)
REVERT: B  333 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8081 (ttpt)
REVERT: B  359 MET cc_start: 0.7494 (tmm) cc_final: 0.7160 (tmm)
REVERT: B  403 ILE cc_start: 0.8953 (mp) cc_final: 0.8523 (tp)
REVERT: B  459 LYS cc_start: 0.8702 (mttm) cc_final: 0.8114 (mtmt)
REVERT: B  472 LEU cc_start: 0.9294 (mm) cc_final: 0.8829 (mt)
REVERT: B  492 PHE cc_start: 0.9261 (m-80) cc_final: 0.8652 (m-80)
REVERT: B  493 MET cc_start: 0.9157 (tmm) cc_final: 0.8537 (tmm)
REVERT: B  494 MET cc_start: 0.9338 (mtp) cc_final: 0.8730 (mtp)
REVERT: B  522 TYR cc_start: 0.8613 (m-80) cc_final: 0.8344 (m-10)
REVERT: B  558 TRP cc_start: 0.8200 (m100) cc_final: 0.7903 (m100)
REVERT: B  585 SER cc_start: 0.8856 (p) cc_final: 0.8467 (t)
REVERT: B  631 ASP cc_start: 0.9174 (t70) cc_final: 0.8894 (t0)
REVERT: C   95 MET cc_start: 0.7646 (tmm) cc_final: 0.6833 (tmm)
REVERT: C   96 MET cc_start: 0.8481 (mmm) cc_final: 0.7970 (mmm)
REVERT: C  137 MET cc_start: 0.7799 (mpp) cc_final: 0.7090 (tpp)
REVERT: C  149 ASP cc_start: 0.8100 (t0) cc_final: 0.7822 (t0)
REVERT: C  151 ILE cc_start: 0.8304 (mm) cc_final: 0.7908 (tp)
REVERT: C  227 PHE cc_start: 0.8620 (t80) cc_final: 0.8388 (t80)
REVERT: C  259 PHE cc_start: 0.6461 (t80) cc_final: 0.5709 (t80)
REVERT: C  276 TYR cc_start: 0.8308 (t80) cc_final: 0.7856 (t80)
REVERT: D   46 TYR cc_start: 0.8289 (t80) cc_final: 0.8045 (t80)
REVERT: D   96 MET cc_start: 0.4118 (tpt) cc_final: 0.3528 (tpp)
REVERT: D  157 MET cc_start: 0.6720 (tmm) cc_final: 0.6402 (tmm)
REVERT: D  169 TYR cc_start: 0.8507 (m-80) cc_final: 0.7836 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 504
  average time/residue: 0.1225
  time to fit residues: 93.3872
Evaluate side-chains
  407 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 407
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   chunk 134 optimal weight:    9.9990
   chunk 153 optimal weight:   20.0000
   chunk 11 optimal weight:   10.0000
   chunk 158 optimal weight:    9.9990
   chunk 97 optimal weight:    2.9990
   chunk 151 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 180 ASN
A 370 ASN
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 ASN
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 645 GLN
C 233 ASN
D  24 GLN
** D  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 127 GLN
D 249 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.120650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.082191 restraints weight = 50692.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.085017 restraints weight = 31565.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.087118 restraints weight = 22037.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.087933 restraints weight = 16894.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.089047 restraints weight = 14557.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.6880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079  16386  Z= 0.267
  Angle     :  0.724   8.585  22134  Z= 0.383
  Chirality :  0.046   0.262   2360
  Planarity :  0.004   0.056   2818
  Dihedral  : 11.093 159.363   2242
  Min Nonbonded Distance : 1.780

Molprobity Statistics.
  All-atom Clashscore : 20.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.99 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.19), residues: 1932
  helix:  0.79 (0.15), residues: 1123
  sheet: -0.56 (0.40), residues: 152
  loop :  0.18 (0.25), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 196 
 TYR   0.038   0.002   TYR D 174 
 PHE   0.032   0.002   PHE B 156 
 TRP   0.019   0.002   TRP B 558 
 HIS   0.018   0.002   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 (16386)
  covalent geometry    : angle       0.72449 (22134)
  hydrogen bonds       : bond        0.04358 (  871)
  hydrogen bonds       : angle       5.26723 ( 2571)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  495 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 494
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 GLU cc_start: 0.8259 (mp0) cc_final: 0.7788 (mp0)
REVERT: A   67 GLU cc_start: 0.9334 (tp30) cc_final: 0.9048 (tp30)
REVERT: A  117 ARG cc_start: 0.9160 (mmt90) cc_final: 0.8796 (mmt180)
REVERT: A  147 GLN cc_start: 0.9129 (mt0) cc_final: 0.8897 (mt0)
REVERT: A  158 ASN cc_start: 0.8977 (m-40) cc_final: 0.8764 (m110)
REVERT: A  236 TYR cc_start: 0.7666 (t80) cc_final: 0.7306 (t80)
REVERT: A  259 ASN cc_start: 0.8135 (p0) cc_final: 0.7897 (p0)
REVERT: A  270 ASP cc_start: 0.8697 (m-30) cc_final: 0.7973 (t0)
REVERT: A  314 MET cc_start: 0.8570 (ppp) cc_final: 0.8243 (ppp)
REVERT: A  322 MET cc_start: 0.8603 (tpp) cc_final: 0.8347 (mmt)
REVERT: A  344 GLU cc_start: 0.9100 (pt0) cc_final: 0.8850 (pp20)
REVERT: A  361 GLN cc_start: 0.9079 (tp40) cc_final: 0.8854 (tp-100)
REVERT: A  375 LYS cc_start: 0.9044 (mmtm) cc_final: 0.8588 (mmtm)
REVERT: A  390 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7675 (tm-30)
REVERT: A  402 GLU cc_start: 0.8836 (mp0) cc_final: 0.8542 (mp0)
REVERT: A  407 ILE cc_start: 0.9102 (mt) cc_final: 0.8545 (mt)
REVERT: A  425 ILE cc_start: 0.9166 (mp) cc_final: 0.8890 (mp)
REVERT: A  455 ASN cc_start: 0.8990 (t0) cc_final: 0.8750 (t0)
REVERT: A  456 LYS cc_start: 0.8903 (mmtm) cc_final: 0.8373 (mmtm)
REVERT: A  498 TYR cc_start: 0.9206 (m-80) cc_final: 0.8900 (m-80)
REVERT: A  501 GLN cc_start: 0.9244 (tp-100) cc_final: 0.8836 (tp-100)
REVERT: A  595 MET cc_start: 0.8844 (tpp) cc_final: 0.8616 (mmm)
REVERT: A  598 MET cc_start: 0.8663 (mtm) cc_final: 0.8460 (ttm)
REVERT: A  599 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7396 (mm-30)
REVERT: A  615 MET cc_start: 0.8252 (mmp) cc_final: 0.7610 (mmp)
REVERT: A  640 MET cc_start: 0.9484 (tpt) cc_final: 0.9021 (tpp)
REVERT: A  650 GLN cc_start: 0.7183 (mm-40) cc_final: 0.6668 (mm-40)
REVERT: A  659 LYS cc_start: 0.8655 (mttt) cc_final: 0.8336 (mmmt)
REVERT: B    8 LYS cc_start: 0.9494 (tttm) cc_final: 0.9156 (tppt)
REVERT: B   12 LEU cc_start: 0.9606 (mt) cc_final: 0.9351 (mt)
REVERT: B   24 PHE cc_start: 0.8947 (m-80) cc_final: 0.8455 (m-80)
REVERT: B   95 MET cc_start: 0.9315 (tpp) cc_final: 0.7923 (tpp)
REVERT: B   98 PHE cc_start: 0.9558 (t80) cc_final: 0.8283 (t80)
REVERT: B   99 LYS cc_start: 0.9677 (mmmt) cc_final: 0.8864 (mmmt)
REVERT: B  115 LEU cc_start: 0.8679 (mp) cc_final: 0.8110 (mp)
REVERT: B  184 ARG cc_start: 0.8743 (mmm160) cc_final: 0.8018 (mmm160)
REVERT: B  187 ASP cc_start: 0.8940 (t0) cc_final: 0.8655 (t0)
REVERT: B  193 SER cc_start: 0.8582 (t) cc_final: 0.8313 (p)
REVERT: B  235 ARG cc_start: 0.8403 (mmt90) cc_final: 0.8037 (mmt90)
REVERT: B  288 PHE cc_start: 0.9423 (t80) cc_final: 0.9079 (t80)
REVERT: B  307 TYR cc_start: 0.9336 (t80) cc_final: 0.8875 (t80)
REVERT: B  317 MET cc_start: 0.8474 (mtm) cc_final: 0.8253 (mtm)
REVERT: B  326 PHE cc_start: 0.9252 (m-10) cc_final: 0.8568 (m-80)
REVERT: B  333 LYS cc_start: 0.8352 (ttpt) cc_final: 0.8019 (ttpt)
REVERT: B  446 ARG cc_start: 0.8943 (mpp80) cc_final: 0.8509 (mtm-85)
REVERT: B  459 LYS cc_start: 0.8930 (mttm) cc_final: 0.8290 (mtmm)
REVERT: B  472 LEU cc_start: 0.9250 (mm) cc_final: 0.9038 (mm)
REVERT: B  493 MET cc_start: 0.9221 (tmm) cc_final: 0.8940 (tmm)
REVERT: B  494 MET cc_start: 0.9372 (mtp) cc_final: 0.8770 (mtp)
REVERT: B  522 TYR cc_start: 0.8803 (m-80) cc_final: 0.8564 (m-10)
REVERT: B  615 MET cc_start: 0.8805 (mmp) cc_final: 0.8425 (mmp)
REVERT: B  640 MET cc_start: 0.9143 (mmp) cc_final: 0.8720 (mmm)
REVERT: B  645 GLN cc_start: 0.9039 (tp40) cc_final: 0.8719 (tp-100)
REVERT: B  662 MET cc_start: 0.9147 (ttt) cc_final: 0.8845 (tmm)
REVERT: C   95 MET cc_start: 0.8248 (tmm) cc_final: 0.7656 (tmm)
REVERT: C   96 MET cc_start: 0.8559 (mmm) cc_final: 0.8012 (mmm)
REVERT: C   98 ASN cc_start: 0.7387 (m-40) cc_final: 0.7116 (m110)
REVERT: C  137 MET cc_start: 0.7709 (mpp) cc_final: 0.6781 (tpp)
REVERT: C  151 ILE cc_start: 0.8241 (mm) cc_final: 0.7930 (tp)
REVERT: C  227 PHE cc_start: 0.8599 (t80) cc_final: 0.8367 (t80)
REVERT: C  259 PHE cc_start: 0.6624 (t80) cc_final: 0.5820 (t80)
REVERT: C  276 TYR cc_start: 0.8276 (t80) cc_final: 0.8008 (t80)
REVERT: D   96 MET cc_start: 0.5075 (tpt) cc_final: 0.4373 (tpp)
REVERT: D  157 MET cc_start: 0.6678 (tmm) cc_final: 0.6346 (tmm)
REVERT: D  169 TYR cc_start: 0.8197 (m-80) cc_final: 0.7298 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 495
  average time/residue: 0.1169
  time to fit residues: 87.5686
Evaluate side-chains
  400 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 400
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 133 optimal weight:    8.9990
   chunk 149 optimal weight:   20.0000
   chunk 16 optimal weight:    3.9990
   chunk 114 optimal weight:    0.9990
   chunk 86 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9980
   chunk 88 optimal weight:    6.9990
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 447 ASN
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 516 GLN
** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.126651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.088106 restraints weight = 50252.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.091360 restraints weight = 31072.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.093299 restraints weight = 21510.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.094804 restraints weight = 16585.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.095802 restraints weight = 13446.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3360
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.6983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  16386  Z= 0.130
  Angle     :  0.635   9.584  22134  Z= 0.331
  Chirality :  0.044   0.324   2360
  Planarity :  0.003   0.042   2818
  Dihedral  : 10.315 145.778   2242
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.19), residues: 1932
  helix:  0.99 (0.15), residues: 1117
  sheet: -0.83 (0.39), residues: 160
  loop :  0.13 (0.25), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 161 
 TYR   0.039   0.002   TYR D 174 
 PHE   0.030   0.002   PHE B 100 
 TRP   0.007   0.001   TRP A 623 
 HIS   0.013   0.001   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (16386)
  covalent geometry    : angle       0.63535 (22134)
  hydrogen bonds       : bond        0.03960 (  871)
  hydrogen bonds       : angle       5.06211 ( 2571)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  514 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 514
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 GLU cc_start: 0.8203 (mp0) cc_final: 0.7649 (mp0)
REVERT: A   67 GLU cc_start: 0.9256 (tp30) cc_final: 0.8838 (tp30)
REVERT: A   71 LEU cc_start: 0.9395 (mt) cc_final: 0.9080 (mt)
REVERT: A  117 ARG cc_start: 0.9161 (mmt90) cc_final: 0.8761 (mmt180)
REVERT: A  147 GLN cc_start: 0.8963 (mt0) cc_final: 0.8538 (mt0)
REVERT: A  158 ASN cc_start: 0.8960 (m-40) cc_final: 0.8730 (m110)
REVERT: A  169 SER cc_start: 0.8048 (p) cc_final: 0.7726 (t)
REVERT: A  202 ASN cc_start: 0.8675 (t0) cc_final: 0.8345 (t0)
REVERT: A  236 TYR cc_start: 0.7178 (t80) cc_final: 0.6971 (t80)
REVERT: A  259 ASN cc_start: 0.8046 (p0) cc_final: 0.7806 (p0)
REVERT: A  270 ASP cc_start: 0.8695 (m-30) cc_final: 0.8049 (t0)
REVERT: A  314 MET cc_start: 0.8503 (ppp) cc_final: 0.8177 (ppp)
REVERT: A  344 GLU cc_start: 0.9136 (pt0) cc_final: 0.8630 (pp20)
REVERT: A  345 LYS cc_start: 0.9333 (mtmm) cc_final: 0.9106 (mttt)
REVERT: A  361 GLN cc_start: 0.9098 (tp40) cc_final: 0.8797 (tp-100)
REVERT: A  375 LYS cc_start: 0.9097 (mmtm) cc_final: 0.8617 (mmtm)
REVERT: A  390 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7794 (tm-30)
REVERT: A  400 GLU cc_start: 0.9420 (mm-30) cc_final: 0.9138 (tp30)
REVERT: A  402 GLU cc_start: 0.8847 (mp0) cc_final: 0.8564 (mp0)
REVERT: A  407 ILE cc_start: 0.8851 (mt) cc_final: 0.8502 (mt)
REVERT: A  456 LYS cc_start: 0.8980 (mmtm) cc_final: 0.8457 (mmtm)
REVERT: A  458 MET cc_start: 0.9129 (mmp) cc_final: 0.8779 (mmp)
REVERT: A  498 TYR cc_start: 0.9195 (m-80) cc_final: 0.8910 (m-80)
REVERT: A  501 GLN cc_start: 0.9264 (tp-100) cc_final: 0.8924 (tp-100)
REVERT: A  595 MET cc_start: 0.8789 (tpp) cc_final: 0.8564 (mmm)
REVERT: A  598 MET cc_start: 0.8610 (mtm) cc_final: 0.8336 (ttm)
REVERT: A  599 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7499 (mm-30)
REVERT: A  615 MET cc_start: 0.8281 (mmp) cc_final: 0.7946 (mmm)
REVERT: A  640 MET cc_start: 0.9466 (tpt) cc_final: 0.9216 (tpp)
REVERT: A  650 GLN cc_start: 0.6935 (mm-40) cc_final: 0.6348 (mm-40)
REVERT: A  659 LYS cc_start: 0.8694 (mttt) cc_final: 0.8417 (mmmt)
REVERT: B    8 LYS cc_start: 0.9480 (tttm) cc_final: 0.9164 (tppt)
REVERT: B   12 LEU cc_start: 0.9627 (mt) cc_final: 0.9338 (mt)
REVERT: B   17 MET cc_start: 0.9234 (mtt) cc_final: 0.8957 (mpp)
REVERT: B   24 PHE cc_start: 0.8951 (m-80) cc_final: 0.8516 (m-80)
REVERT: B   95 MET cc_start: 0.9052 (tpp) cc_final: 0.7867 (tpp)
REVERT: B   98 PHE cc_start: 0.9518 (t80) cc_final: 0.9036 (t80)
REVERT: B   99 LYS cc_start: 0.9590 (mmmt) cc_final: 0.8884 (mmmt)
REVERT: B  117 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8318 (mmm160)
REVERT: B  189 SER cc_start: 0.9143 (p) cc_final: 0.8939 (p)
REVERT: B  193 SER cc_start: 0.8614 (t) cc_final: 0.8302 (p)
REVERT: B  235 ARG cc_start: 0.8447 (mmt90) cc_final: 0.8084 (mmt90)
REVERT: B  259 ASN cc_start: 0.8708 (m-40) cc_final: 0.8493 (p0)
REVERT: B  288 PHE cc_start: 0.9388 (t80) cc_final: 0.9060 (t80)
REVERT: B  307 TYR cc_start: 0.9326 (t80) cc_final: 0.8828 (t80)
REVERT: B  317 MET cc_start: 0.8456 (mtm) cc_final: 0.8033 (mpp)
REVERT: B  319 MET cc_start: 0.8581 (tpp) cc_final: 0.8255 (tpp)
REVERT: B  326 PHE cc_start: 0.9219 (m-10) cc_final: 0.8685 (m-80)
REVERT: B  333 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8083 (ttpt)
REVERT: B  359 MET cc_start: 0.7497 (tmm) cc_final: 0.7243 (tmm)
REVERT: B  373 ILE cc_start: 0.9435 (tp) cc_final: 0.8899 (tp)
REVERT: B  375 LYS cc_start: 0.8947 (mmtm) cc_final: 0.8733 (mmtm)
REVERT: B  403 ILE cc_start: 0.8987 (mp) cc_final: 0.8520 (tp)
REVERT: B  436 LEU cc_start: 0.8950 (mp) cc_final: 0.8615 (mp)
REVERT: B  444 ASP cc_start: 0.8819 (t70) cc_final: 0.8562 (t70)
REVERT: B  458 MET cc_start: 0.9326 (mmm) cc_final: 0.8910 (mmm)
REVERT: B  459 LYS cc_start: 0.8806 (mttm) cc_final: 0.8135 (mtmm)
REVERT: B  472 LEU cc_start: 0.9277 (mm) cc_final: 0.9023 (mm)
REVERT: B  492 PHE cc_start: 0.9268 (m-80) cc_final: 0.8917 (m-80)
REVERT: B  493 MET cc_start: 0.9130 (tmm) cc_final: 0.8701 (tmm)
REVERT: B  494 MET cc_start: 0.9346 (mtp) cc_final: 0.8770 (mtp)
REVERT: B  516 GLN cc_start: 0.9254 (tt0) cc_final: 0.9040 (tt0)
REVERT: B  522 TYR cc_start: 0.8739 (m-80) cc_final: 0.8460 (m-10)
REVERT: B  605 THR cc_start: 0.9351 (p) cc_final: 0.9092 (p)
REVERT: B  615 MET cc_start: 0.8722 (mmp) cc_final: 0.8496 (mmm)
REVERT: B  640 MET cc_start: 0.9083 (mmp) cc_final: 0.8777 (mmm)
REVERT: B  645 GLN cc_start: 0.9076 (tp40) cc_final: 0.8869 (tp-100)
REVERT: B  662 MET cc_start: 0.8953 (ttt) cc_final: 0.8716 (tmm)
REVERT: B  684 TYR cc_start: 0.6976 (t80) cc_final: 0.6722 (t80)
REVERT: C   95 MET cc_start: 0.8020 (tmm) cc_final: 0.7184 (tmm)
REVERT: C  137 MET cc_start: 0.7858 (mpp) cc_final: 0.6823 (tpp)
REVERT: C  151 ILE cc_start: 0.8309 (mm) cc_final: 0.7931 (tp)
REVERT: C  227 PHE cc_start: 0.8624 (t80) cc_final: 0.8411 (t80)
REVERT: C  259 PHE cc_start: 0.6522 (t80) cc_final: 0.5737 (t80)
REVERT: C  276 TYR cc_start: 0.8337 (t80) cc_final: 0.8037 (t80)
REVERT: D   96 MET cc_start: 0.4663 (tpt) cc_final: 0.4100 (tpp)
REVERT: D  157 MET cc_start: 0.6661 (tmm) cc_final: 0.6394 (tmm)
REVERT: D  169 TYR cc_start: 0.8519 (m-80) cc_final: 0.7867 (m-80)
REVERT: D  201 HIS cc_start: 0.8368 (m90) cc_final: 0.8158 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 514
  average time/residue: 0.1139
  time to fit residues: 88.3296
Evaluate side-chains
  414 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 414
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 33 optimal weight:    0.3980
   chunk 35 optimal weight:    6.9990
   chunk 189 optimal weight:   20.0000
   chunk 181 optimal weight:   30.0000
   chunk 165 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0570
   chunk 132 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.8902

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 ASN
** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 GLN
** D  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.128819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.089698 restraints weight = 50634.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.093002 restraints weight = 31444.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.095024 restraints weight = 21603.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.096700 restraints weight = 16367.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.097846 restraints weight = 13018.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3438
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3438 r_free = 0.3438    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3438 r_free = 0.3438    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3438
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.7148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073  16386  Z= 0.132
  Angle     :  0.640   8.630  22134  Z= 0.334
  Chirality :  0.043   0.282   2360
  Planarity :  0.004   0.051   2818
  Dihedral  : 10.038 141.262   2242
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.19), residues: 1932
  helix:  0.98 (0.15), residues: 1134
  sheet: -0.96 (0.39), residues: 160
  loop :  0.12 (0.25), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG D 196 
 TYR   0.040   0.002   TYR D 174 
 PHE   0.026   0.001   PHE A  81 
 TRP   0.018   0.001   TRP B 558 
 HIS   0.011   0.001   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (16386)
  covalent geometry    : angle       0.63972 (22134)
  hydrogen bonds       : bond        0.03918 (  871)
  hydrogen bonds       : angle       5.04144 ( 2571)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  493 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 493
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 GLU cc_start: 0.8166 (mp0) cc_final: 0.7614 (mp0)
REVERT: A   67 GLU cc_start: 0.9223 (tp30) cc_final: 0.8840 (tp30)
REVERT: A   71 LEU cc_start: 0.9424 (mt) cc_final: 0.9123 (mt)
REVERT: A  117 ARG cc_start: 0.9170 (mmt90) cc_final: 0.8844 (mtp85)
REVERT: A  139 GLU cc_start: 0.9004 (mp0) cc_final: 0.8803 (mp0)
REVERT: A  147 GLN cc_start: 0.8891 (mt0) cc_final: 0.8449 (mt0)
REVERT: A  169 SER cc_start: 0.8213 (p) cc_final: 0.7932 (t)
REVERT: A  202 ASN cc_start: 0.8678 (t0) cc_final: 0.8281 (t0)
REVERT: A  270 ASP cc_start: 0.8744 (m-30) cc_final: 0.8085 (t0)
REVERT: A  314 MET cc_start: 0.8496 (ppp) cc_final: 0.8161 (ppp)
REVERT: A  359 MET cc_start: 0.8328 (ttp) cc_final: 0.7684 (ttp)
REVERT: A  361 GLN cc_start: 0.9066 (tp40) cc_final: 0.8785 (tp-100)
REVERT: A  375 LYS cc_start: 0.9083 (mmtm) cc_final: 0.8700 (mmtm)
REVERT: A  402 GLU cc_start: 0.8827 (mp0) cc_final: 0.8561 (mp0)
REVERT: A  444 ASP cc_start: 0.8024 (t0) cc_final: 0.7538 (t0)
REVERT: A  455 ASN cc_start: 0.9101 (t0) cc_final: 0.8886 (t0)
REVERT: A  456 LYS cc_start: 0.9081 (mmtm) cc_final: 0.8436 (mmtm)
REVERT: A  498 TYR cc_start: 0.9184 (m-80) cc_final: 0.8873 (m-80)
REVERT: A  501 GLN cc_start: 0.9277 (tp-100) cc_final: 0.8942 (tp-100)
REVERT: A  595 MET cc_start: 0.8735 (tpp) cc_final: 0.8520 (mmm)
REVERT: A  615 MET cc_start: 0.8300 (mmp) cc_final: 0.7994 (mmm)
REVERT: A  640 MET cc_start: 0.9433 (tpt) cc_final: 0.9142 (tpp)
REVERT: A  650 GLN cc_start: 0.6939 (mm-40) cc_final: 0.6328 (mm-40)
REVERT: B    8 LYS cc_start: 0.9481 (tttm) cc_final: 0.9175 (tppt)
REVERT: B   12 LEU cc_start: 0.9654 (mt) cc_final: 0.9344 (mt)
REVERT: B   17 MET cc_start: 0.9232 (mtt) cc_final: 0.8993 (mpp)
REVERT: B   24 PHE cc_start: 0.8878 (m-80) cc_final: 0.8528 (m-80)
REVERT: B   41 ILE cc_start: 0.9463 (mm) cc_final: 0.9253 (mm)
REVERT: B   95 MET cc_start: 0.9030 (tpp) cc_final: 0.7829 (tpp)
REVERT: B   98 PHE cc_start: 0.9494 (t80) cc_final: 0.9045 (t80)
REVERT: B   99 LYS cc_start: 0.9600 (mmmt) cc_final: 0.8899 (mmmt)
REVERT: B  117 ARG cc_start: 0.8456 (mmm160) cc_final: 0.8192 (mmm160)
REVERT: B  193 SER cc_start: 0.8619 (t) cc_final: 0.8291 (p)
REVERT: B  259 ASN cc_start: 0.8695 (m-40) cc_final: 0.8398 (p0)
REVERT: B  288 PHE cc_start: 0.9374 (t80) cc_final: 0.9123 (t80)
REVERT: B  307 TYR cc_start: 0.9315 (t80) cc_final: 0.8781 (t80)
REVERT: B  326 PHE cc_start: 0.9157 (m-10) cc_final: 0.8581 (m-80)
REVERT: B  333 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8182 (ttpt)
REVERT: B  359 MET cc_start: 0.7652 (tmm) cc_final: 0.7347 (tmm)
REVERT: B  373 ILE cc_start: 0.9427 (tp) cc_final: 0.8885 (tp)
REVERT: B  375 LYS cc_start: 0.8977 (mmtm) cc_final: 0.8718 (mmtm)
REVERT: B  403 ILE cc_start: 0.9006 (mp) cc_final: 0.8555 (tp)
REVERT: B  444 ASP cc_start: 0.8749 (t70) cc_final: 0.8537 (t70)
REVERT: B  458 MET cc_start: 0.9303 (mmm) cc_final: 0.8909 (mmm)
REVERT: B  459 LYS cc_start: 0.8770 (mttm) cc_final: 0.8094 (mtmm)
REVERT: B  466 MET cc_start: 0.8785 (ptp) cc_final: 0.8493 (ptp)
REVERT: B  492 PHE cc_start: 0.9258 (m-80) cc_final: 0.8671 (m-80)
REVERT: B  493 MET cc_start: 0.9172 (tmm) cc_final: 0.8855 (tmm)
REVERT: B  494 MET cc_start: 0.9403 (mtp) cc_final: 0.8930 (mtp)
REVERT: B  516 GLN cc_start: 0.9259 (tt0) cc_final: 0.9026 (tt0)
REVERT: B  522 TYR cc_start: 0.8722 (m-80) cc_final: 0.8453 (m-10)
REVERT: B  584 ILE cc_start: 0.9128 (tp) cc_final: 0.8769 (tp)
REVERT: B  615 MET cc_start: 0.8727 (mmp) cc_final: 0.8510 (mmm)
REVERT: B  640 MET cc_start: 0.9126 (mmp) cc_final: 0.8835 (mmm)
REVERT: B  645 GLN cc_start: 0.9091 (tp40) cc_final: 0.8752 (tp-100)
REVERT: B  686 ARG cc_start: 0.8685 (mmm160) cc_final: 0.8474 (mmm-85)
REVERT: C   95 MET cc_start: 0.7894 (tmm) cc_final: 0.7082 (tmm)
REVERT: C   96 MET cc_start: 0.8313 (mmm) cc_final: 0.7773 (mmm)
REVERT: C  137 MET cc_start: 0.7868 (mpp) cc_final: 0.6782 (tpp)
REVERT: C  138 ILE cc_start: 0.9046 (mm) cc_final: 0.8828 (pt)
REVERT: C  151 ILE cc_start: 0.8255 (mm) cc_final: 0.7956 (tp)
REVERT: C  227 PHE cc_start: 0.8655 (t80) cc_final: 0.8453 (t80)
REVERT: C  259 PHE cc_start: 0.6515 (t80) cc_final: 0.5738 (t80)
REVERT: C  276 TYR cc_start: 0.8391 (t80) cc_final: 0.8096 (t80)
REVERT: D   96 MET cc_start: 0.4559 (tpt) cc_final: 0.3900 (tpp)
REVERT: D  157 MET cc_start: 0.6369 (tmm) cc_final: 0.6115 (tmm)
REVERT: D  169 TYR cc_start: 0.8586 (m-80) cc_final: 0.7935 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 493
  average time/residue: 0.1267
  time to fit residues: 94.0806
Evaluate side-chains
  407 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 407
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 93 optimal weight:    9.9990
   chunk 1 optimal weight:    0.1980
   chunk 48 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 148 optimal weight:    3.9990
   chunk 125 optimal weight:    7.9990
   chunk 28 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  69 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.128016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.088752 restraints weight = 49839.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.091985 restraints weight = 31521.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.094094 restraints weight = 22141.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.095586 restraints weight = 16912.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.096510 restraints weight = 13767.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3389
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3390
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.7311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  16386  Z= 0.130
  Angle     :  0.643   8.605  22134  Z= 0.335
  Chirality :  0.044   0.272   2360
  Planarity :  0.004   0.052   2818
  Dihedral  :  9.746 135.110   2242
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.23 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.19), residues: 1932
  helix:  0.95 (0.15), residues: 1135
  sheet: -0.91 (0.39), residues: 160
  loop :  0.05 (0.24), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 161 
 TYR   0.038   0.001   TYR D 174 
 PHE   0.023   0.001   PHE B 254 
 TRP   0.014   0.001   TRP B 558 
 HIS   0.010   0.001   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (16386)
  covalent geometry    : angle       0.64276 (22134)
  hydrogen bonds       : bond        0.03952 (  871)
  hydrogen bonds       : angle       5.01424 ( 2571)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3079.11 seconds
wall clock time: 54 minutes 11.90 seconds (3251.90 seconds total)