Starting phenix.real_space_refine
on Sat May 17 16:51:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bz3_45052/05_2025/9bz3_45052_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bz3_45052/05_2025/9bz3_45052.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bz3_45052/05_2025/9bz3_45052.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bz3_45052/05_2025/9bz3_45052.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bz3_45052/05_2025/9bz3_45052_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bz3_45052/05_2025/9bz3_45052_neut.cif"
  }
  resolution = 4.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.52, per 1000 atoms: 0.59
  Number of scatterers: 16038
  At special positions: 0
  Unit cell: (96.615, 129.159, 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: 3.78
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  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: 1.65
  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: 4.094A  pdb=" N   LYS A  30 " --> pdb=" O   PHE A  26 " (cutoff:3.500A)
      removed outlier: 3.515A  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: 3.986A  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: 4.118A  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: 3.579A  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: 3.729A  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: 5.117A  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: 4.068A  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: 3.881A  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: 4.936A  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: 4.876A  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: 6.359A  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: 6.199A  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: 6.479A  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: 8.393A  pdb=" N   ASN A 252 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
      removed outlier: 6.453A  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: 6.192A  pdb=" N   ALA A 249 " --> pdb=" O   GLY A 281 " (cutoff:3.500A)
      removed outlier: 7.500A  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: 6.063A  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: 6.564A  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: 6.549A  pdb=" N   LEU B 201 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
      removed outlier: 8.345A  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: 7.806A  pdb=" N   GLY B 281 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   ALA B 249 " --> pdb=" O   GLY B 281 " (cutoff:3.500A)
      removed outlier: 7.592A  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: 5.29

  Time building geometry restraints manager: 4.44 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: 4851
        1.34 -     1.46: 3061
        1.46 -     1.58: 8293
        1.58 -     1.70: 25
        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  1.601 -0.061 1.25e-02 6.40e+03 2.39e+01
  bond pdb=" CA  ILE D 138 "
       pdb=" CB  ILE D 138 "
    ideal  model  delta    sigma   weight residual
    1.539  1.578 -0.039 1.20e-02 6.94e+03 1.04e+01
  bond pdb=" CA  VAL C 250 "
       pdb=" CB  VAL C 250 "
    ideal  model  delta    sigma   weight residual
    1.542  1.575 -0.032 1.08e-02 8.57e+03 8.87e+00
  bond pdb=" CA  ILE D  35 "
       pdb=" CB  ILE D  35 "
    ideal  model  delta    sigma   weight residual
    1.537  1.569 -0.032 1.17e-02 7.31e+03 7.33e+00
  bond pdb=" CA  VAL D 203 "
       pdb=" CB  VAL D 203 "
    ideal  model  delta    sigma   weight residual
    1.540  1.573 -0.033 1.25e-02 6.40e+03 6.81e+00
  ... (remaining 16381 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 21581
        2.09 -     4.18: 511
        4.18 -     6.27: 36
        6.27 -     8.36: 2
        8.36 -    10.45: 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  116.63   -6.09 1.36e+00 5.41e-01 2.00e+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  116.17   -4.46 1.15e+00 7.56e-01 1.50e+01
  angle pdb=" N   SER D 253 "
        pdb=" CA  SER D 253 "
        pdb=" C   SER D 253 "
      ideal   model   delta    sigma   weight residual
     111.28  115.25   -3.97 1.09e+00 8.42e-01 1.33e+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  117.85   -4.35 1.23e+00 6.61e-01 1.25e+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  115.71   -4.00 1.15e+00 7.56e-01 1.21e+01
  ... (remaining 22129 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.80: 9468
       35.80 -    71.59: 339
       71.59 -   107.39: 37
      107.39 -   143.19: 3
      143.19 -   178.99: 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  120.67 -178.99     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  151.15  150.53     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   31.87  148.10     1      2.00e+01 2.50e-03 4.44e+01
  ... (remaining 9847 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 2149
       0.094 -    0.187: 178
       0.187 -    0.281: 29
       0.281 -    0.375: 2
       0.375 -    0.469: 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    2.04    0.47 2.00e-01 2.50e+01 5.49e+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 4.56e+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    0.35 2.00e-01 2.50e+01 2.98e+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   4.13e-02 2.73e+00
        pdb=" N   PRO D  75 "    0.071 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 2.18e+00
        pdb=" CG  PHE D  92 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  92 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  92 "   -0.007 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 D 179 "   -0.017 2.00e-02 2.50e+03   9.83e-03 1.93e+00
        pdb=" CG  TYR D 179 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 179 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 179 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 179 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 179 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 179 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR D 179 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 2815 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 129
        2.51 -     3.11: 11559
        3.11 -     3.70: 27043
        3.70 -     4.30: 41517
        4.30 -     4.90: 65377
  Nonbonded interactions: 145625
  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
     1.960 2.320
  nonbonded pdb=" OE2 GLU C 164 "
            pdb="MN    MN C 401 "
     model   vdw
     1.966 2.320
  nonbonded pdb=" OE1 GLU D  97 "
            pdb="MN    MN D 402 "
     model   vdw
     1.990 2.320
  nonbonded pdb=" OG1 THR A 108 "
            pdb=" OD1 ASP A 110 "
     model   vdw
     2.012 3.040
  ... (remaining 145620 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: 0.02
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:             0.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     36.150
  Find NCS groups from input model:        0.960
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6486
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   0.061  16386  Z= 0.315
  Angle     :  0.740  10.455  22134  Z= 0.463
  Chirality :  0.058   0.469   2360
  Planarity :  0.003   0.041   2818
  Dihedral  : 17.952 178.987   6154
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 15.27 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (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
 TRP   0.008   0.002   TRP D  44 
 HIS   0.006   0.001   HIS C 254 
 PHE   0.021   0.002   PHE C 227 
 TYR   0.020   0.002   TYR D 179 
 ARG   0.004   0.000   ARG D 196 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15421 (  871)
  hydrogen bonds       : angle       6.51731 ( 2571)
  covalent geometry    : bond        0.00554 (16386)
  covalent geometry    : angle       0.74040 (22134)

*********************** 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
  822 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 799
  time to evaluate  : 1.919 
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   29 ASP cc_start: 0.8448 (t0) cc_final: 0.8233 (t70)
REVERT: A   68 PHE cc_start: 0.8635 (p90) cc_final: 0.8321 (p90)
REVERT: A  106 LEU cc_start: 0.9003 (tp) cc_final: 0.8678 (tp)
REVERT: A  120 ASP cc_start: 0.7014 (m-30) cc_final: 0.6695 (m-30)
REVERT: A  122 ILE cc_start: 0.9216 (mt) cc_final: 0.8938 (mt)
REVERT: A  134 THR cc_start: 0.7929 (t) cc_final: 0.7572 (t)
REVERT: A  186 ILE cc_start: 0.9310 (mt) cc_final: 0.9058 (mt)
REVERT: A  200 SER cc_start: 0.9120 (t) cc_final: 0.8885 (p)
REVERT: A  202 ASN cc_start: 0.9124 (t0) cc_final: 0.8608 (t0)
REVERT: A  204 SER cc_start: 0.8970 (m) cc_final: 0.8633 (p)
REVERT: A  227 MET cc_start: 0.8293 (mtp) cc_final: 0.7907 (mtp)
REVERT: A  322 MET cc_start: 0.8217 (mmp) cc_final: 0.7943 (mmp)
REVERT: A  362 ASP cc_start: 0.6331 (m-30) cc_final: 0.6082 (m-30)
REVERT: A  367 VAL cc_start: 0.9095 (m) cc_final: 0.8753 (p)
REVERT: A  417 LEU cc_start: 0.8510 (tt) cc_final: 0.7869 (tt)
REVERT: A  425 ILE cc_start: 0.8978 (mt) cc_final: 0.8496 (mt)
REVERT: A  436 LEU cc_start: 0.9194 (mt) cc_final: 0.8982 (mm)
REVERT: A  447 ASN cc_start: 0.7972 (m-40) cc_final: 0.7770 (m-40)
REVERT: A  458 MET cc_start: 0.8831 (mmm) cc_final: 0.8314 (mtm)
REVERT: A  576 LEU cc_start: 0.8899 (mt) cc_final: 0.8676 (mt)
REVERT: A  606 TYR cc_start: 0.6769 (m-80) cc_final: 0.6553 (m-80)
REVERT: A  618 LEU cc_start: 0.9218 (tp) cc_final: 0.8982 (tp)
REVERT: A  630 TYR cc_start: 0.7539 (m-80) cc_final: 0.6529 (m-80)
REVERT: A  634 MET cc_start: 0.8587 (mmp) cc_final: 0.8324 (mmm)
REVERT: A  640 MET cc_start: 0.7738 (tpp) cc_final: 0.7280 (tpp)
REVERT: A  670 ILE cc_start: 0.9244 (mt) cc_final: 0.9021 (mt)
REVERT: B   51 LEU cc_start: 0.8434 (tp) cc_final: 0.8203 (tp)
REVERT: B  116 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7299 (mt-10)
REVERT: B  156 PHE cc_start: 0.8455 (t80) cc_final: 0.8206 (t80)
REVERT: B  167 LEU cc_start: 0.8207 (mt) cc_final: 0.7977 (mt)
REVERT: B  190 MET cc_start: 0.8381 (mtm) cc_final: 0.8117 (mtm)
REVERT: B  322 MET cc_start: 0.8152 (mmm) cc_final: 0.7775 (tpp)
REVERT: B  362 ASP cc_start: 0.6823 (m-30) cc_final: 0.6128 (m-30)
REVERT: B  373 ILE cc_start: 0.8899 (mt) cc_final: 0.8608 (mt)
REVERT: B  466 MET cc_start: 0.8431 (ptp) cc_final: 0.8108 (ptm)
REVERT: B  467 ASN cc_start: 0.8888 (t0) cc_final: 0.8472 (t0)
REVERT: B  471 TYR cc_start: 0.8362 (t80) cc_final: 0.8154 (t80)
REVERT: B  500 ILE cc_start: 0.9270 (mt) cc_final: 0.9049 (mt)
REVERT: B  522 TYR cc_start: 0.8492 (m-80) cc_final: 0.8089 (m-10)
REVERT: B  550 MET cc_start: 0.8179 (mtm) cc_final: 0.7351 (mtp)
REVERT: B  570 MET cc_start: 0.7240 (mtm) cc_final: 0.6749 (mtm)
REVERT: B  576 LEU cc_start: 0.9116 (mt) cc_final: 0.8821 (mt)
REVERT: B  590 SER cc_start: 0.8860 (p) cc_final: 0.8200 (t)
REVERT: B  591 THR cc_start: 0.9291 (p) cc_final: 0.8607 (m)
REVERT: B  597 ILE cc_start: 0.9135 (pt) cc_final: 0.8771 (pt)
REVERT: C   31 LEU cc_start: 0.5709 (mt) cc_final: 0.5448 (mt)
REVERT: C  155 LYS cc_start: 0.7170 (mttt) cc_final: 0.6918 (mttm)
REVERT: D  136 GLN cc_start: 0.1070 (mm-40) cc_final: 0.0606 (tm-30)
REVERT: D  137 MET cc_start: -0.0170 (mtp) cc_final: -0.0738 (mtp)
REVERT: D  256 VAL cc_start: 0.5301 (t) cc_final: 0.4495 (t)
  outliers start: 23
  outliers final: 7
  residues processed: 810
  average time/residue: 0.2928
  time to fit residues: 340.7483
Evaluate side-chains
  554 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 547
  time to evaluate  : 1.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 162 optimal weight:    3.9990
   chunk 145 optimal weight:    7.9990
   chunk 80 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 77 optimal weight:    0.6980
   chunk 150 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 112 optimal weight:    2.9990
   chunk 174 optimal weight:    5.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
A 242 GLN
A 320 ASN
A 370 ASN
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 GLN
B 410 ASN
** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 645 GLN
B 668 ASN
** D  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  71 ASN
D  80 HIS
** D  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.163350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.110901 restraints weight = 33115.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.114550 restraints weight = 15948.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.116894 restraints weight = 9571.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3308
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3308 r_free = 0.3308    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3308 r_free = 0.3308    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3308
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.3785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  16386  Z= 0.217
  Angle     :  0.611   7.212  22134  Z= 0.329
  Chirality :  0.043   0.281   2360
  Planarity :  0.004   0.036   2818
  Dihedral  : 11.377 178.464   2242
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.21 %
    Favored  : 96.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.19), residues: 1932
  helix:  1.45 (0.15), residues: 1128
  sheet: -0.05 (0.41), residues: 146
  loop :  0.53 (0.24), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 623 
 HIS   0.009   0.001   HIS A 438 
 PHE   0.030   0.002   PHE C 227 
 TYR   0.026   0.002   TYR D 130 
 ARG   0.006   0.001   ARG B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04648 (  871)
  hydrogen bonds       : angle       5.01974 ( 2571)
  covalent geometry    : bond        0.00455 (16386)
  covalent geometry    : angle       0.61077 (22134)

*********************** 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
  622 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 620
  time to evaluate  : 1.942 
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  122 ILE cc_start: 0.9340 (mt) cc_final: 0.9069 (mt)
REVERT: A  150 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8795 (tm-30)
REVERT: A  188 ILE cc_start: 0.9606 (mt) cc_final: 0.9361 (mm)
REVERT: A  202 ASN cc_start: 0.9293 (t0) cc_final: 0.9029 (t0)
REVERT: A  204 SER cc_start: 0.9190 (m) cc_final: 0.8605 (t)
REVERT: A  232 ASN cc_start: 0.8454 (m-40) cc_final: 0.8232 (m110)
REVERT: A  286 ASP cc_start: 0.8094 (m-30) cc_final: 0.7744 (m-30)
REVERT: A  308 LYS cc_start: 0.9580 (mtmt) cc_final: 0.9359 (mtmm)
REVERT: A  362 ASP cc_start: 0.7271 (m-30) cc_final: 0.7067 (m-30)
REVERT: A  367 VAL cc_start: 0.9705 (m) cc_final: 0.9477 (p)
REVERT: A  447 ASN cc_start: 0.8408 (m-40) cc_final: 0.7312 (m-40)
REVERT: A  458 MET cc_start: 0.9332 (mmm) cc_final: 0.8471 (mmm)
REVERT: A  485 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.7442 (mtm-85)
REVERT: A  494 MET cc_start: 0.8718 (mtp) cc_final: 0.8371 (mtp)
REVERT: A  576 LEU cc_start: 0.9036 (mt) cc_final: 0.8789 (mt)
REVERT: A  583 SER cc_start: 0.9141 (m) cc_final: 0.8739 (t)
REVERT: A  586 TYR cc_start: 0.8470 (m-80) cc_final: 0.8199 (m-10)
REVERT: A  590 SER cc_start: 0.9258 (t) cc_final: 0.9004 (t)
REVERT: A  602 GLU cc_start: 0.7273 (pt0) cc_final: 0.6585 (pt0)
REVERT: A  606 TYR cc_start: 0.8030 (m-80) cc_final: 0.7739 (m-10)
REVERT: A  630 TYR cc_start: 0.8575 (m-80) cc_final: 0.8367 (m-80)
REVERT: A  640 MET cc_start: 0.9051 (tpp) cc_final: 0.8653 (tpp)
REVERT: A  662 MET cc_start: 0.8432 (pmm) cc_final: 0.8182 (pmm)
REVERT: A  667 LEU cc_start: 0.9031 (tt) cc_final: 0.8324 (tt)
REVERT: A  668 ASN cc_start: 0.8902 (m110) cc_final: 0.8491 (m110)
REVERT: B   51 LEU cc_start: 0.9103 (tp) cc_final: 0.8871 (tp)
REVERT: B  108 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8496 (p)
REVERT: B  147 GLN cc_start: 0.8765 (mt0) cc_final: 0.8485 (mt0)
REVERT: B  156 PHE cc_start: 0.9206 (t80) cc_final: 0.8931 (t80)
REVERT: B  190 MET cc_start: 0.9268 (mtm) cc_final: 0.9001 (mtm)
REVERT: B  253 ILE cc_start: 0.9461 (tt) cc_final: 0.9232 (tt)
REVERT: B  257 ASP cc_start: 0.8908 (m-30) cc_final: 0.8674 (m-30)
REVERT: B  288 PHE cc_start: 0.9429 (t80) cc_final: 0.9182 (t80)
REVERT: B  291 LEU cc_start: 0.9556 (mt) cc_final: 0.9354 (mt)
REVERT: B  318 ASP cc_start: 0.8825 (t0) cc_final: 0.8547 (p0)
REVERT: B  333 LYS cc_start: 0.8827 (tptp) cc_final: 0.7833 (tttp)
REVERT: B  358 ILE cc_start: 0.9468 (mm) cc_final: 0.9182 (mm)
REVERT: B  362 ASP cc_start: 0.8134 (m-30) cc_final: 0.7410 (m-30)
REVERT: B  393 SER cc_start: 0.9543 (m) cc_final: 0.9259 (p)
REVERT: B  396 ASP cc_start: 0.8084 (m-30) cc_final: 0.7854 (m-30)
REVERT: B  471 TYR cc_start: 0.9003 (t80) cc_final: 0.8592 (t80)
REVERT: B  493 MET cc_start: 0.9320 (tmm) cc_final: 0.9004 (tmm)
REVERT: B  512 GLU cc_start: 0.8698 (pt0) cc_final: 0.8414 (pt0)
REVERT: B  550 MET cc_start: 0.8410 (mtm) cc_final: 0.8152 (mtp)
REVERT: B  561 LEU cc_start: 0.9393 (tp) cc_final: 0.9122 (tp)
REVERT: B  597 ILE cc_start: 0.9345 (pt) cc_final: 0.9142 (pt)
REVERT: B  610 LYS cc_start: 0.8810 (ptmt) cc_final: 0.8605 (ptpt)
REVERT: B  615 MET cc_start: 0.9098 (mmp) cc_final: 0.8858 (mmm)
REVERT: B  627 LYS cc_start: 0.9149 (tttt) cc_final: 0.8787 (tttp)
REVERT: B  662 MET cc_start: 0.8293 (ptp) cc_final: 0.7965 (ptp)
REVERT: C   74 MET cc_start: 0.7248 (mtt) cc_final: 0.6459 (mtt)
REVERT: C  154 PHE cc_start: 0.8616 (t80) cc_final: 0.8278 (t80)
REVERT: C  239 GLU cc_start: 0.9029 (tp30) cc_final: 0.8569 (tp30)
REVERT: D   95 MET cc_start: 0.7159 (ttp) cc_final: 0.6831 (ttp)
REVERT: D  208 LEU cc_start: 0.9290 (mm) cc_final: 0.9056 (mm)
REVERT: D  242 TYR cc_start: 0.7843 (t80) cc_final: 0.7120 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 621
  average time/residue: 0.2737
  time to fit residues: 251.4212
Evaluate side-chains
  479 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 478
  time to evaluate  : 1.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 168 optimal weight:    3.9990
   chunk 175 optimal weight:    7.9990
   chunk 34 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 191 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 171 optimal weight:    1.9990
   chunk 189 optimal weight:    9.9990
   chunk 141 optimal weight:    9.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 676 HIS
D  24 GLN
** D  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.164666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.114113 restraints weight = 33498.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.117780 restraints weight = 16222.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.120043 restraints weight = 9660.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3280
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3281 r_free = 0.3281    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3281
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.4439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  16386  Z= 0.185
  Angle     :  0.580   9.071  22134  Z= 0.306
  Chirality :  0.042   0.198   2360
  Planarity :  0.003   0.041   2818
  Dihedral  : 11.140 178.135   2242
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.68 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.19), residues: 1932
  helix:  1.60 (0.15), residues: 1128
  sheet: -0.20 (0.39), residues: 146
  loop :  0.53 (0.24), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 623 
 HIS   0.005   0.001   HIS A 438 
 PHE   0.037   0.002   PHE C 109 
 TYR   0.021   0.002   TYR D  22 
 ARG   0.006   0.001   ARG A 669 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04124 (  871)
  hydrogen bonds       : angle       4.79182 ( 2571)
  covalent geometry    : bond        0.00407 (16386)
  covalent geometry    : angle       0.57973 (22134)

*********************** 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
  593 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 591
  time to evaluate  : 1.702 
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: A   55 LEU cc_start: 0.9650 (mt) cc_final: 0.9258 (pp)
REVERT: A  158 ASN cc_start: 0.9065 (m110) cc_final: 0.8850 (m110)
REVERT: A  204 SER cc_start: 0.9246 (m) cc_final: 0.8654 (t)
REVERT: A  205 LYS cc_start: 0.8098 (mttm) cc_final: 0.7495 (mtpp)
REVERT: A  232 ASN cc_start: 0.8423 (m-40) cc_final: 0.8132 (m110)
REVERT: A  286 ASP cc_start: 0.8248 (m-30) cc_final: 0.7651 (m-30)
REVERT: A  308 LYS cc_start: 0.9577 (mtmt) cc_final: 0.9325 (mtmm)
REVERT: A  362 ASP cc_start: 0.7314 (m-30) cc_final: 0.7072 (m-30)
REVERT: A  406 ASP cc_start: 0.8462 (m-30) cc_final: 0.8163 (m-30)
REVERT: A  417 LEU cc_start: 0.9382 (tt) cc_final: 0.8468 (tt)
REVERT: A  425 ILE cc_start: 0.9461 (mt) cc_final: 0.9256 (mt)
REVERT: A  443 THR cc_start: 0.9124 (m) cc_final: 0.8912 (t)
REVERT: A  447 ASN cc_start: 0.8145 (m-40) cc_final: 0.7687 (m-40)
REVERT: A  458 MET cc_start: 0.9291 (mmm) cc_final: 0.8519 (mmm)
REVERT: A  494 MET cc_start: 0.8766 (mtp) cc_final: 0.8544 (mtp)
REVERT: A  557 ASP cc_start: 0.8858 (m-30) cc_final: 0.8658 (m-30)
REVERT: A  576 LEU cc_start: 0.9108 (mt) cc_final: 0.8869 (mt)
REVERT: A  583 SER cc_start: 0.9121 (m) cc_final: 0.8831 (t)
REVERT: A  586 TYR cc_start: 0.8492 (m-80) cc_final: 0.8161 (m-10)
REVERT: A  602 GLU cc_start: 0.7046 (pt0) cc_final: 0.6128 (pt0)
REVERT: A  604 ARG cc_start: 0.8527 (tpp-160) cc_final: 0.8293 (tpp-160)
REVERT: A  645 GLN cc_start: 0.8900 (tp40) cc_final: 0.8648 (tp-100)
REVERT: A  667 LEU cc_start: 0.9191 (tt) cc_final: 0.8606 (tt)
REVERT: B   51 LEU cc_start: 0.9112 (tp) cc_final: 0.8864 (tp)
REVERT: B  120 ASP cc_start: 0.8649 (m-30) cc_final: 0.8429 (m-30)
REVERT: B  235 ARG cc_start: 0.8634 (ttm-80) cc_final: 0.8329 (ttm110)
REVERT: B  276 LYS cc_start: 0.8818 (ptmt) cc_final: 0.8432 (ptpp)
REVERT: B  288 PHE cc_start: 0.9495 (t80) cc_final: 0.9226 (t80)
REVERT: B  291 LEU cc_start: 0.9531 (mt) cc_final: 0.9318 (mt)
REVERT: B  333 LYS cc_start: 0.8879 (tptp) cc_final: 0.7833 (tptp)
REVERT: B  348 MET cc_start: 0.8007 (tpp) cc_final: 0.7771 (tpp)
REVERT: B  362 ASP cc_start: 0.8152 (m-30) cc_final: 0.7321 (m-30)
REVERT: B  393 SER cc_start: 0.9486 (m) cc_final: 0.9212 (p)
REVERT: B  471 TYR cc_start: 0.9092 (t80) cc_final: 0.8818 (t80)
REVERT: B  493 MET cc_start: 0.9340 (tmm) cc_final: 0.9034 (tmm)
REVERT: B  550 MET cc_start: 0.8427 (mtm) cc_final: 0.8150 (mtp)
REVERT: B  561 LEU cc_start: 0.9484 (tp) cc_final: 0.9229 (tp)
REVERT: B  615 MET cc_start: 0.9161 (mmp) cc_final: 0.8941 (mmm)
REVERT: B  627 LYS cc_start: 0.9331 (tttt) cc_final: 0.8823 (tttp)
REVERT: B  628 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8069 (mm-30)
REVERT: B  640 MET cc_start: 0.8954 (tpp) cc_final: 0.8277 (tpp)
REVERT: B  662 MET cc_start: 0.8609 (ptp) cc_final: 0.8265 (ptp)
REVERT: C   74 MET cc_start: 0.7009 (mtt) cc_final: 0.6404 (mtt)
REVERT: C  154 PHE cc_start: 0.8590 (t80) cc_final: 0.8209 (t80)
REVERT: C  239 GLU cc_start: 0.8978 (tp30) cc_final: 0.8549 (tp30)
REVERT: D  117 THR cc_start: 0.8498 (p) cc_final: 0.8198 (p)
REVERT: D  173 TYR cc_start: 0.7271 (t80) cc_final: 0.6759 (t80)
REVERT: D  242 TYR cc_start: 0.7715 (t80) cc_final: 0.7464 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 591
  average time/residue: 0.2703
  time to fit residues: 235.8512
Evaluate side-chains
  475 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 475
  time to evaluate  : 1.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 180 optimal weight:   10.0000
   chunk 99 optimal weight:    6.9990
   chunk 1 optimal weight:    0.4980
   chunk 39 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   chunk 69 optimal weight:    7.9990
   chunk 71 optimal weight:    6.9990
   chunk 74 optimal weight:    5.9990
   chunk 148 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 94 optimal weight:    8.9990
   overall best weight:    4.8988

-------------------------------------------------------------------------------
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 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  11 GLN
B  25 GLN
B 370 ASN
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 210 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.153448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.104213 restraints weight = 34353.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.107533 restraints weight = 16958.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.109599 restraints weight = 10092.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.5245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.095  16386  Z= 0.377
  Angle     :  0.735   7.019  22134  Z= 0.388
  Chirality :  0.046   0.175   2360
  Planarity :  0.004   0.041   2818
  Dihedral  : 11.396 174.597   2242
  Min Nonbonded Distance : 1.753

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.32 %
    Favored  : 96.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.19), residues: 1932
  helix:  1.12 (0.15), residues: 1132
  sheet: -0.60 (0.40), residues: 140
  loop :  0.42 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A 623 
 HIS   0.006   0.001   HIS A 438 
 PHE   0.030   0.003   PHE C 109 
 TYR   0.025   0.002   TYR B 118 
 ARG   0.007   0.001   ARG B 453 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04490 (  871)
  hydrogen bonds       : angle       5.05780 ( 2571)
  covalent geometry    : bond        0.00820 (16386)
  covalent geometry    : angle       0.73494 (22134)

*********************** 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: 4
    poor density    : 530
  time to evaluate  : 1.846 
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: 0.8533 (mm-30) cc_final: 0.8089 (mp0)
REVERT: A  139 GLU cc_start: 0.8204 (mp0) cc_final: 0.7979 (mp0)
REVERT: A  144 MET cc_start: 0.8964 (mtm) cc_final: 0.8713 (mtm)
REVERT: A  172 LEU cc_start: 0.9164 (mp) cc_final: 0.8824 (mp)
REVERT: A  174 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7677 (mt-10)
REVERT: A  204 SER cc_start: 0.9227 (m) cc_final: 0.8814 (t)
REVERT: A  286 ASP cc_start: 0.8055 (m-30) cc_final: 0.7754 (m-30)
REVERT: A  308 LYS cc_start: 0.9596 (mtmt) cc_final: 0.9389 (mtmm)
REVERT: A  319 MET cc_start: 0.9272 (tpp) cc_final: 0.8944 (tpp)
REVERT: A  362 ASP cc_start: 0.7434 (m-30) cc_final: 0.7138 (m-30)
REVERT: A  383 SER cc_start: 0.8859 (p) cc_final: 0.8422 (t)
REVERT: A  406 ASP cc_start: 0.8633 (m-30) cc_final: 0.8292 (m-30)
REVERT: A  447 ASN cc_start: 0.8107 (m-40) cc_final: 0.7620 (m-40)
REVERT: A  456 LYS cc_start: 0.8930 (ptpp) cc_final: 0.8486 (ptpp)
REVERT: A  458 MET cc_start: 0.9306 (mmm) cc_final: 0.8467 (mtm)
REVERT: A  479 TYR cc_start: 0.9141 (t80) cc_final: 0.8912 (t80)
REVERT: A  494 MET cc_start: 0.8806 (mtp) cc_final: 0.8430 (mtp)
REVERT: A  557 ASP cc_start: 0.8731 (m-30) cc_final: 0.8514 (m-30)
REVERT: A  576 LEU cc_start: 0.9115 (mt) cc_final: 0.8854 (mt)
REVERT: A  583 SER cc_start: 0.9186 (m) cc_final: 0.8706 (t)
REVERT: A  604 ARG cc_start: 0.8562 (tpp-160) cc_final: 0.8015 (tpp80)
REVERT: A  606 TYR cc_start: 0.8057 (m-10) cc_final: 0.7788 (m-10)
REVERT: A  645 GLN cc_start: 0.8981 (tp40) cc_final: 0.8663 (tp-100)
REVERT: A  667 LEU cc_start: 0.9362 (tt) cc_final: 0.8809 (tt)
REVERT: B   51 LEU cc_start: 0.9239 (tp) cc_final: 0.9021 (tp)
REVERT: B  102 ASN cc_start: 0.9249 (m110) cc_final: 0.8916 (m110)
REVERT: B  114 ILE cc_start: 0.9609 (mt) cc_final: 0.9396 (mp)
REVERT: B  117 ARG cc_start: 0.8709 (mtt-85) cc_final: 0.8159 (mmm-85)
REVERT: B  120 ASP cc_start: 0.8813 (m-30) cc_final: 0.8516 (m-30)
REVERT: B  150 GLN cc_start: 0.9186 (tp40) cc_final: 0.8894 (tp-100)
REVERT: B  214 LYS cc_start: 0.8034 (mmtm) cc_final: 0.7745 (mmtm)
REVERT: B  235 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8436 (ttm110)
REVERT: B  276 LYS cc_start: 0.8872 (ptmt) cc_final: 0.8566 (ptpp)
REVERT: B  286 ASP cc_start: 0.8410 (m-30) cc_final: 0.8192 (m-30)
REVERT: B  358 ILE cc_start: 0.9422 (mm) cc_final: 0.9148 (mm)
REVERT: B  393 SER cc_start: 0.9472 (m) cc_final: 0.9226 (p)
REVERT: B  410 ASN cc_start: 0.9068 (m-40) cc_final: 0.8856 (m-40)
REVERT: B  467 ASN cc_start: 0.9478 (t0) cc_final: 0.9105 (t0)
REVERT: B  493 MET cc_start: 0.9324 (tmm) cc_final: 0.9019 (tmm)
REVERT: B  595 MET cc_start: 0.9076 (mmp) cc_final: 0.8874 (mmt)
REVERT: B  604 ARG cc_start: 0.8776 (tpp80) cc_final: 0.7986 (tpp80)
REVERT: B  610 LYS cc_start: 0.8948 (ptmt) cc_final: 0.8717 (ptpt)
REVERT: B  615 MET cc_start: 0.9122 (mmp) cc_final: 0.8905 (mmm)
REVERT: B  627 LYS cc_start: 0.9379 (tttt) cc_final: 0.8967 (tttp)
REVERT: B  640 MET cc_start: 0.8915 (tpp) cc_final: 0.8443 (tpp)
REVERT: B  650 GLN cc_start: 0.7941 (mt0) cc_final: 0.7720 (mt0)
REVERT: B  686 ARG cc_start: 0.7525 (mmt180) cc_final: 0.7225 (mmt180)
REVERT: D   95 MET cc_start: 0.7479 (ttp) cc_final: 0.7046 (ttt)
REVERT: D  173 TYR cc_start: 0.6972 (t80) cc_final: 0.6632 (t80)
  outliers start: 4
  outliers final: 0
  residues processed: 531
  average time/residue: 0.2666
  time to fit residues: 210.3841
Evaluate side-chains
  424 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 424
  time to evaluate  : 1.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 175 optimal weight:    5.9990
   chunk 182 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 320 ASN
** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 361 GLN
B 668 ASN
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 238 ASN
** D  91 ASN ** 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 = 0.3977 r_free = 0.3977 target = 0.161277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.112213 restraints weight = 33731.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.115734 restraints weight = 16218.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.117964 restraints weight = 9558.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3302
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3302
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.5395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16386  Z= 0.134
  Angle     :  0.578   7.286  22134  Z= 0.304
  Chirality :  0.041   0.237   2360
  Planarity :  0.003   0.040   2818
  Dihedral  : 10.816 171.755   2242
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.19), residues: 1932
  helix:  1.48 (0.15), residues: 1121
  sheet: -0.77 (0.39), residues: 148
  loop :  0.34 (0.24), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP D 124 
 HIS   0.004   0.001   HIS A 438 
 PHE   0.041   0.002   PHE C 109 
 TYR   0.023   0.001   TYR A 522 
 ARG   0.007   0.001   ARG B 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03888 (  871)
  hydrogen bonds       : angle       4.75127 ( 2571)
  covalent geometry    : bond        0.00293 (16386)
  covalent geometry    : angle       0.57764 (22134)

*********************** 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
  547 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 547
  time to evaluate  : 1.793 
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: 0.8425 (mm-30) cc_final: 0.7858 (mp0)
REVERT: A  144 MET cc_start: 0.8760 (mtm) cc_final: 0.8444 (mtm)
REVERT: A  150 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8512 (tm-30)
REVERT: A  168 VAL cc_start: 0.8752 (t) cc_final: 0.8534 (m)
REVERT: A  174 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7756 (mt-10)
REVERT: A  204 SER cc_start: 0.9202 (m) cc_final: 0.8687 (t)
REVERT: A  214 LYS cc_start: 0.7946 (tppt) cc_final: 0.7511 (mmtp)
REVERT: A  257 ASP cc_start: 0.8992 (m-30) cc_final: 0.8704 (m-30)
REVERT: A  286 ASP cc_start: 0.8137 (m-30) cc_final: 0.7832 (m-30)
REVERT: A  308 LYS cc_start: 0.9559 (mtmt) cc_final: 0.9344 (mtmm)
REVERT: A  319 MET cc_start: 0.9297 (tpp) cc_final: 0.8901 (tpp)
REVERT: A  417 LEU cc_start: 0.9450 (tt) cc_final: 0.8590 (tt)
REVERT: A  456 LYS cc_start: 0.8878 (ptpp) cc_final: 0.8442 (ptpp)
REVERT: A  458 MET cc_start: 0.9181 (mmm) cc_final: 0.8354 (mtm)
REVERT: A  557 ASP cc_start: 0.8720 (m-30) cc_final: 0.8512 (m-30)
REVERT: A  576 LEU cc_start: 0.9083 (mt) cc_final: 0.8822 (mt)
REVERT: A  584 ILE cc_start: 0.8983 (pt) cc_final: 0.8708 (pt)
REVERT: A  604 ARG cc_start: 0.8375 (tpp-160) cc_final: 0.8040 (ttm-80)
REVERT: A  645 GLN cc_start: 0.8712 (tp40) cc_final: 0.8470 (tp-100)
REVERT: A  667 LEU cc_start: 0.9173 (tt) cc_final: 0.8576 (tt)
REVERT: B   16 ILE cc_start: 0.9405 (mm) cc_final: 0.9167 (mm)
REVERT: B   95 MET cc_start: 0.8481 (tpp) cc_final: 0.8213 (tpp)
REVERT: B  102 ASN cc_start: 0.9248 (m110) cc_final: 0.8914 (m110)
REVERT: B  117 ARG cc_start: 0.8669 (mtt-85) cc_final: 0.8112 (mmm-85)
REVERT: B  120 ASP cc_start: 0.8643 (m-30) cc_final: 0.8403 (m-30)
REVERT: B  147 GLN cc_start: 0.8989 (mt0) cc_final: 0.8391 (mt0)
REVERT: B  150 GLN cc_start: 0.9187 (tp40) cc_final: 0.8983 (tp-100)
REVERT: B  179 LEU cc_start: 0.9470 (tp) cc_final: 0.9224 (tp)
REVERT: B  190 MET cc_start: 0.9138 (mtm) cc_final: 0.8851 (mtm)
REVERT: B  235 ARG cc_start: 0.8610 (ttm-80) cc_final: 0.8157 (ttm110)
REVERT: B  276 LYS cc_start: 0.8813 (ptmt) cc_final: 0.8475 (ptpp)
REVERT: B  286 ASP cc_start: 0.8478 (m-30) cc_final: 0.8231 (m-30)
REVERT: B  288 PHE cc_start: 0.9481 (t80) cc_final: 0.9190 (t80)
REVERT: B  312 GLN cc_start: 0.8878 (mt0) cc_final: 0.8424 (pt0)
REVERT: B  348 MET cc_start: 0.7544 (tpp) cc_final: 0.7224 (tpp)
REVERT: B  359 MET cc_start: 0.9068 (ttp) cc_final: 0.8767 (tmm)
REVERT: B  379 SER cc_start: 0.8950 (t) cc_final: 0.8730 (t)
REVERT: B  393 SER cc_start: 0.9495 (m) cc_final: 0.9146 (p)
REVERT: B  427 LYS cc_start: 0.9434 (pttt) cc_final: 0.9216 (pttt)
REVERT: B  467 ASN cc_start: 0.9292 (t0) cc_final: 0.8801 (t0)
REVERT: B  493 MET cc_start: 0.9220 (tmm) cc_final: 0.9007 (tmm)
REVERT: B  550 MET cc_start: 0.8513 (mtp) cc_final: 0.7974 (mtm)
REVERT: B  604 ARG cc_start: 0.8611 (tpp80) cc_final: 0.8068 (tpp80)
REVERT: B  615 MET cc_start: 0.9091 (mmp) cc_final: 0.8845 (mmm)
REVERT: B  627 LYS cc_start: 0.9177 (tttt) cc_final: 0.8921 (tttp)
REVERT: B  640 MET cc_start: 0.8936 (tpp) cc_final: 0.8376 (tpp)
REVERT: B  650 GLN cc_start: 0.7836 (mt0) cc_final: 0.7619 (mt0)
REVERT: C   89 VAL cc_start: 0.5327 (m) cc_final: 0.4779 (m)
REVERT: D   95 MET cc_start: 0.7586 (ttp) cc_final: 0.7132 (ttt)
REVERT: D  173 TYR cc_start: 0.7044 (t80) cc_final: 0.6751 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 547
  average time/residue: 0.2827
  time to fit residues: 229.1447
Evaluate side-chains
  439 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 439
  time to evaluate  : 1.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 31 optimal weight:    7.9990
   chunk 126 optimal weight:    0.8980
   chunk 62 optimal weight:    7.9990
   chunk 69 optimal weight:    5.9990
   chunk 156 optimal weight:    9.9990
   chunk 21 optimal weight:    8.9990
   chunk 115 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 169 optimal weight:    6.9990
   chunk 113 optimal weight:    6.9990
   chunk 177 optimal weight:    6.9990
   overall best weight:    4.9788

-------------------------------------------------------------------------------
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 239 GLN
** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 361 GLN
B 501 GLN
B 668 ASN
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 201 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.156433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.108146 restraints weight = 34764.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.111428 restraints weight = 16901.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.113530 restraints weight = 10115.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.5753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.084  16386  Z= 0.369
  Angle     :  0.714   8.040  22134  Z= 0.380
  Chirality :  0.047   0.199   2360
  Planarity :  0.004   0.047   2818
  Dihedral  : 11.098 172.576   2242
  Min Nonbonded Distance : 1.730

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.19), residues: 1932
  helix:  1.12 (0.15), residues: 1120
  sheet: -0.62 (0.42), residues: 126
  loop :  0.17 (0.24), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP D 124 
 HIS   0.006   0.001   HIS A 438 
 PHE   0.037   0.003   PHE C 109 
 TYR   0.017   0.002   TYR B 498 
 ARG   0.005   0.001   ARG B 453 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04381 (  871)
  hydrogen bonds       : angle       5.07271 ( 2571)
  covalent geometry    : bond        0.00801 (16386)
  covalent geometry    : angle       0.71449 (22134)

*********************** 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
  489 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 489
  time to evaluate  : 1.786 
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: 0.8437 (mm-30) cc_final: 0.8174 (mp0)
REVERT: A  144 MET cc_start: 0.8851 (mtm) cc_final: 0.8574 (mtm)
REVERT: A  214 LYS cc_start: 0.8240 (tppt) cc_final: 0.8033 (tppt)
REVERT: A  286 ASP cc_start: 0.8134 (m-30) cc_final: 0.7891 (m-30)
REVERT: A  319 MET cc_start: 0.9317 (tpp) cc_final: 0.8763 (tpp)
REVERT: A  344 GLU cc_start: 0.8919 (pt0) cc_final: 0.8650 (pt0)
REVERT: A  362 ASP cc_start: 0.7596 (m-30) cc_final: 0.7341 (m-30)
REVERT: A  447 ASN cc_start: 0.8179 (m-40) cc_final: 0.7634 (m-40)
REVERT: A  458 MET cc_start: 0.9238 (mmm) cc_final: 0.8475 (mtm)
REVERT: A  557 ASP cc_start: 0.8667 (m-30) cc_final: 0.8452 (m-30)
REVERT: A  576 LEU cc_start: 0.9101 (mt) cc_final: 0.8803 (mt)
REVERT: A  645 GLN cc_start: 0.8853 (tp40) cc_final: 0.8519 (tp-100)
REVERT: A  667 LEU cc_start: 0.9339 (tt) cc_final: 0.8737 (tt)
REVERT: B   95 MET cc_start: 0.8605 (tpp) cc_final: 0.8379 (tpp)
REVERT: B  102 ASN cc_start: 0.9242 (m110) cc_final: 0.8881 (m110)
REVERT: B  104 TYR cc_start: 0.9043 (m-80) cc_final: 0.8763 (m-80)
REVERT: B  120 ASP cc_start: 0.8819 (m-30) cc_final: 0.8585 (m-30)
REVERT: B  147 GLN cc_start: 0.9184 (mt0) cc_final: 0.8873 (mt0)
REVERT: B  150 GLN cc_start: 0.9122 (tp40) cc_final: 0.8837 (tp-100)
REVERT: B  190 MET cc_start: 0.9248 (mtm) cc_final: 0.8868 (mtm)
REVERT: B  214 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7730 (mmtp)
REVERT: B  235 ARG cc_start: 0.8668 (ttm-80) cc_final: 0.8346 (ttm110)
REVERT: B  258 ILE cc_start: 0.9531 (tp) cc_final: 0.9219 (tp)
REVERT: B  276 LYS cc_start: 0.8879 (ptmt) cc_final: 0.8564 (ptpp)
REVERT: B  362 ASP cc_start: 0.8108 (m-30) cc_final: 0.7189 (m-30)
REVERT: B  393 SER cc_start: 0.9473 (m) cc_final: 0.9239 (p)
REVERT: B  467 ASN cc_start: 0.9391 (t0) cc_final: 0.9024 (t0)
REVERT: B  493 MET cc_start: 0.9368 (tmm) cc_final: 0.9038 (tmm)
REVERT: B  604 ARG cc_start: 0.8671 (tpp80) cc_final: 0.7831 (tpp80)
REVERT: B  610 LYS cc_start: 0.8935 (ptmt) cc_final: 0.8670 (ptpt)
REVERT: B  615 MET cc_start: 0.9141 (mmp) cc_final: 0.8928 (mmm)
REVERT: B  627 LYS cc_start: 0.9371 (tttt) cc_final: 0.8959 (tttp)
REVERT: B  640 MET cc_start: 0.8912 (tpp) cc_final: 0.8421 (tpp)
REVERT: C   74 MET cc_start: 0.6870 (mtt) cc_final: 0.6438 (mtp)
REVERT: C   89 VAL cc_start: 0.5441 (m) cc_final: 0.4968 (m)
REVERT: C   95 MET cc_start: 0.7024 (tmm) cc_final: 0.6696 (tmm)
REVERT: C  157 MET cc_start: 0.8853 (mpp) cc_final: 0.8059 (ptp)
REVERT: D   95 MET cc_start: 0.8602 (ttp) cc_final: 0.8131 (ttt)
REVERT: D  173 TYR cc_start: 0.6493 (t80) cc_final: 0.6245 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 489
  average time/residue: 0.2714
  time to fit residues: 198.0205
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  : 1.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 161 optimal weight:    9.9990
   chunk 23 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 146 optimal weight:    7.9990
   chunk 184 optimal weight:   20.0000
   chunk 119 optimal weight:    0.9990
   chunk 175 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 410 ASN
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  69 GLN
** D  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 210 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.158474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.109905 restraints weight = 33852.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.113299 restraints weight = 16332.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.115503 restraints weight = 9750.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3273
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3273
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.5863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  16386  Z= 0.165
  Angle     :  0.606   8.140  22134  Z= 0.320
  Chirality :  0.042   0.161   2360
  Planarity :  0.003   0.043   2818
  Dihedral  : 10.657 170.534   2242
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  1.40 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.19), residues: 1932
  helix:  1.23 (0.15), residues: 1124
  sheet: -0.69 (0.43), residues: 126
  loop :  0.15 (0.24), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP D 124 
 HIS   0.005   0.001   HIS B 438 
 PHE   0.045   0.002   PHE C 109 
 TYR   0.019   0.002   TYR C 242 
 ARG   0.007   0.001   ARG A 686 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03960 (  871)
  hydrogen bonds       : angle       4.86481 ( 2571)
  covalent geometry    : bond        0.00362 (16386)
  covalent geometry    : angle       0.60581 (22134)

*********************** 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
  533 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 532
  time to evaluate  : 1.788 
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  188 ILE cc_start: 0.9424 (mm) cc_final: 0.9019 (mm)
REVERT: A  214 LYS cc_start: 0.8295 (tppt) cc_final: 0.8067 (tppt)
REVERT: A  231 ASP cc_start: 0.8473 (t0) cc_final: 0.8261 (t0)
REVERT: A  232 ASN cc_start: 0.8754 (m-40) cc_final: 0.8230 (m110)
REVERT: A  257 ASP cc_start: 0.8871 (m-30) cc_final: 0.8487 (m-30)
REVERT: A  308 LYS cc_start: 0.9544 (mtmt) cc_final: 0.9326 (mtmm)
REVERT: A  319 MET cc_start: 0.9296 (tpp) cc_final: 0.8794 (tpp)
REVERT: A  344 GLU cc_start: 0.8890 (pt0) cc_final: 0.8597 (pt0)
REVERT: A  447 ASN cc_start: 0.8090 (m-40) cc_final: 0.7647 (m-40)
REVERT: A  458 MET cc_start: 0.9212 (mmm) cc_final: 0.8454 (mtm)
REVERT: A  576 LEU cc_start: 0.9066 (mt) cc_final: 0.8808 (mt)
REVERT: A  645 GLN cc_start: 0.8732 (tp40) cc_final: 0.8461 (tp-100)
REVERT: A  667 LEU cc_start: 0.9241 (tt) cc_final: 0.8608 (tt)
REVERT: A  671 ASP cc_start: 0.8297 (m-30) cc_final: 0.8090 (m-30)
REVERT: A  686 ARG cc_start: 0.8448 (mtp-110) cc_final: 0.7926 (mtp-110)
REVERT: B   95 MET cc_start: 0.8492 (tpp) cc_final: 0.8212 (tpp)
REVERT: B  102 ASN cc_start: 0.9295 (m110) cc_final: 0.8969 (m110)
REVERT: B  147 GLN cc_start: 0.9157 (mt0) cc_final: 0.8801 (mt0)
REVERT: B  150 GLN cc_start: 0.9192 (tp40) cc_final: 0.8884 (tp-100)
REVERT: B  190 MET cc_start: 0.9251 (mtm) cc_final: 0.8863 (mtm)
REVERT: B  191 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8115 (mm-40)
REVERT: B  258 ILE cc_start: 0.9489 (tp) cc_final: 0.9231 (tp)
REVERT: B  262 LEU cc_start: 0.9477 (mm) cc_final: 0.9243 (mm)
REVERT: B  276 LYS cc_start: 0.8841 (ptmt) cc_final: 0.8470 (ptpp)
REVERT: B  288 PHE cc_start: 0.9456 (t80) cc_final: 0.9183 (t80)
REVERT: B  320 ASN cc_start: 0.8694 (p0) cc_final: 0.8391 (p0)
REVERT: B  359 MET cc_start: 0.9120 (ttp) cc_final: 0.8741 (tmm)
REVERT: B  362 ASP cc_start: 0.7967 (m-30) cc_final: 0.7110 (m-30)
REVERT: B  379 SER cc_start: 0.8995 (t) cc_final: 0.8759 (t)
REVERT: B  392 SER cc_start: 0.9280 (m) cc_final: 0.8822 (m)
REVERT: B  393 SER cc_start: 0.9487 (m) cc_final: 0.9192 (p)
REVERT: B  467 ASN cc_start: 0.9221 (t0) cc_final: 0.8725 (t0)
REVERT: B  493 MET cc_start: 0.9250 (tmm) cc_final: 0.9015 (tmm)
REVERT: B  550 MET cc_start: 0.8504 (mtp) cc_final: 0.7808 (mtp)
REVERT: B  604 ARG cc_start: 0.8540 (tpp80) cc_final: 0.7640 (tpp80)
REVERT: B  615 MET cc_start: 0.9105 (mmp) cc_final: 0.8828 (mmm)
REVERT: B  627 LYS cc_start: 0.9296 (tttt) cc_final: 0.8955 (tttp)
REVERT: B  640 MET cc_start: 0.9005 (tpp) cc_final: 0.8480 (tpp)
REVERT: C   89 VAL cc_start: 0.6097 (m) cc_final: 0.5652 (m)
REVERT: C   95 MET cc_start: 0.6624 (tmm) cc_final: 0.6363 (tmm)
REVERT: C  157 MET cc_start: 0.8802 (mpp) cc_final: 0.8173 (ptp)
REVERT: D   95 MET cc_start: 0.8347 (ttp) cc_final: 0.7844 (ttt)
REVERT: D  173 TYR cc_start: 0.6387 (t80) cc_final: 0.6170 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 533
  average time/residue: 0.2617
  time to fit residues: 207.7151
Evaluate side-chains
  436 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 435
  time to evaluate  : 1.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 159 optimal weight:   20.0000
   chunk 72 optimal weight:    6.9990
   chunk 18 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 183 optimal weight:    6.9990
   chunk 52 optimal weight:    0.7980
   chunk 180 optimal weight:   10.0000
   chunk 108 optimal weight:    0.6980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
A 232 ASN
** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 438 HIS
** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 233 ASN
** D  91 ASN ** 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 = 0.3960 r_free = 0.3960 target = 0.159039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.111140 restraints weight = 33256.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.114495 restraints weight = 16054.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.116762 restraints weight = 9565.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3305
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3305
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.6032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  16386  Z= 0.139
  Angle     :  0.598   8.311  22134  Z= 0.315
  Chirality :  0.042   0.157   2360
  Planarity :  0.003   0.041   2818
  Dihedral  : 10.385 171.252   2242
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.19), residues: 1932
  helix:  1.37 (0.15), residues: 1126
  sheet: -0.15 (0.45), residues: 106
  loop :  0.03 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP D 124 
 HIS   0.004   0.001   HIS B 438 
 PHE   0.043   0.002   PHE C 109 
 TYR   0.027   0.002   TYR A 571 
 ARG   0.006   0.001   ARG A 686 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03887 (  871)
  hydrogen bonds       : angle       4.77747 ( 2571)
  covalent geometry    : bond        0.00307 (16386)
  covalent geometry    : angle       0.59752 (22134)

*********************** 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
  520 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 520
  time to evaluate  : 1.816 
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   64 TYR cc_start: 0.8896 (m-10) cc_final: 0.8593 (m-10)
REVERT: A   65 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8101 (mp0)
REVERT: A  172 LEU cc_start: 0.9260 (mp) cc_final: 0.8865 (mp)
REVERT: A  188 ILE cc_start: 0.9447 (mm) cc_final: 0.9079 (mm)
REVERT: A  214 LYS cc_start: 0.8203 (tppt) cc_final: 0.7970 (tppt)
REVERT: A  231 ASP cc_start: 0.8472 (t0) cc_final: 0.8231 (t0)
REVERT: A  232 ASN cc_start: 0.8608 (m-40) cc_final: 0.8171 (m110)
REVERT: A  236 TYR cc_start: 0.9017 (t80) cc_final: 0.8642 (t80)
REVERT: A  286 ASP cc_start: 0.8281 (m-30) cc_final: 0.7890 (m-30)
REVERT: A  319 MET cc_start: 0.9306 (tpp) cc_final: 0.8856 (tpp)
REVERT: A  344 GLU cc_start: 0.8909 (pt0) cc_final: 0.8616 (pt0)
REVERT: A  357 TYR cc_start: 0.8314 (m-80) cc_final: 0.7837 (m-80)
REVERT: A  362 ASP cc_start: 0.7333 (m-30) cc_final: 0.7071 (m-30)
REVERT: A  456 LYS cc_start: 0.8896 (ptpp) cc_final: 0.8620 (ptpp)
REVERT: A  458 MET cc_start: 0.9225 (mmm) cc_final: 0.8497 (mtm)
REVERT: A  576 LEU cc_start: 0.9129 (mt) cc_final: 0.8898 (mt)
REVERT: A  645 GLN cc_start: 0.8655 (tp40) cc_final: 0.8397 (tp-100)
REVERT: A  667 LEU cc_start: 0.9249 (tt) cc_final: 0.8632 (tt)
REVERT: A  686 ARG cc_start: 0.8414 (mtp-110) cc_final: 0.7898 (mtp-110)
REVERT: B   16 ILE cc_start: 0.9345 (mm) cc_final: 0.9040 (mm)
REVERT: B  102 ASN cc_start: 0.9217 (m110) cc_final: 0.8928 (m110)
REVERT: B  120 ASP cc_start: 0.8693 (m-30) cc_final: 0.8393 (m-30)
REVERT: B  150 GLN cc_start: 0.9204 (tp40) cc_final: 0.8962 (tp-100)
REVERT: B  156 PHE cc_start: 0.9157 (t80) cc_final: 0.8920 (t80)
REVERT: B  190 MET cc_start: 0.9186 (mtm) cc_final: 0.8837 (mtm)
REVERT: B  191 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8146 (mm-40)
REVERT: B  253 ILE cc_start: 0.9347 (tt) cc_final: 0.9086 (tt)
REVERT: B  276 LYS cc_start: 0.8774 (ptmt) cc_final: 0.8466 (ptpp)
REVERT: B  286 ASP cc_start: 0.8368 (m-30) cc_final: 0.8114 (m-30)
REVERT: B  288 PHE cc_start: 0.9413 (t80) cc_final: 0.9127 (t80)
REVERT: B  348 MET cc_start: 0.8047 (tpp) cc_final: 0.7590 (tpp)
REVERT: B  359 MET cc_start: 0.9025 (ttp) cc_final: 0.8678 (tmm)
REVERT: B  392 SER cc_start: 0.9233 (m) cc_final: 0.8989 (m)
REVERT: B  467 ASN cc_start: 0.9233 (t0) cc_final: 0.8763 (t0)
REVERT: B  493 MET cc_start: 0.9212 (tmm) cc_final: 0.8976 (tmm)
REVERT: B  576 LEU cc_start: 0.9289 (mt) cc_final: 0.9042 (mt)
REVERT: B  588 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8774 (mm-40)
REVERT: B  604 ARG cc_start: 0.8549 (tpp80) cc_final: 0.7692 (tpp80)
REVERT: B  615 MET cc_start: 0.9086 (mmp) cc_final: 0.8831 (mmm)
REVERT: B  627 LYS cc_start: 0.9200 (tttt) cc_final: 0.8858 (tttp)
REVERT: B  640 MET cc_start: 0.8983 (tpp) cc_final: 0.8231 (tpp)
REVERT: B  652 ILE cc_start: 0.8914 (mt) cc_final: 0.8698 (mt)
REVERT: C   89 VAL cc_start: 0.5360 (m) cc_final: 0.4806 (m)
REVERT: C   95 MET cc_start: 0.6381 (tmm) cc_final: 0.6134 (tmm)
REVERT: C  154 PHE cc_start: 0.8568 (t80) cc_final: 0.7486 (t80)
REVERT: C  157 MET cc_start: 0.8750 (mpp) cc_final: 0.8211 (ptp)
REVERT: D   56 MET cc_start: -0.1028 (mmm) cc_final: -0.1395 (mmm)
REVERT: D   95 MET cc_start: 0.8342 (ttp) cc_final: 0.7865 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 520
  average time/residue: 0.2652
  time to fit residues: 208.1312
Evaluate side-chains
  429 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 429
  time to evaluate  : 1.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 102 optimal weight:    0.9990
   chunk 182 optimal weight:    5.9990
   chunk 107 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9980
   chunk 115 optimal weight:    5.9990
   chunk 127 optimal weight:    5.9990
   chunk 188 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 50 optimal weight:    0.0010
   overall best weight:    2.3992

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

Flipped N/Q/H residues before XYZ refinement:
** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 ASN
A 646 GLN
B 668 ASN
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.156050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.107913 restraints weight = 33743.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.111256 restraints weight = 16379.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.113415 restraints weight = 9790.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3259
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.6190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079  16386  Z= 0.213
  Angle     :  0.654  10.778  22134  Z= 0.344
  Chirality :  0.044   0.308   2360
  Planarity :  0.004   0.041   2818
  Dihedral  : 10.418 170.630   2242
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.19), residues: 1932
  helix:  1.34 (0.15), residues: 1115
  sheet: -0.02 (0.45), residues: 106
  loop :  0.06 (0.23), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP D 124 
 HIS   0.004   0.001   HIS A 438 
 PHE   0.046   0.002   PHE C 109 
 TYR   0.023   0.002   TYR A 571 
 ARG   0.010   0.001   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04042 (  871)
  hydrogen bonds       : angle       4.90453 ( 2571)
  covalent geometry    : bond        0.00470 (16386)
  covalent geometry    : angle       0.65432 (22134)

*********************** 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
  492 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 492
  time to evaluate  : 1.836 
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  139 GLU cc_start: 0.8297 (mp0) cc_final: 0.7933 (mp0)
REVERT: A  158 ASN cc_start: 0.8978 (m-40) cc_final: 0.8772 (m-40)
REVERT: A  172 LEU cc_start: 0.9206 (mp) cc_final: 0.8906 (mp)
REVERT: A  214 LYS cc_start: 0.8248 (tppt) cc_final: 0.7863 (tppt)
REVERT: A  228 LYS cc_start: 0.8570 (mmtm) cc_final: 0.8207 (mmtt)
REVERT: A  286 ASP cc_start: 0.8220 (m-30) cc_final: 0.7832 (m-30)
REVERT: A  319 MET cc_start: 0.9299 (tpp) cc_final: 0.8776 (tpp)
REVERT: A  344 GLU cc_start: 0.8927 (pt0) cc_final: 0.8664 (pt0)
REVERT: A  362 ASP cc_start: 0.7333 (m-30) cc_final: 0.7123 (m-30)
REVERT: A  456 LYS cc_start: 0.8903 (ptpp) cc_final: 0.8586 (ptpp)
REVERT: A  458 MET cc_start: 0.9211 (mmm) cc_final: 0.8474 (mtm)
REVERT: A  557 ASP cc_start: 0.8709 (m-30) cc_final: 0.8508 (m-30)
REVERT: A  576 LEU cc_start: 0.9145 (mt) cc_final: 0.8896 (mt)
REVERT: A  584 ILE cc_start: 0.9061 (pt) cc_final: 0.8818 (pt)
REVERT: A  645 GLN cc_start: 0.8767 (tp40) cc_final: 0.8470 (tp-100)
REVERT: A  667 LEU cc_start: 0.9340 (tt) cc_final: 0.8689 (tt)
REVERT: A  686 ARG cc_start: 0.8490 (mtp-110) cc_final: 0.7924 (mtp-110)
REVERT: B  102 ASN cc_start: 0.9183 (m110) cc_final: 0.8831 (m110)
REVERT: B  120 ASP cc_start: 0.8736 (m-30) cc_final: 0.8419 (m-30)
REVERT: B  125 VAL cc_start: 0.9251 (t) cc_final: 0.9048 (m)
REVERT: B  150 GLN cc_start: 0.9205 (tp40) cc_final: 0.8993 (tp-100)
REVERT: B  172 LEU cc_start: 0.9169 (mp) cc_final: 0.8891 (mp)
REVERT: B  190 MET cc_start: 0.9234 (mtm) cc_final: 0.8958 (mtm)
REVERT: B  235 ARG cc_start: 0.8586 (ttm110) cc_final: 0.8341 (mtm110)
REVERT: B  253 ILE cc_start: 0.9338 (tt) cc_final: 0.9128 (tt)
REVERT: B  274 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7512 (ttm-80)
REVERT: B  276 LYS cc_start: 0.8980 (ptmt) cc_final: 0.8622 (ptpp)
REVERT: B  288 PHE cc_start: 0.9502 (t80) cc_final: 0.9227 (t80)
REVERT: B  348 MET cc_start: 0.8332 (tpp) cc_final: 0.7961 (tpp)
REVERT: B  358 ILE cc_start: 0.9493 (mm) cc_final: 0.9181 (mm)
REVERT: B  359 MET cc_start: 0.9051 (ttp) cc_final: 0.8632 (tmm)
REVERT: B  362 ASP cc_start: 0.7867 (m-30) cc_final: 0.6924 (m-30)
REVERT: B  392 SER cc_start: 0.9245 (m) cc_final: 0.8975 (m)
REVERT: B  467 ASN cc_start: 0.9214 (t0) cc_final: 0.8788 (t0)
REVERT: B  493 MET cc_start: 0.9266 (tmm) cc_final: 0.9001 (tmm)
REVERT: B  576 LEU cc_start: 0.9290 (mt) cc_final: 0.9051 (mt)
REVERT: B  586 TYR cc_start: 0.8474 (m-10) cc_final: 0.8151 (m-10)
REVERT: B  602 GLU cc_start: 0.7240 (pt0) cc_final: 0.6936 (pt0)
REVERT: B  604 ARG cc_start: 0.8598 (tpp80) cc_final: 0.7709 (tpp80)
REVERT: B  615 MET cc_start: 0.9063 (mmp) cc_final: 0.8850 (mmm)
REVERT: B  627 LYS cc_start: 0.9196 (tttt) cc_final: 0.8831 (tttp)
REVERT: B  640 MET cc_start: 0.8941 (tpp) cc_final: 0.8398 (tpp)
REVERT: B  652 ILE cc_start: 0.9030 (mt) cc_final: 0.8828 (mt)
REVERT: C   90 LEU cc_start: 0.7411 (mt) cc_final: 0.6995 (tt)
REVERT: C   95 MET cc_start: 0.6799 (tmm) cc_final: 0.6471 (tmm)
REVERT: C  154 PHE cc_start: 0.8662 (t80) cc_final: 0.7425 (t80)
REVERT: C  157 MET cc_start: 0.8819 (mpp) cc_final: 0.8240 (ptp)
REVERT: D   56 MET cc_start: -0.1006 (mmm) cc_final: -0.1364 (mmm)
REVERT: D   95 MET cc_start: 0.8569 (ttp) cc_final: 0.8121 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 492
  average time/residue: 0.2648
  time to fit residues: 195.9908
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  : 1.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 137 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 79 optimal weight:    1.9990
   chunk 160 optimal weight:   30.0000
   chunk 106 optimal weight:    0.5980
   chunk 120 optimal weight:    0.9980
   chunk 135 optimal weight:    0.6980
   chunk 148 optimal weight:    7.9990
   chunk 127 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.158787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.110356 restraints weight = 33551.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.113796 restraints weight = 16079.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.116005 restraints weight = 9537.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3305
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3305
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.6313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  16386  Z= 0.152
  Angle     :  0.625  11.918  22134  Z= 0.328
  Chirality :  0.043   0.231   2360
  Planarity :  0.003   0.039   2818
  Dihedral  : 10.151 167.867   2242
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.19), residues: 1932
  helix:  1.35 (0.15), residues: 1120
  sheet:  0.01 (0.44), residues: 106
  loop :  0.06 (0.23), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP D 124 
 HIS   0.007   0.001   HIS A 438 
 PHE   0.049   0.002   PHE C 109 
 TYR   0.043   0.002   TYR B 118 
 ARG   0.009   0.001   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03885 (  871)
  hydrogen bonds       : angle       4.89598 ( 2571)
  covalent geometry    : bond        0.00340 (16386)
  covalent geometry    : angle       0.62542 (22134)

********************** 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
  472 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 472
  time to evaluate  : 1.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8222 (mp0)
REVERT: A  172 LEU cc_start: 0.9184 (mp) cc_final: 0.8910 (mp)
REVERT: A  228 LYS cc_start: 0.8496 (mmtm) cc_final: 0.8222 (mmtt)
REVERT: A  236 TYR cc_start: 0.9034 (t80) cc_final: 0.8754 (t80)
REVERT: A  286 ASP cc_start: 0.8277 (m-30) cc_final: 0.7887 (m-30)
REVERT: A  319 MET cc_start: 0.9292 (tpp) cc_final: 0.8806 (tpp)
REVERT: A  344 GLU cc_start: 0.8926 (pt0) cc_final: 0.8626 (pt0)
REVERT: A  357 TYR cc_start: 0.8246 (m-80) cc_final: 0.7772 (m-80)
REVERT: A  456 LYS cc_start: 0.8894 (ptpp) cc_final: 0.8568 (ptpp)
REVERT: A  458 MET cc_start: 0.9237 (mmm) cc_final: 0.8496 (mtm)
REVERT: A  576 LEU cc_start: 0.9164 (mt) cc_final: 0.8942 (mt)
REVERT: A  584 ILE cc_start: 0.9069 (pt) cc_final: 0.8840 (pt)
REVERT: A  645 GLN cc_start: 0.8598 (tp40) cc_final: 0.8326 (tp-100)
REVERT: A  667 LEU cc_start: 0.9300 (tt) cc_final: 0.8643 (tt)
REVERT: A  686 ARG cc_start: 0.8401 (mtp-110) cc_final: 0.7863 (mtp-110)
REVERT: A  687 THR cc_start: 0.8407 (m) cc_final: 0.8165 (p)
REVERT: B  120 ASP cc_start: 0.8678 (m-30) cc_final: 0.8371 (m-30)
REVERT: B  150 GLN cc_start: 0.9194 (tp40) cc_final: 0.8963 (tp-100)
REVERT: B  190 MET cc_start: 0.9197 (mtm) cc_final: 0.8926 (mtm)
REVERT: B  191 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8257 (mm-40)
REVERT: B  235 ARG cc_start: 0.8585 (ttm110) cc_final: 0.8136 (mtm110)
REVERT: B  253 ILE cc_start: 0.9326 (tt) cc_final: 0.9106 (tt)
REVERT: B  262 LEU cc_start: 0.9496 (mm) cc_final: 0.9289 (mm)
REVERT: B  274 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7415 (ttm-80)
REVERT: B  276 LYS cc_start: 0.8947 (ptmt) cc_final: 0.8597 (ptpp)
REVERT: B  288 PHE cc_start: 0.9453 (t80) cc_final: 0.9155 (t80)
REVERT: B  348 MET cc_start: 0.8312 (tpp) cc_final: 0.7850 (tpp)
REVERT: B  359 MET cc_start: 0.9034 (ttp) cc_final: 0.8582 (tmm)
REVERT: B  362 ASP cc_start: 0.7807 (m-30) cc_final: 0.6941 (m-30)
REVERT: B  392 SER cc_start: 0.9252 (m) cc_final: 0.9018 (m)
REVERT: B  410 ASN cc_start: 0.9089 (m-40) cc_final: 0.8699 (m-40)
REVERT: B  467 ASN cc_start: 0.9208 (t0) cc_final: 0.8744 (t0)
REVERT: B  493 MET cc_start: 0.9215 (tmm) cc_final: 0.8975 (tmm)
REVERT: B  604 ARG cc_start: 0.8557 (tpp80) cc_final: 0.7634 (tpp80)
REVERT: B  615 MET cc_start: 0.9078 (mmp) cc_final: 0.8851 (mmm)
REVERT: B  627 LYS cc_start: 0.9147 (tttt) cc_final: 0.8748 (tttp)
REVERT: B  640 MET cc_start: 0.8985 (tpp) cc_final: 0.8220 (tpp)
REVERT: B  652 ILE cc_start: 0.8952 (mt) cc_final: 0.8742 (mt)
REVERT: C   90 LEU cc_start: 0.7553 (mt) cc_final: 0.7328 (tt)
REVERT: C   93 MET cc_start: 0.9334 (ppp) cc_final: 0.9117 (ppp)
REVERT: C   95 MET cc_start: 0.6771 (tmm) cc_final: 0.6395 (tmm)
REVERT: C  154 PHE cc_start: 0.8728 (t80) cc_final: 0.7490 (t80)
REVERT: C  157 MET cc_start: 0.8696 (mpp) cc_final: 0.8196 (ptp)
REVERT: D   56 MET cc_start: -0.0915 (mmm) cc_final: -0.1248 (mmm)
REVERT: D   95 MET cc_start: 0.8499 (ttp) cc_final: 0.8026 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 472
  average time/residue: 0.2705
  time to fit residues: 191.5035
Evaluate side-chains
  411 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 411
  time to evaluate  : 1.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 179 optimal weight:    7.9990
   chunk 190 optimal weight:    9.9990
   chunk 58 optimal weight:    0.1980
   chunk 180 optimal weight:    9.9990
   chunk 108 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.6388

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

Flipped N/Q/H residues before XYZ refinement:
** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.157621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.109140 restraints weight = 33395.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.112547 restraints weight = 16360.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.114739 restraints weight = 9684.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3292
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.6404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  16386  Z= 0.170
  Angle     :  0.627   9.520  22134  Z= 0.330
  Chirality :  0.043   0.202   2360
  Planarity :  0.003   0.039   2818
  Dihedral  : 10.051 166.590   2242
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.19), residues: 1932
  helix:  1.36 (0.15), residues: 1126
  sheet:  0.24 (0.45), residues: 96
  loop : -0.01 (0.23), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP D 124 
 HIS   0.007   0.001   HIS A 438 
 PHE   0.050   0.002   PHE C 109 
 TYR   0.028   0.002   TYR B 612 
 ARG   0.009   0.001   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03910 (  871)
  hydrogen bonds       : angle       4.89340 ( 2571)
  covalent geometry    : bond        0.00377 (16386)
  covalent geometry    : angle       0.62688 (22134)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6315.94 seconds
wall clock time: 111 minutes 16.94 seconds (6676.94 seconds total)