Starting phenix.real_space_refine
on Fri Feb 14 23:52:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qwl_4660/02_2025/6qwl_4660.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qwl_4660/02_2025/6qwl_4660.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qwl_4660/02_2025/6qwl_4660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qwl_4660/02_2025/6qwl_4660.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qwl_4660/02_2025/6qwl_4660.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qwl_4660/02_2025/6qwl_4660.cif"
  }
  resolution = 4.1
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      26      5.49       5
     S      74      5.16       5
     C    6498      2.51       5
     N    1787      2.21       5
     O    2023      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10408
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "E"
      Number of atoms: 4084
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 511, 4084
          Classifications: {'peptide': 511}
          Link IDs: {'PTRANS': 21, 'TRANS': 489}
    Chain: "K"
      Number of atoms: 4206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 539, 4206
          Classifications: {'peptide': 539}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 24, 'TRANS': 514}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "Q"
      Number of atoms: 1565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1565
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
    Chain: "T"
      Number of atoms: 249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 249
          Classifications: {'RNA': 12}
          Modifications used: {'rna2p_pyr': 4, 'rna3p_pur': 3, 'rna3p_pyr': 5}
          Link IDs: {'rna2p': 4, 'rna3p': 7}
    Chain: "W"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 304
          Classifications: {'RNA': 14}
          Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 2, 'rna3p': 11}
  Time building chain proxies: 6.73, per 1000 atoms: 0.65
  Number of scatterers: 10408
  At special positions: 0
  Unit cell: (99.36, 104.76, 113.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      74     16.00
     P      26     15.00
     O    2023      8.00
     N    1787      7.00
     C    6498      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: 2.56
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2312

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 13 sheets defined
      50.2% alpha, 7.8% beta
      6 base pairs and 10 stacking pairs defined.
    Time for finding SS restraints: 3.67
  Creating SS restraints...
    Processing helix  chain 'E' and resid 206 through 215
    Processing helix  chain 'E' and resid 222 through 232
    Processing helix  chain 'E' and resid 239 through 246
    Processing helix  chain 'E' and resid 258 through 262
      removed outlier: 3.846A  pdb=" N   ASP E 261 " --> pdb=" O   LYS E 258 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 266 through 270
      removed outlier: 3.584A  pdb=" N   ILE E 269 " --> pdb=" O   GLY E 266 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 301 through 313
      removed outlier: 4.179A  pdb=" N   GLU E 311 " --> pdb=" O   LYS E 307 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 314 through 317
    Processing helix  chain 'E' and resid 332 through 345
      removed outlier: 3.900A  pdb=" N   LEU E 336 " --> pdb=" O   ASN E 332 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   LYS E 338 " --> pdb=" O   ASN E 334 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 359 through 366
      removed outlier: 3.627A  pdb=" N   LYS E 363 " --> pdb=" O   THR E 359 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 376 through 380
      removed outlier: 3.809A  pdb=" N   VAL E 379 " --> pdb=" O   MET E 376 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 402 through 410
    Processing helix  chain 'E' and resid 429 through 447
      removed outlier: 3.511A  pdb=" N   ASN E 447 " --> pdb=" O   VAL E 443 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 450 through 472
    Processing helix  chain 'E' and resid 529 through 533
      removed outlier: 3.513A  pdb=" N   TRP E 533 " --> pdb=" O   SER E 530 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 564 through 572
      removed outlier: 3.509A  pdb=" N   GLU E 572 " --> pdb=" O   LYS E 568 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 575 through 596
      removed outlier: 3.636A  pdb=" N   GLN E 579 " --> pdb=" O   ARG E 575 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 600 through 605
      removed outlier: 3.702A  pdb=" N   LYS E 605 " --> pdb=" O   LYS E 601 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 628 through 646
      removed outlier: 3.581A  pdb=" N   TYR E 644 " --> pdb=" O   CYS E 640 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   PHE E 646 " --> pdb=" O   MET E 642 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 648 through 670
      removed outlier: 3.734A  pdb=" N   GLU E 652 " --> pdb=" O   ASN E 648 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   ARG E 660 " --> pdb=" O   ALA E 656 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   LEU E 661 " --> pdb=" O   GLU E 657 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 678 through 688
    Processing helix  chain 'E' and resid 693 through 714
      removed outlier: 3.513A  pdb=" N   ILE E 697 " --> pdb=" O   ASN E 693 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLN E 698 " --> pdb=" O   PRO E 694 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 5 through 11
      removed outlier: 3.839A  pdb=" N   LEU K   8 " --> pdb=" O   PRO K   5 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE K  10 " --> pdb=" O   PHE K   7 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 13 through 17
    Processing helix  chain 'K' and resid 37 through 48
    Processing helix  chain 'K' and resid 49 through 51
      No H-bonds generated for 'chain 'K' and resid 49 through 51'
    Processing helix  chain 'K' and resid 85 through 98
    Processing helix  chain 'K' and resid 101 through 116
      removed outlier: 3.743A  pdb=" N   MET K 115 " --> pdb=" O   MET K 111 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   VAL K 116 " --> pdb=" O   GLU K 112 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 119 through 123
      removed outlier: 3.973A  pdb=" N   LEU K 122 " --> pdb=" O   VAL K 119 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   THR K 123 " --> pdb=" O   ASP K 120 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 119 through 123'
    Processing helix  chain 'K' and resid 141 through 151
    Processing helix  chain 'K' and resid 152 through 154
      No H-bonds generated for 'chain 'K' and resid 152 through 154'
    Processing helix  chain 'K' and resid 162 through 172
      removed outlier: 3.851A  pdb=" N   PHE K 166 " --> pdb=" O   GLY K 162 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 173 through 176
    Processing helix  chain 'K' and resid 214 through 223
      removed outlier: 3.922A  pdb=" N   ALA K 221 " --> pdb=" O   TYR K 217 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 245 through 264
      removed outlier: 4.462A  pdb=" N   GLY K 250 " --> pdb=" O   ILE K 246 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   PHE K 251 " --> pdb=" O   GLN K 247 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 314 through 326
      removed outlier: 3.751A  pdb=" N   PHE K 318 " --> pdb=" O   ASN K 314 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 327 through 329
      No H-bonds generated for 'chain 'K' and resid 327 through 329'
    Processing helix  chain 'K' and resid 330 through 338
      removed outlier: 3.535A  pdb=" N   ARG K 334 " --> pdb=" O   PRO K 330 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   SER K 338 " --> pdb=" O   ARG K 334 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 339 through 344
    Processing helix  chain 'K' and resid 377 through 381
      removed outlier: 4.068A  pdb=" N   TYR K 381 " --> pdb=" O   LEU K 378 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 382 through 393
      removed outlier: 3.636A  pdb=" N   ARG K 386 " --> pdb=" O   ASN K 382 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   LYS K 391 " --> pdb=" O   ALA K 387 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 394 through 396
      No H-bonds generated for 'chain 'K' and resid 394 through 396'
    Processing helix  chain 'K' and resid 413 through 426
    Processing helix  chain 'K' and resid 454 through 471
    Processing helix  chain 'K' and resid 518 through 537
      removed outlier: 4.165A  pdb=" N   ASN K 536 " --> pdb=" O   ASN K 532 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLY K 537 " --> pdb=" O   MET K 533 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 539 through 558
      removed outlier: 3.680A  pdb=" N   GLN K 548 " --> pdb=" O   GLN K 544 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 571 through 582
      removed outlier: 3.825A  pdb=" N   ILE K 575 " --> pdb=" O   ARG K 571 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 589 through 593
    Processing helix  chain 'K' and resid 607 through 612
    Processing helix  chain 'K' and resid 616 through 624
    Processing helix  chain 'Q' and resid 64 through 69
      removed outlier: 3.941A  pdb=" N   ARG Q  69 " --> pdb=" O   MET Q  66 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 95 through 105
      removed outlier: 4.079A  pdb=" N   ASN Q 102 " --> pdb=" O   VAL Q  98 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLY Q 105 " --> pdb=" O   TRP Q 101 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 112 through 117
      removed outlier: 4.133A  pdb=" N   TYR Q 117 " --> pdb=" O   PHE Q 113 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 118 through 129
    Processing helix  chain 'Q' and resid 157 through 170
    Processing helix  chain 'Q' and resid 178 through 193
      removed outlier: 5.077A  pdb=" N   GLU Q 186 " --> pdb=" O   TRP Q 182 " (cutoff:3.500A)
      removed outlier: 5.143A  pdb=" N   LEU Q 187 " --> pdb=" O   ILE Q 183 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LYS Q 191 " --> pdb=" O   LEU Q 187 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 194 through 198
      removed outlier: 4.225A  pdb=" N   GLY Q 197 " --> pdb=" O   LYS Q 194 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   THR Q 198 " --> pdb=" O   LEU Q 195 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Q' and resid 194 through 198'
    Processing helix  chain 'Q' and resid 201 through 214
      removed outlier: 3.594A  pdb=" N   VAL Q 214 " --> pdb=" O   GLU Q 210 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 227 through 233
    Processing helix  chain 'Q' and resid 233 through 238
    Processing sheet with id=AA1, first strand: chain 'E' and resid 373 through 374
      removed outlier: 6.659A  pdb=" N   GLN E 373 " --> pdb=" O   LYS K 365 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'E' and resid 480 through 486
      removed outlier: 4.799A  pdb=" N   ILE E 481 " --> pdb=" O   TYR E 497 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ASN E 483 " --> pdb=" O   MET E 495 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   MET E 495 " --> pdb=" O   ASN E 483 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU E 499 " --> pdb=" O   PHE E 519 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 521 through 522
      removed outlier: 3.923A  pdb=" N   TYR E 554 " --> pdb=" O   SER E 522 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   THR E 537 " --> pdb=" O   CYS E 557 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 521 through 522
      removed outlier: 3.923A  pdb=" N   TYR E 554 " --> pdb=" O   SER E 522 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 623 through 627
      removed outlier: 3.859A  pdb=" N   GLY E 618 " --> pdb=" O   VAL E 625 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   GLY E 627 " --> pdb=" O   SER E 616 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   SER E 616 " --> pdb=" O   GLY E 627 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ASN K   2 " --> pdb=" O   THR E 619 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 54 through 55
    Processing sheet with id=AA7, first strand: chain 'K' and resid 128 through 129
    Processing sheet with id=AA8, first strand: chain 'K' and resid 178 through 181
    Processing sheet with id=AA9, first strand: chain 'K' and resid 435 through 437
      removed outlier: 3.721A  pdb=" N   MET K 300 " --> pdb=" O   VAL K 450 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'K' and resid 348 through 350
    Processing sheet with id=AB2, first strand: chain 'Q' and resid 73 through 74
    Processing sheet with id=AB3, first strand: chain 'Q' and resid 131 through 135
      removed outlier: 5.691A  pdb=" N   ILE Q 245 " --> pdb=" O   GLY Q 133 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'Q' and resid 143 through 148
      removed outlier: 3.845A  pdb=" N   ARG Q 218 " --> pdb=" O   VAL Q 147 " (cutoff:3.500A)

    402 hydrogen bonds defined for protein.
    1128 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      18 hydrogen bonds
      36 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      10 stacking parallelities
  Total time for adding SS restraints: 3.41

  Time building geometry restraints manager: 2.92 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2799
        1.33 -     1.46: 2522
        1.46 -     1.58: 5173
        1.58 -     1.70: 50
        1.70 -     1.83: 124
  Bond restraints: 10668
  Sorted by residual:
  bond pdb=" CB  TRP E 340 "
       pdb=" CG  TRP E 340 "
    ideal  model  delta    sigma   weight residual
    1.498  1.428  0.070 3.10e-02 1.04e+03 5.09e+00
  bond pdb=" CA  ILE E 479 "
       pdb=" C   ILE E 479 "
    ideal  model  delta    sigma   weight residual
    1.525  1.506  0.019 8.80e-03 1.29e+04 4.60e+00
  bond pdb=" CG  MET E 407 "
       pdb=" SD  MET E 407 "
    ideal  model  delta    sigma   weight residual
    1.803  1.751  0.052 2.50e-02 1.60e+03 4.33e+00
  bond pdb=" CB  ASN E 560 "
       pdb=" CG  ASN E 560 "
    ideal  model  delta    sigma   weight residual
    1.516  1.465  0.051 2.50e-02 1.60e+03 4.09e+00
  bond pdb=" C   ILE E 479 "
       pdb=" N   PRO E 480 "
    ideal  model  delta    sigma   weight residual
    1.333  1.312  0.021 1.17e-02 7.31e+03 3.27e+00
  ... (remaining 10663 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 13620
        1.91 -     3.81: 757
        3.81 -     5.72: 114
        5.72 -     7.63: 23
        7.63 -     9.54: 9
  Bond angle restraints: 14523
  Sorted by residual:
  angle pdb=" N   ILE E 347 "
        pdb=" CA  ILE E 347 "
        pdb=" C   ILE E 347 "
      ideal   model   delta    sigma   weight residual
     112.12  107.85    4.27 8.40e-01 1.42e+00 2.58e+01
  angle pdb=" N   LYS K 393 "
        pdb=" CA  LYS K 393 "
        pdb=" C   LYS K 393 "
      ideal   model   delta    sigma   weight residual
     109.81  119.35   -9.54 2.21e+00 2.05e-01 1.86e+01
  angle pdb=" C3'   G T   2 "
        pdb=" O3'   G T   2 "
        pdb=" P     C T   3 "
      ideal   model   delta    sigma   weight residual
     120.20  126.48   -6.28 1.50e+00 4.44e-01 1.75e+01
  angle pdb=" N   GLY E 367 "
        pdb=" CA  GLY E 367 "
        pdb=" C   GLY E 367 "
      ideal   model   delta    sigma   weight residual
     113.18  122.07   -8.89 2.37e+00 1.78e-01 1.41e+01
  angle pdb=" C   ASN K 153 "
        pdb=" N   ASP K 154 "
        pdb=" CA  ASP K 154 "
      ideal   model   delta    sigma   weight residual
     122.08  127.43   -5.35 1.47e+00 4.63e-01 1.32e+01
  ... (remaining 14518 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.58: 6302
       35.58 -    71.16: 183
       71.16 -   106.74: 16
      106.74 -   142.32: 1
      142.32 -   177.90: 1
  Dihedral angle restraints: 6503
    sinusoidal: 2917
      harmonic: 3586
  Sorted by residual:
  dihedral pdb=" O4'   U T   6 "
           pdb=" C1'   U T   6 "
           pdb=" N1    U T   6 "
           pdb=" C2    U T   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   49.90 -177.90     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" CA  GLU K 399 "
           pdb=" C   GLU K 399 "
           pdb=" N   GLY K 400 "
           pdb=" CA  GLY K 400 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.97   27.03     0      5.00e+00 4.00e-02 2.92e+01
  dihedral pdb=" CA  THR E 366 "
           pdb=" C   THR E 366 "
           pdb=" N   GLY E 367 "
           pdb=" CA  GLY E 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.47   26.53     0      5.00e+00 4.00e-02 2.81e+01
  ... (remaining 6500 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1098
       0.056 -    0.112: 404
       0.112 -    0.168: 94
       0.168 -    0.224: 27
       0.224 -    0.280: 2
  Chirality restraints: 1625
  Sorted by residual:
  chirality pdb=" CB  VAL K 116 "
            pdb=" CA  VAL K 116 "
            pdb=" CG1 VAL K 116 "
            pdb=" CG2 VAL K 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CB  THR K 401 "
            pdb=" CA  THR K 401 "
            pdb=" OG1 THR K 401 "
            pdb=" CG2 THR K 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CG  LEU Q  79 "
            pdb=" CB  LEU Q  79 "
            pdb=" CD1 LEU Q  79 "
            pdb=" CD2 LEU Q  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 1622 not shown)

  Planarity restraints: 1767
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE Q  70 "    0.049 5.00e-02 4.00e+02   7.51e-02 9.03e+00
        pdb=" N   PRO Q  71 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO Q  71 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO Q  71 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE K 605 "   -0.048 5.00e-02 4.00e+02   7.19e-02 8.28e+00
        pdb=" N   PRO K 606 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO K 606 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO K 606 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER K 405 "    0.047 5.00e-02 4.00e+02   7.01e-02 7.86e+00
        pdb=" N   PRO K 406 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO K 406 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO K 406 "    0.040 5.00e-02 4.00e+02
  ... (remaining 1764 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1704
        2.75 -     3.29: 10241
        3.29 -     3.83: 18346
        3.83 -     4.36: 19733
        4.36 -     4.90: 32328
  Nonbonded interactions: 82352
  Sorted by model distance:
  nonbonded pdb=" O   ASP K 553 "
            pdb=" OG1 THR K 557 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   LEU K 114 "
            pdb=" OG1 THR K 117 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   SER E 215 "
            pdb=" OG  SER E 215 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   ALA E 362 "
            pdb=" OG1 THR E 366 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG  SER E 328 "
            pdb=" OE1 GLU E 329 "
     model   vdw
     2.269 3.040
  ... (remaining 82347 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.610
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
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      :  0.008   0.077  10668  Z= 0.493
  Angle     :  1.013   9.537  14523  Z= 0.547
  Chirality :  0.062   0.280   1625
  Planarity :  0.008   0.075   1767
  Dihedral  : 17.049 177.903   4191
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 10.85 %
    Favored  : 89.07 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 12.05 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.69 (0.18), residues: 1226
  helix: -2.72 (0.16), residues: 530
  sheet: -3.72 (0.51), residues: 73
  loop : -3.44 (0.20), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP E 364 
 HIS   0.016   0.002   HIS K  99 
 PHE   0.035   0.003   PHE E 604 
 TYR   0.029   0.003   TYR K 554 
 ARG   0.007   0.001   ARG K 316 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 171
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  246 MET cc_start: 0.7373 (tpp) cc_final: 0.7093 (tpp)
REVERT: E  271 ASN cc_start: 0.8572 (t0) cc_final: 0.8185 (t0)
REVERT: E  473 MET cc_start: 0.5168 (ttm) cc_final: 0.4880 (ttt)
REVERT: E  477 LYS cc_start: 0.8610 (ptpp) cc_final: 0.8172 (ptpp)
REVERT: E  483 ASN cc_start: 0.8372 (t0) cc_final: 0.8082 (t0)
REVERT: E  584 MET cc_start: 0.8118 (ttp) cc_final: 0.7561 (tmm)
REVERT: E  599 MET cc_start: 0.4518 (mmt) cc_final: 0.3800 (mpp)
REVERT: E  659 ARG cc_start: 0.8575 (ttm110) cc_final: 0.8147 (ttm110)
REVERT: K   65 MET cc_start: 0.8627 (mtt) cc_final: 0.8235 (mtm)
REVERT: K  111 MET cc_start: 0.8449 (mtm) cc_final: 0.7766 (mtp)
REVERT: K  114 LEU cc_start: 0.8625 (tp) cc_final: 0.8328 (tp)
REVERT: K  163 LEU cc_start: 0.8817 (tt) cc_final: 0.8383 (tp)
REVERT: K  174 LEU cc_start: 0.8699 (pt) cc_final: 0.8393 (pt)
REVERT: K  217 TYR cc_start: 0.7725 (t80) cc_final: 0.7292 (t80)
REVERT: K  300 MET cc_start: 0.7350 (mtm) cc_final: 0.6749 (mtm)
REVERT: K  331 ILE cc_start: 0.8242 (mp) cc_final: 0.8036 (tp)
REVERT: K  412 MET cc_start: 0.7646 (ptp) cc_final: 0.7430 (ptt)
REVERT: K  459 MET cc_start: 0.8121 (mmt) cc_final: 0.7652 (mmt)
REVERT: K  538 MET cc_start: 0.7336 (ttm) cc_final: 0.6566 (ttm)
REVERT: Q  166 MET cc_start: 0.4454 (mtt) cc_final: 0.3921 (mmt)
REVERT: Q  233 MET cc_start: 0.5615 (mmm) cc_final: 0.5024 (mmm)
  outliers start: 10
  outliers final: 2
  residues processed: 179
  average time/residue: 0.2645
  time to fit residues: 65.4475
Evaluate side-chains
  116 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 1.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    0.3980
   chunk 94 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 63 optimal weight:   20.0000
   chunk 50 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0870
   chunk 37 optimal weight:    0.8980
   chunk 59 optimal weight:    9.9990
   chunk 72 optimal weight:    0.0470
   chunk 113 optimal weight:    4.9990
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
E 206 GLN
E 271 ASN
E 349 ASN
E 447 ASN
E 643 HIS
K 261 ASN
Q 184 HIS
Q 235 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.122076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.099714 restraints weight = 26834.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.098989 restraints weight = 25125.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.100266 restraints weight = 21217.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10668  Z= 0.168
  Angle     :  0.646   7.678  14523  Z= 0.337
  Chirality :  0.043   0.209   1625
  Planarity :  0.005   0.064   1767
  Dihedral  : 14.867 178.076   1738
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.93 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.36 %
    Favored  : 95.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.40 (0.21), residues: 1226
  helix: -1.19 (0.20), residues: 543
  sheet: -3.64 (0.47), residues: 82
  loop : -3.14 (0.22), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 533 
 HIS   0.007   0.001   HIS K 604 
 PHE   0.023   0.001   PHE E 604 
 TYR   0.016   0.001   TYR E 497 
 ARG   0.003   0.000   ARG Q 146 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 1.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  246 MET cc_start: 0.8248 (tpp) cc_final: 0.7874 (tpp)
REVERT: E  473 MET cc_start: 0.6514 (ttm) cc_final: 0.5736 (ttp)
REVERT: E  533 TRP cc_start: 0.7257 (m-10) cc_final: 0.6494 (m-10)
REVERT: E  580 SER cc_start: 0.8839 (p) cc_final: 0.8604 (t)
REVERT: E  584 MET cc_start: 0.6947 (ttp) cc_final: 0.6674 (tmm)
REVERT: E  599 MET cc_start: 0.3956 (mmm) cc_final: 0.3574 (mmt)
REVERT: K  111 MET cc_start: 0.7440 (mtm) cc_final: 0.7198 (mtp)
REVERT: K  300 MET cc_start: 0.6981 (mtm) cc_final: 0.6350 (mtm)
REVERT: K  392 LEU cc_start: 0.7772 (tp) cc_final: 0.7467 (tt)
REVERT: K  459 MET cc_start: 0.7612 (mmt) cc_final: 0.7156 (mmt)
REVERT: Q  166 MET cc_start: 0.4862 (mtt) cc_final: 0.3990 (mmt)
REVERT: Q  217 ARG cc_start: 0.7432 (mtt-85) cc_final: 0.6929 (mtp85)
  outliers start: 1
  outliers final: 0
  residues processed: 166
  average time/residue: 0.2313
  time to fit residues: 54.4729
Evaluate side-chains
  128 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9990
   chunk 80 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 98 optimal weight:    5.9990
   chunk 112 optimal weight:    7.9990
   chunk 109 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
E 242 ASN
** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 648 ASN
E 693 ASN
E 704 ASN
** K 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 561 HIS
K 663 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.115925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.094234 restraints weight = 28214.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.093705 restraints weight = 26505.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.094709 restraints weight = 23497.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071  10668  Z= 0.412
  Angle     :  0.793   8.103  14523  Z= 0.416
  Chirality :  0.049   0.188   1625
  Planarity :  0.006   0.058   1767
  Dihedral  : 14.956 178.692   1738
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  6.67 %
    Favored  : 93.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.22), residues: 1226
  helix: -0.87 (0.21), residues: 552
  sheet: -3.61 (0.47), residues: 94
  loop : -3.16 (0.23), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 364 
 HIS   0.008   0.002   HIS E 643 
 PHE   0.027   0.003   PHE E 646 
 TYR   0.022   0.002   TYR K 556 
 ARG   0.009   0.001   ARG E 659 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  246 MET cc_start: 0.8267 (tpp) cc_final: 0.7798 (tpp)
REVERT: E  279 TYR cc_start: 0.7902 (t80) cc_final: 0.7371 (t80)
REVERT: E  285 MET cc_start: 0.8075 (mtm) cc_final: 0.7676 (ttm)
REVERT: E  473 MET cc_start: 0.6349 (ttm) cc_final: 0.5991 (ttt)
REVERT: E  584 MET cc_start: 0.7282 (ttp) cc_final: 0.6834 (tmm)
REVERT: E  659 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7641 (mtm180)
REVERT: K  111 MET cc_start: 0.7559 (mtm) cc_final: 0.7216 (mtp)
REVERT: K  392 LEU cc_start: 0.7699 (tp) cc_final: 0.7425 (tt)
REVERT: K  415 MET cc_start: 0.8062 (mmt) cc_final: 0.7639 (mmt)
REVERT: K  459 MET cc_start: 0.7787 (mmt) cc_final: 0.7175 (mmt)
REVERT: K  572 MET cc_start: 0.8145 (tpp) cc_final: 0.7017 (tpp)
REVERT: Q  163 ASN cc_start: 0.7713 (t0) cc_final: 0.7211 (t0)
REVERT: Q  166 MET cc_start: 0.4731 (mtt) cc_final: 0.3794 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 136
  average time/residue: 0.2290
  time to fit residues: 45.0347
Evaluate side-chains
  112 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0870
   chunk 118 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.9160

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

Flipped N/Q/H residues before XYZ refinement:
E 408 ASN
E 666 GLN
** K 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.118940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.097450 restraints weight = 27114.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.097279 restraints weight = 28222.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.098184 restraints weight = 24539.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10668  Z= 0.178
  Angle     :  0.623   7.399  14523  Z= 0.322
  Chirality :  0.043   0.162   1625
  Planarity :  0.005   0.058   1767
  Dihedral  : 14.655 177.774   1738
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.23), residues: 1226
  helix: -0.24 (0.22), residues: 544
  sheet: -3.63 (0.49), residues: 83
  loop : -2.82 (0.23), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E 533 
 HIS   0.008   0.001   HIS K  99 
 PHE   0.021   0.001   PHE E 604 
 TYR   0.013   0.001   TYR E 497 
 ARG   0.008   0.000   ARG Q 216 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  246 MET cc_start: 0.8211 (tpp) cc_final: 0.7832 (tpp)
REVERT: E  285 MET cc_start: 0.7783 (mtm) cc_final: 0.7557 (ttm)
REVERT: E  473 MET cc_start: 0.6792 (ttm) cc_final: 0.6531 (ttt)
REVERT: E  483 ASN cc_start: 0.8182 (t0) cc_final: 0.7982 (t0)
REVERT: E  599 MET cc_start: 0.4132 (mmt) cc_final: 0.3679 (tpp)
REVERT: K  130 ASP cc_start: 0.7222 (t0) cc_final: 0.6752 (t70)
REVERT: K  300 MET cc_start: 0.7096 (mtp) cc_final: 0.6764 (mtp)
REVERT: K  392 LEU cc_start: 0.7668 (tp) cc_final: 0.7228 (tt)
REVERT: K  459 MET cc_start: 0.7387 (mmt) cc_final: 0.6934 (mmt)
REVERT: Q  163 ASN cc_start: 0.7566 (t0) cc_final: 0.7063 (t0)
REVERT: Q  166 MET cc_start: 0.4712 (mtt) cc_final: 0.3806 (mmt)
REVERT: Q  211 ARG cc_start: 0.6502 (tpt90) cc_final: 0.5934 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2283
  time to fit residues: 49.5785
Evaluate side-chains
  120 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 123 optimal weight:   10.0000
   chunk 86 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 81 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0570
   chunk 118 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    2.2106

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

Flipped N/Q/H residues before XYZ refinement:
E 467 ASN
** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 693 ASN
** K 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.117700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.096806 restraints weight = 27840.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.096963 restraints weight = 27384.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.097616 restraints weight = 27816.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10668  Z= 0.243
  Angle     :  0.660   8.656  14523  Z= 0.340
  Chirality :  0.045   0.164   1625
  Planarity :  0.005   0.053   1767
  Dihedral  : 14.573 177.558   1738
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.32 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.26 %
    Favored  : 95.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.23), residues: 1226
  helix: -0.04 (0.22), residues: 541
  sheet: -3.83 (0.46), residues: 83
  loop : -2.77 (0.23), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 533 
 HIS   0.004   0.001   HIS Q 184 
 PHE   0.023   0.002   PHE E 604 
 TYR   0.013   0.001   TYR K 556 
 ARG   0.005   0.000   ARG Q 192 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 1.062 
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: E  246 MET cc_start: 0.8250 (tpp) cc_final: 0.7879 (tpp)
REVERT: E  285 MET cc_start: 0.7943 (mtm) cc_final: 0.7711 (ttm)
REVERT: E  580 SER cc_start: 0.8783 (m) cc_final: 0.8000 (t)
REVERT: E  582 GLN cc_start: 0.8357 (pt0) cc_final: 0.8065 (pt0)
REVERT: K  300 MET cc_start: 0.7267 (mtp) cc_final: 0.7062 (mtp)
REVERT: K  392 LEU cc_start: 0.7586 (tp) cc_final: 0.7339 (tt)
REVERT: K  459 MET cc_start: 0.7316 (mmt) cc_final: 0.6934 (mmt)
REVERT: Q  156 MET cc_start: 0.6658 (pmm) cc_final: 0.6122 (ptp)
REVERT: Q  163 ASN cc_start: 0.7592 (t0) cc_final: 0.7077 (t0)
REVERT: Q  166 MET cc_start: 0.4642 (mtt) cc_final: 0.3737 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 145
  average time/residue: 0.2167
  time to fit residues: 45.5124
Evaluate side-chains
  120 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 116 optimal weight:    5.9990
   chunk 120 optimal weight:    6.9990
   chunk 41 optimal weight:    0.1980
   chunk 10 optimal weight:    0.3980
   chunk 98 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 107 optimal weight:   20.0000
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
E 408 ASN
** K 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 150 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.120951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.099281 restraints weight = 27722.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.098874 restraints weight = 27564.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.099877 restraints weight = 25268.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10668  Z= 0.163
  Angle     :  0.607   8.098  14523  Z= 0.310
  Chirality :  0.042   0.192   1625
  Planarity :  0.004   0.052   1767
  Dihedral  : 14.415 177.086   1738
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.67 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.24), residues: 1226
  helix:  0.33 (0.23), residues: 531
  sheet: -3.47 (0.53), residues: 73
  loop : -2.62 (0.23), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP E 533 
 HIS   0.003   0.001   HIS K  99 
 PHE   0.020   0.001   PHE E 604 
 TYR   0.019   0.001   TYR E 644 
 ARG   0.005   0.000   ARG Q 216 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 1.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  246 MET cc_start: 0.8171 (tpp) cc_final: 0.7782 (tpp)
REVERT: E  580 SER cc_start: 0.8923 (m) cc_final: 0.8226 (t)
REVERT: E  599 MET cc_start: 0.3890 (mmt) cc_final: 0.3541 (tpp)
REVERT: K  300 MET cc_start: 0.7168 (mtp) cc_final: 0.6925 (mtp)
REVERT: Q  150 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.8024 (p0)
REVERT: Q  163 ASN cc_start: 0.7907 (t0) cc_final: 0.7349 (t0)
REVERT: Q  166 MET cc_start: 0.4388 (mtt) cc_final: 0.3568 (mmt)
REVERT: Q  211 ARG cc_start: 0.6611 (tpt90) cc_final: 0.6071 (tpm170)
  outliers start: 1
  outliers final: 0
  residues processed: 159
  average time/residue: 0.2101
  time to fit residues: 48.7072
Evaluate side-chains
  125 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 27 optimal weight:    0.3980
   chunk 78 optimal weight:    9.9990
   chunk 6 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   chunk 124 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0270
   chunk 9 optimal weight:    0.7980
   chunk 114 optimal weight:    2.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
E 467 ASN
E 582 GLN
E 704 ASN
K 429 ASN
Q 150 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.121846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.101018 restraints weight = 28126.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.100217 restraints weight = 31632.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.101295 restraints weight = 26799.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.3390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  10668  Z= 0.162
  Angle     :  0.594   8.517  14523  Z= 0.303
  Chirality :  0.041   0.178   1625
  Planarity :  0.004   0.054   1767
  Dihedral  : 14.283 177.045   1738
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.20 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.24), residues: 1226
  helix:  0.28 (0.23), residues: 547
  sheet: -3.27 (0.53), residues: 73
  loop : -2.42 (0.24), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP K 131 
 HIS   0.008   0.001   HIS K  99 
 PHE   0.021   0.001   PHE E 604 
 TYR   0.018   0.001   TYR E 361 
 ARG   0.003   0.000   ARG Q 211 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 150
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  246 MET cc_start: 0.8124 (tpp) cc_final: 0.7792 (tpp)
REVERT: E  580 SER cc_start: 0.8934 (m) cc_final: 0.8198 (t)
REVERT: K  300 MET cc_start: 0.7180 (mtp) cc_final: 0.6894 (mtp)
REVERT: K  412 MET cc_start: 0.6543 (mtm) cc_final: 0.6076 (mpp)
REVERT: K  556 TYR cc_start: 0.8577 (t80) cc_final: 0.8356 (t80)
REVERT: K  572 MET cc_start: 0.7980 (mmm) cc_final: 0.7434 (tpp)
REVERT: Q   78 GLN cc_start: 0.7644 (mp10) cc_final: 0.7423 (mp10)
REVERT: Q  156 MET cc_start: 0.6527 (pmm) cc_final: 0.5976 (ptp)
REVERT: Q  163 ASN cc_start: 0.7774 (t0) cc_final: 0.7269 (t0)
REVERT: Q  166 MET cc_start: 0.4467 (mtt) cc_final: 0.3574 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2045
  time to fit residues: 45.6011
Evaluate side-chains
  124 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 39 optimal weight:   20.0000
   chunk 4 optimal weight:    7.9990
   chunk 80 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 124 optimal weight:    9.9990
   chunk 79 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9990
   chunk 1 optimal weight:    0.4980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
E 467 ASN
Q 150 ASN
Q 244 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.121114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.099730 restraints weight = 27124.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.099349 restraints weight = 26371.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.100449 restraints weight = 23769.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10668  Z= 0.164
  Angle     :  0.593   9.141  14523  Z= 0.303
  Chirality :  0.042   0.180   1625
  Planarity :  0.004   0.054   1767
  Dihedral  : 14.193 177.052   1738
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.76 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.24), residues: 1226
  helix:  0.38 (0.23), residues: 547
  sheet: -3.28 (0.50), residues: 81
  loop : -2.35 (0.24), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP K 131 
 HIS   0.002   0.001   HIS K  99 
 PHE   0.021   0.001   PHE E 604 
 TYR   0.017   0.001   TYR E 361 
 ARG   0.006   0.000   ARG K  94 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 1.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  246 MET cc_start: 0.8167 (tpp) cc_final: 0.7797 (tpp)
REVERT: E  580 SER cc_start: 0.8927 (m) cc_final: 0.8181 (t)
REVERT: E  599 MET cc_start: 0.3782 (mmt) cc_final: 0.3419 (tpp)
REVERT: K  300 MET cc_start: 0.7064 (mtp) cc_final: 0.6757 (mtp)
REVERT: K  412 MET cc_start: 0.6456 (mtm) cc_final: 0.6012 (mpp)
REVERT: K  572 MET cc_start: 0.7927 (mmm) cc_final: 0.7438 (tpp)
REVERT: Q   78 GLN cc_start: 0.7640 (mp10) cc_final: 0.7422 (mp10)
REVERT: Q  156 MET cc_start: 0.6794 (pmm) cc_final: 0.6293 (ptp)
REVERT: Q  163 ASN cc_start: 0.7796 (t0) cc_final: 0.7304 (t0)
REVERT: Q  166 MET cc_start: 0.4468 (mtt) cc_final: 0.3580 (mmt)
REVERT: Q  199 MET cc_start: 0.7144 (ptm) cc_final: 0.6923 (ptm)
  outliers start: 1
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2289
  time to fit residues: 48.7735
Evaluate side-chains
  127 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 85 optimal weight:    0.4980
   chunk 62 optimal weight:    9.9990
   chunk 14 optimal weight:    5.9990
   chunk 67 optimal weight:    7.9990
   chunk 120 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 59 optimal weight:    4.9990
   chunk 83 optimal weight:    8.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.120800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.099941 restraints weight = 27478.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.099613 restraints weight = 29732.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.100685 restraints weight = 26475.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.3651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10668  Z= 0.192
  Angle     :  0.615   9.391  14523  Z= 0.315
  Chirality :  0.043   0.180   1625
  Planarity :  0.004   0.054   1767
  Dihedral  : 14.172 176.955   1738
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.37 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.24), residues: 1226
  helix:  0.32 (0.22), residues: 549
  sheet: -3.08 (0.54), residues: 74
  loop : -2.36 (0.24), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP E 533 
 HIS   0.003   0.001   HIS Q 184 
 PHE   0.021   0.001   PHE E 604 
 TYR   0.025   0.002   TYR K 482 
 ARG   0.003   0.000   ARG K  94 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  246 MET cc_start: 0.8233 (tpp) cc_final: 0.7854 (tpp)
REVERT: E  571 MET cc_start: 0.8615 (mtp) cc_final: 0.8352 (mtp)
REVERT: E  580 SER cc_start: 0.8830 (m) cc_final: 0.8143 (t)
REVERT: E  599 MET cc_start: 0.3800 (mmt) cc_final: 0.3471 (tpp)
REVERT: Q   78 GLN cc_start: 0.7618 (mp10) cc_final: 0.7400 (mp10)
REVERT: Q  163 ASN cc_start: 0.7723 (t0) cc_final: 0.7289 (t0)
REVERT: Q  166 MET cc_start: 0.4438 (mtt) cc_final: 0.3518 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 151
  average time/residue: 0.2060
  time to fit residues: 46.2432
Evaluate side-chains
  127 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 67 optimal weight:    0.3980
   chunk 82 optimal weight:    0.1980
   chunk 104 optimal weight:   10.0000
   chunk 76 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0870
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.123205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.101522 restraints weight = 27312.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.100800 restraints weight = 28854.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.102085 restraints weight = 23670.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.3898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  10668  Z= 0.152
  Angle     :  0.592   9.577  14523  Z= 0.301
  Chirality :  0.041   0.171   1625
  Planarity :  0.004   0.055   1767
  Dihedral  : 14.083 176.830   1738
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.19 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.24), residues: 1226
  helix:  0.39 (0.22), residues: 551
  sheet: -2.98 (0.54), residues: 71
  loop : -2.26 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP E 533 
 HIS   0.003   0.001   HIS E 462 
 PHE   0.026   0.001   PHE E 646 
 TYR   0.017   0.001   TYR E 497 
 ARG   0.006   0.000   ARG E 227 

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 1.142 
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: E  246 MET cc_start: 0.8149 (tpp) cc_final: 0.7779 (tpp)
REVERT: E  571 MET cc_start: 0.8577 (mtp) cc_final: 0.8351 (mtp)
REVERT: E  580 SER cc_start: 0.8937 (m) cc_final: 0.8130 (t)
REVERT: E  599 MET cc_start: 0.3817 (mmt) cc_final: 0.3466 (tpp)
REVERT: K  572 MET cc_start: 0.7942 (mmm) cc_final: 0.7203 (tpp)
REVERT: Q   78 GLN cc_start: 0.7649 (mp10) cc_final: 0.7396 (mp10)
REVERT: Q  163 ASN cc_start: 0.7753 (t0) cc_final: 0.7306 (t0)
REVERT: Q  166 MET cc_start: 0.4439 (mtt) cc_final: 0.3547 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2085
  time to fit residues: 46.8896
Evaluate side-chains
  125 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 117 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 54 optimal weight:    0.4980
   chunk 67 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 82 optimal weight:    0.0670
   chunk 31 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    0.6722

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

Flipped N/Q/H residues before XYZ refinement:
** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.123020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.101060 restraints weight = 27185.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.101201 restraints weight = 23298.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.101951 restraints weight = 21414.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.4038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  10668  Z= 0.158
  Angle     :  0.605  10.482  14523  Z= 0.304
  Chirality :  0.041   0.172   1625
  Planarity :  0.004   0.055   1767
  Dihedral  : 14.015 176.880   1738
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.19 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.24), residues: 1226
  helix:  0.38 (0.22), residues: 552
  sheet: -3.03 (0.53), residues: 71
  loop : -2.19 (0.24), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP K 131 
 HIS   0.006   0.001   HIS K 604 
 PHE   0.023   0.001   PHE E 646 
 TYR   0.016   0.001   TYR E 497 
 ARG   0.002   0.000   ARG E 575 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2710.98 seconds
wall clock time: 49 minutes 59.52 seconds (2999.52 seconds total)