Starting phenix.real_space_refine
on Tue Mar  3 18:37:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f4u_31454/03_2026/7f4u_31454.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f4u_31454/03_2026/7f4u_31454.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f4u_31454/03_2026/7f4u_31454.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f4u_31454/03_2026/7f4u_31454.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f4u_31454/03_2026/7f4u_31454.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f4u_31454/03_2026/7f4u_31454.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
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: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    5059      2.51       5
     N    1476      2.21       5
     O    1510      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8079
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 3416
          Classifications: {'peptide': 440}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 24, 'TRANS': 415}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 3298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 514, 3298
          Classifications: {'peptide': 514}
          Incomplete info: {'truncation_to_alanine': 232}
          Link IDs: {'PTRANS': 12, 'TRANS': 501}
          Chain breaks: 6
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 760
          Unresolved non-hydrogen angles: 992
          Unresolved non-hydrogen dihedrals: 600
          Unresolved non-hydrogen chiralities: 61
          Planarities with less than four sites: {'UNK:plan-1': 50, 'PHE:plan': 7, 'TYR:plan': 4, 'ASP:plan': 14, 'GLU:plan': 20, 'GLN:plan1': 10, 'ARG:plan': 8, 'HIS:plan': 6, 'TRP:plan': 4, 'ASN:plan1': 5}
          Unresolved non-hydrogen planarities: 403
    Chain: "B"
      Number of atoms: 880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 880
          Classifications: {'peptide': 176}
          Incomplete info: {'truncation_to_alanine': 176}
          Link IDs: {'TRANS': 175}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 352
          Unresolved non-hydrogen angles: 528
          Unresolved non-hydrogen dihedrals: 176
          Planarities with less than four sites: {'UNK:plan-1': 176}
          Unresolved non-hydrogen planarities: 176
    Chain: "C"
      Number of atoms: 485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 485
          Classifications: {'peptide': 97}
          Incomplete info: {'truncation_to_alanine': 97}
          Link IDs: {'TRANS': 96}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 194
          Unresolved non-hydrogen angles: 291
          Unresolved non-hydrogen dihedrals: 97
          Planarities with less than four sites: {'UNK:plan-1': 97}
          Unresolved non-hydrogen planarities: 97
  Time building chain proxies: 1.87, per 1000 atoms: 0.23
  Number of scatterers: 8079
  At special positions: 0
  Unit cell: (78.11, 121.98, 189.39, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1510      8.00
     N    1476      7.00
     C    5059      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: 0.93
  Conformation dependent library (CDL) restraints added in 298.9 milliseconds
  

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2364

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 0 sheets defined
      105.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 21
    Processing helix  chain 'A' and resid 24 through 38
    Processing helix  chain 'A' and resid 48 through 56
    Processing helix  chain 'A' and resid 58 through 68
    Processing helix  chain 'A' and resid 73 through 78
      removed outlier: 3.957A  pdb=" N   LEU A  78 " --> pdb=" O   TRP A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 93
      removed outlier: 3.564A  pdb=" N   PHE A  91 " --> pdb=" O   TRP A  87 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   GLU A  93 " --> pdb=" O   SER A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 110
      removed outlier: 4.442A  pdb=" N   PHE A 100 " --> pdb=" O   ALA A  96 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU A 101 " --> pdb=" O   ASP A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 130
      removed outlier: 3.602A  pdb=" N   GLU A 130 " --> pdb=" O   ARG A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 140
      removed outlier: 4.423A  pdb=" N   GLN A 140 " --> pdb=" O   MET A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 167
      removed outlier: 6.424A  pdb=" N   VAL A 160 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   VAL A 161 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
      Proline residue:  A 164  - end of helix
      removed outlier: 3.968A  pdb=" N   LEU A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 176
    Processing helix  chain 'A' and resid 183 through 203
      removed outlier: 4.074A  pdb=" N   LEU A 203 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 225
      removed outlier: 3.560A  pdb=" N   LYS A 220 " --> pdb=" O   GLN A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 243
      Proline residue:  A 236  - end of helix
      removed outlier: 4.323A  pdb=" N   GLN A 243 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 258
      removed outlier: 3.506A  pdb=" N   GLN A 258 " --> pdb=" O   ARG A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 274
    Processing helix  chain 'A' and resid 277 through 286
      removed outlier: 3.966A  pdb=" N   GLY A 286 " --> pdb=" O   SER A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 306
    Processing helix  chain 'A' and resid 313 through 326
    Processing helix  chain 'A' and resid 331 through 349
    Processing helix  chain 'A' and resid 353 through 370
      removed outlier: 4.440A  pdb=" N   GLN A 370 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 395
      removed outlier: 4.072A  pdb=" N   CYS A 393 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   LEU A 395 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 416
      removed outlier: 4.053A  pdb=" N   ARG A 403 " --> pdb=" O   LEU A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 430
      removed outlier: 3.544A  pdb=" N   LYS A 425 " --> pdb=" O   GLY A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 449
    Processing helix  chain 'B' and resid 167 through 185
    Processing helix  chain 'B' and resid 193 through 197
    Processing helix  chain 'B' and resid 198 through 208
      removed outlier: 3.813A  pdb=" N   UNK B 202 " --> pdb=" O   UNK B 198 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   UNK B 208 " --> pdb=" O   UNK B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 222
      removed outlier: 3.536A  pdb=" N   UNK B 216 " --> pdb=" O   UNK B 213 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   UNK B 217 " --> pdb=" O   UNK B 214 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   UNK B 222 " --> pdb=" O   UNK B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 261
      removed outlier: 4.687A  pdb=" N   ASP B 249 " --> pdb=" O   PHE B 245 " (cutoff:3.500A)
      removed outlier: 5.811A  pdb=" N   GLU B 250 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLN B 251 " --> pdb=" O   MET B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 280
      removed outlier: 3.998A  pdb=" N   ALA B 269 " --> pdb=" O   GLU B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 301
    Processing helix  chain 'B' and resid 302 through 305
    Processing helix  chain 'B' and resid 309 through 325
      removed outlier: 3.525A  pdb=" N   LEU B 318 " --> pdb=" O   VAL B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 341
      removed outlier: 3.819A  pdb=" N   ALA B 335 " --> pdb=" O   PRO B 331 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL B 337 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 359
    Processing helix  chain 'B' and resid 368 through 385
      removed outlier: 3.602A  pdb=" N   ASP B 372 " --> pdb=" O   LYS B 368 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU B 381 " --> pdb=" O   SER B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 390
      removed outlier: 3.797A  pdb=" N   ASN B 390 " --> pdb=" O   PRO B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 411
      removed outlier: 3.674A  pdb=" N   THR B 400 " --> pdb=" O   GLY B 396 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU B 411 " --> pdb=" O   TYR B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 420
    Processing helix  chain 'B' and resid 421 through 436
      removed outlier: 3.864A  pdb=" N   GLN B 434 " --> pdb=" O   LYS B 430 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU B 436 " --> pdb=" O   LEU B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 495
      removed outlier: 3.987A  pdb=" N   LEU B 487 " --> pdb=" O   ARG B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 515
      removed outlier: 3.537A  pdb=" N   LEU B 511 " --> pdb=" O   HIS B 507 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   SER B 515 " --> pdb=" O   LEU B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 535
      removed outlier: 3.697A  pdb=" N   ALA B 522 " --> pdb=" O   TYR B 518 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLY B 535 " --> pdb=" O   THR B 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 549 through 568
    Processing helix  chain 'B' and resid 617 through 641
    Processing helix  chain 'B' and resid 643 through 647
      removed outlier: 3.760A  pdb=" N   CYS B 646 " --> pdb=" O   LYS B 643 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LEU B 647 " --> pdb=" O   ASP B 644 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 643 through 647'
    Processing helix  chain 'B' and resid 648 through 660
      removed outlier: 3.657A  pdb=" N   ALA B 652 " --> pdb=" O   LEU B 648 " (cutoff:3.500A)
      Proline residue:  B 655  - end of helix
    Processing helix  chain 'B' and resid 665 through 683
    Processing helix  chain 'B' and resid 687 through 693
      removed outlier: 3.642A  pdb=" N   ILE B 691 " --> pdb=" O   LEU B 687 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ASN B 692 " --> pdb=" O   GLN B 688 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 695 through 708
    Processing helix  chain 'B' and resid 715 through 723
      removed outlier: 4.281A  pdb=" N   LEU B 719 " --> pdb=" O   THR B 715 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 727 through 729
      No H-bonds generated for 'chain 'B' and resid 727 through 729'
    Processing helix  chain 'B' and resid 730 through 748
      removed outlier: 5.027A  pdb=" N   ASP B 736 " --> pdb=" O   PRO B 732 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   VAL B 737 " --> pdb=" O   LEU B 733 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LEU B 745 " --> pdb=" O   VAL B 741 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASP B 746 " --> pdb=" O   LEU B 742 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   PHE B 748 " --> pdb=" O   THR B 744 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 751 through 771
      removed outlier: 3.736A  pdb=" N   VAL B 757 " --> pdb=" O   ALA B 753 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 858 through 873
    Processing helix  chain 'B' and resid 878 through 892
      removed outlier: 4.064A  pdb=" N   UNK B 882 " --> pdb=" O   UNK B 878 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 898 through 915
    Processing helix  chain 'B' and resid 924 through 935
    Processing helix  chain 'B' and resid 939 through 954
    Processing helix  chain 'B' and resid 978 through 991
      removed outlier: 4.492A  pdb=" N   UNK B 990 " --> pdb=" O   UNK B 986 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 995 through 1003
      removed outlier: 3.800A  pdb=" N   UNK B 999 " --> pdb=" O   UNK B 995 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1022 through 1028
    Processing helix  chain 'B' and resid 1046 through 1051
      removed outlier: 3.510A  pdb=" N   UNK B1051 " --> pdb=" O   UNK B1047 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1059 through 1067
    Processing helix  chain 'B' and resid 1068 through 1070
      No H-bonds generated for 'chain 'B' and resid 1068 through 1070'
    Processing helix  chain 'C' and resid 42 through 48
      removed outlier: 4.769A  pdb=" N   UNK C  47 " --> pdb=" O   UNK C  43 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   UNK C  48 " --> pdb=" O   UNK C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 76
      removed outlier: 4.543A  pdb=" N   UNK C  76 " --> pdb=" O   UNK C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 111
    Processing helix  chain 'C' and resid 122 through 131
    Processing helix  chain 'C' and resid 144 through 163
    Processing helix  chain 'C' and resid 177 through 188
      removed outlier: 4.750A  pdb=" N   UNK C 186 " --> pdb=" O   UNK C 182 " (cutoff:3.500A)

    596 hydrogen bonds defined for protein.
    1764 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: 1.42

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2841
        1.34 -     1.46: 1508
        1.46 -     1.58: 3756
        1.58 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 8159
  Sorted by residual:
  bond pdb=" N   ASP B 540 "
       pdb=" CA  ASP B 540 "
    ideal  model  delta    sigma   weight residual
    1.455  1.482 -0.027 1.21e-02 6.83e+03 5.07e+00
  bond pdb=" N   GLU B 539 "
       pdb=" CA  GLU B 539 "
    ideal  model  delta    sigma   weight residual
    1.457  1.482 -0.025 1.29e-02 6.01e+03 3.65e+00
  bond pdb=" CA  ASP B 540 "
       pdb=" CB  ASP B 540 "
    ideal  model  delta    sigma   weight residual
    1.533  1.509  0.024 1.72e-02 3.38e+03 1.95e+00
  bond pdb=" CA  VAL B 306 "
       pdb=" CB  VAL B 306 "
    ideal  model  delta    sigma   weight residual
    1.540  1.521  0.019 1.36e-02 5.41e+03 1.95e+00
  bond pdb=" C   PRO A 400 "
       pdb=" N   PRO A 401 "
    ideal  model  delta    sigma   weight residual
    1.334  1.366 -0.032 2.34e-02 1.83e+03 1.91e+00
  ... (remaining 8154 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 10675
        1.88 -     3.75: 387
        3.75 -     5.63: 63
        5.63 -     7.51: 17
        7.51 -     9.38: 4
  Bond angle restraints: 11146
  Sorted by residual:
  angle pdb=" N   PRO B 331 "
        pdb=" CA  PRO B 331 "
        pdb=" CB  PRO B 331 "
      ideal   model   delta    sigma   weight residual
     103.46  110.27   -6.81 9.30e-01 1.16e+00 5.36e+01
  angle pdb=" N   PRO B 302 "
        pdb=" CA  PRO B 302 "
        pdb=" CB  PRO B 302 "
      ideal   model   delta    sigma   weight residual
     103.51  110.24   -6.73 9.60e-01 1.09e+00 4.91e+01
  angle pdb=" N   PRO B 345 "
        pdb=" CA  PRO B 345 "
        pdb=" CB  PRO B 345 "
      ideal   model   delta    sigma   weight residual
     103.25  110.49   -7.24 1.05e+00 9.07e-01 4.75e+01
  angle pdb=" N   PRO B 262 "
        pdb=" CA  PRO B 262 "
        pdb=" CB  PRO B 262 "
      ideal   model   delta    sigma   weight residual
     103.25  110.23   -6.98 1.05e+00 9.07e-01 4.42e+01
  angle pdb=" N   PRO B 732 "
        pdb=" CA  PRO B 732 "
        pdb=" CB  PRO B 732 "
      ideal   model   delta    sigma   weight residual
     103.39  110.17   -6.78 1.08e+00 8.57e-01 3.94e+01
  ... (remaining 11141 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4521
       17.95 -    35.90: 343
       35.90 -    53.85: 56
       53.85 -    71.80: 16
       71.80 -    89.75: 6
  Dihedral angle restraints: 4942
    sinusoidal: 1355
      harmonic: 3587
  Sorted by residual:
  dihedral pdb=" CA  VAL B 364 "
           pdb=" C   VAL B 364 "
           pdb=" N   VAL B 365 "
           pdb=" CA  VAL B 365 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.58   34.42     0      5.00e+00 4.00e-02 4.74e+01
  dihedral pdb=" CA  PHE A 180 "
           pdb=" C   PHE A 180 "
           pdb=" N   PRO A 181 "
           pdb=" CA  PRO A 181 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.60   34.40     0      5.00e+00 4.00e-02 4.73e+01
  dihedral pdb=" CA  LYS B 281 "
           pdb=" C   LYS B 281 "
           pdb=" N   LYS B 282 "
           pdb=" CA  LYS B 282 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.13   29.87     0      5.00e+00 4.00e-02 3.57e+01
  ... (remaining 4939 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1136
       0.051 -    0.101: 247
       0.101 -    0.152: 24
       0.152 -    0.203: 0
       0.203 -    0.254: 6
  Chirality restraints: 1413
  Sorted by residual:
  chirality pdb=" CA  PRO B 331 "
            pdb=" N   PRO B 331 "
            pdb=" C   PRO B 331 "
            pdb=" CB  PRO B 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA  PRO B 302 "
            pdb=" N   PRO B 302 "
            pdb=" C   PRO B 302 "
            pdb=" CB  PRO B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  PRO B 772 "
            pdb=" N   PRO B 772 "
            pdb=" C   PRO B 772 "
            pdb=" CB  PRO B 772 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1410 not shown)

  Planarity restraints: 1469
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 180 "    0.064 5.00e-02 4.00e+02   9.64e-02 1.49e+01
        pdb=" N   PRO A 181 "   -0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO A 181 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 181 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 385 "   -0.041 5.00e-02 4.00e+02   6.18e-02 6.11e+00
        pdb=" N   PRO B 386 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO B 386 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 386 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 400 "   -0.033 5.00e-02 4.00e+02   4.99e-02 3.99e+00
        pdb=" N   PRO A 401 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 401 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 401 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1466 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 133
        2.65 -     3.21: 8929
        3.21 -     3.77: 12493
        3.77 -     4.34: 15878
        4.34 -     4.90: 23816
  Nonbonded interactions: 61249
  Sorted by model distance:
  nonbonded pdb=" O   SER A 346 "
            pdb=" ND1 HIS A 351 "
     model   vdw
     2.087 3.120
  nonbonded pdb=" O   GLU B 568 "
            pdb=" NZ  LYS B 659 "
     model   vdw
     2.135 3.120
  nonbonded pdb=" O   VAL A 199 "
            pdb=" OG  SER A 202 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" O   LEU A 133 "
            pdb=" N   VAL A 135 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" O   ARG A 358 "
            pdb=" OG  SER A 361 "
     model   vdw
     2.214 3.040
  ... (remaining 61244 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:             3.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.210
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6152
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      :  0.004   0.032   8159  Z= 0.222
  Angle     :  0.874   9.382  11146  Z= 0.493
  Chirality :  0.042   0.254   1413
  Planarity :  0.005   0.096   1469
  Dihedral  : 14.593  89.746   2578
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 18.00
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  : 14.38 %
    Favored  : 85.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.17 (0.21), residues: 890
  helix: -2.52 (0.17), residues: 613
  sheet:  None (None), residues: 0
  loop : -5.38 (0.23), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 170 
 TYR   0.021   0.002   TYR B 498 
 PHE   0.019   0.001   PHE A 297 
 TRP   0.007   0.001   TRP A 343 
 HIS   0.007   0.001   HIS A 351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 8159)
  covalent geometry    : angle       0.87365 (11146)
  hydrogen bonds       : bond        0.17735 (  596)
  hydrogen bonds       : angle       6.72060 ( 1764)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.261 
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: A   12 VAL cc_start: 0.7831 (t) cc_final: 0.7583 (t)
REVERT: A  107 ILE cc_start: 0.6438 (pt) cc_final: 0.6070 (pt)
REVERT: A  118 MET cc_start: 0.3965 (tpt) cc_final: 0.3653 (tpt)
REVERT: A  128 LEU cc_start: 0.6937 (mt) cc_final: 0.6434 (mt)
REVERT: A  151 LEU cc_start: 0.6727 (tp) cc_final: 0.6315 (tp)
REVERT: A  253 TRP cc_start: 0.6033 (m-10) cc_final: 0.5779 (m-10)
REVERT: A  291 LYS cc_start: 0.6070 (ttmt) cc_final: 0.5772 (ttmt)
REVERT: A  292 ASN cc_start: 0.7909 (t0) cc_final: 0.7653 (t0)
REVERT: A  331 LEU cc_start: 0.7969 (tp) cc_final: 0.7701 (tt)
REVERT: A  334 GLN cc_start: 0.5620 (tm-30) cc_final: 0.5203 (tm-30)
REVERT: A  337 LYS cc_start: 0.7167 (mtmm) cc_final: 0.6882 (ttmm)
REVERT: B  354 VAL cc_start: 0.7453 (p) cc_final: 0.6217 (p)
REVERT: B  380 SER cc_start: 0.7770 (m) cc_final: 0.7294 (p)
REVERT: B  389 MET cc_start: 0.5060 (mtp) cc_final: 0.4819 (mtp)
REVERT: B  422 VAL cc_start: 0.7892 (t) cc_final: 0.7685 (p)
REVERT: B  427 ARG cc_start: 0.7217 (mmm160) cc_final: 0.7001 (mmm160)
REVERT: B  524 MET cc_start: 0.6972 (ttm) cc_final: 0.6608 (ttm)
REVERT: B  525 ILE cc_start: 0.8146 (mm) cc_final: 0.7924 (mm)
REVERT: B  564 TYR cc_start: 0.5305 (m-10) cc_final: 0.5055 (m-10)
REVERT: B  691 ILE cc_start: 0.8153 (mm) cc_final: 0.7921 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 269
  average time/residue: 0.0946
  time to fit residues: 33.3001
Evaluate side-chains
  244 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0040
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
A 140 GLN
A 228 GLN
A 258 GLN
** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 GLN
B 352 ASN
B 434 GLN
B 513 HIS
B 626 GLN
B 663 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.130236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.105967 restraints weight = 22569.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.108718 restraints weight = 15913.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.110764 restraints weight = 12050.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.112387 restraints weight = 9637.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.113638 restraints weight = 7994.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8159  Z= 0.185
  Angle     :  0.788  10.962  11146  Z= 0.391
  Chirality :  0.039   0.198   1413
  Planarity :  0.006   0.096   1469
  Dihedral  :  5.551  33.566   1264
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 12.81 %
    Favored  : 86.85 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  6.00 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.09 (0.25), residues: 890
  helix: -0.86 (0.19), residues: 620
  sheet:  None (None), residues: 0
  loop : -4.91 (0.29), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  49 
 TYR   0.026   0.002   TYR B 498 
 PHE   0.024   0.002   PHE B 417 
 TRP   0.008   0.001   TRP A  74 
 HIS   0.006   0.001   HIS A 351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8159)
  covalent geometry    : angle       0.78755 (11146)
  hydrogen bonds       : bond        0.04772 (  596)
  hydrogen bonds       : angle       5.36507 ( 1764)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 254
  time to evaluate  : 0.266 
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   13 ARG cc_start: 0.8559 (mmt-90) cc_final: 0.8172 (mmt180)
REVERT: A   27 HIS cc_start: 0.8480 (m90) cc_final: 0.8269 (m90)
REVERT: A   52 GLU cc_start: 0.8367 (pt0) cc_final: 0.7759 (pp20)
REVERT: A   59 PHE cc_start: 0.8104 (t80) cc_final: 0.7838 (t80)
REVERT: A   66 LEU cc_start: 0.8142 (tp) cc_final: 0.7929 (pp)
REVERT: A   84 GLU cc_start: 0.8629 (pm20) cc_final: 0.8291 (pm20)
REVERT: A  104 MET cc_start: 0.8578 (mmm) cc_final: 0.8179 (mmm)
REVERT: A  108 GLU cc_start: 0.8374 (pt0) cc_final: 0.8018 (pt0)
REVERT: A  120 MET cc_start: 0.8555 (mtm) cc_final: 0.8306 (ptp)
REVERT: A  186 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8010 (ttp80)
REVERT: A  190 GLU cc_start: 0.8315 (tt0) cc_final: 0.7553 (tt0)
REVERT: A  252 CYS cc_start: 0.8580 (t) cc_final: 0.8195 (p)
REVERT: A  256 VAL cc_start: 0.8809 (m) cc_final: 0.8537 (p)
REVERT: A  261 ASP cc_start: 0.7855 (m-30) cc_final: 0.7627 (m-30)
REVERT: A  265 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7320 (tm-30)
REVERT: A  293 LYS cc_start: 0.7747 (tttp) cc_final: 0.7443 (tttp)
REVERT: A  297 PHE cc_start: 0.7346 (m-80) cc_final: 0.6999 (m-80)
REVERT: A  305 PHE cc_start: 0.6853 (m-10) cc_final: 0.6585 (m-10)
REVERT: A  319 LEU cc_start: 0.8678 (tt) cc_final: 0.8279 (tt)
REVERT: A  359 HIS cc_start: 0.8207 (t70) cc_final: 0.7637 (t70)
REVERT: A  362 LYS cc_start: 0.9086 (mtmm) cc_final: 0.8869 (mtmm)
REVERT: A  388 MET cc_start: 0.6857 (ppp) cc_final: 0.6576 (ppp)
REVERT: A  404 ARG cc_start: 0.8815 (mmt180) cc_final: 0.8463 (mmt180)
REVERT: A  448 ASP cc_start: 0.8585 (t70) cc_final: 0.8329 (t70)
REVERT: B  358 PHE cc_start: 0.8769 (m-10) cc_final: 0.8468 (m-10)
REVERT: B  385 LEU cc_start: 0.8487 (pp) cc_final: 0.8205 (pp)
REVERT: B  387 ARG cc_start: 0.8674 (ptt-90) cc_final: 0.8346 (ptt-90)
REVERT: B  389 MET cc_start: 0.8008 (mtp) cc_final: 0.7698 (mtp)
REVERT: B  409 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8175 (tppp)
REVERT: B  414 LYS cc_start: 0.8401 (tppt) cc_final: 0.8050 (tppt)
REVERT: B  426 GLN cc_start: 0.7660 (mt0) cc_final: 0.7350 (mt0)
REVERT: B  427 ARG cc_start: 0.8609 (mmm160) cc_final: 0.8292 (mmm160)
REVERT: B  486 MET cc_start: 0.7743 (mpp) cc_final: 0.7099 (mpp)
REVERT: B  526 LEU cc_start: 0.8883 (mm) cc_final: 0.8440 (mm)
REVERT: B  549 ASN cc_start: 0.8495 (m-40) cc_final: 0.7887 (t0)
REVERT: B  564 TYR cc_start: 0.7402 (m-10) cc_final: 0.7182 (m-10)
REVERT: B  631 LEU cc_start: 0.9361 (mt) cc_final: 0.9161 (mm)
REVERT: B  636 GLN cc_start: 0.8351 (mm110) cc_final: 0.8131 (mm110)
REVERT: B  641 LEU cc_start: 0.8584 (tp) cc_final: 0.8124 (tp)
REVERT: B  653 LEU cc_start: 0.8125 (mt) cc_final: 0.7845 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 254
  average time/residue: 0.0924
  time to fit residues: 30.7062
Evaluate side-chains
  236 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 235
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 119 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 86 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 54 optimal weight:    0.1980
   chunk 83 optimal weight:    0.9980
   chunk 120 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 228 GLN
A 258 GLN
A 357 GLN
B 513 HIS
B 623 ASN
B 626 GLN
B 630 GLN
** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.121316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.095602 restraints weight = 22887.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.098281 restraints weight = 16694.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.100327 restraints weight = 12941.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.101913 restraints weight = 10501.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.103138 restraints weight = 8851.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8159  Z= 0.182
  Angle     :  0.758   9.836  11146  Z= 0.376
  Chirality :  0.039   0.154   1413
  Planarity :  0.006   0.095   1469
  Dihedral  :  5.292  32.531   1264
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 12.92 %
    Favored  : 86.85 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  5.67 %
    Favored  : 94.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.27), residues: 890
  helix: -0.09 (0.20), residues: 616
  sheet:  None (None), residues: 0
  loop : -4.58 (0.31), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 329 
 TYR   0.029   0.002   TYR B 498 
 PHE   0.023   0.002   PHE A 297 
 TRP   0.011   0.002   TRP A  74 
 HIS   0.010   0.001   HIS A 351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8159)
  covalent geometry    : angle       0.75800 (11146)
  hydrogen bonds       : bond        0.04260 (  596)
  hydrogen bonds       : angle       5.08292 ( 1764)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 254
  time to evaluate  : 0.261 
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   13 ARG cc_start: 0.8582 (mmt-90) cc_final: 0.7883 (mmt180)
REVERT: A   17 HIS cc_start: 0.8542 (m170) cc_final: 0.8055 (m170)
REVERT: A   27 HIS cc_start: 0.8484 (m90) cc_final: 0.8278 (m90)
REVERT: A   59 PHE cc_start: 0.7950 (t80) cc_final: 0.7657 (t80)
REVERT: A   84 GLU cc_start: 0.8591 (pm20) cc_final: 0.8262 (pm20)
REVERT: A   93 GLU cc_start: 0.6826 (mp0) cc_final: 0.6623 (mp0)
REVERT: A  104 MET cc_start: 0.8631 (mmm) cc_final: 0.8139 (mmm)
REVERT: A  108 GLU cc_start: 0.8368 (pt0) cc_final: 0.7927 (pt0)
REVERT: A  118 MET cc_start: 0.7801 (tpt) cc_final: 0.7342 (tpt)
REVERT: A  186 ARG cc_start: 0.8349 (ttp80) cc_final: 0.7948 (ttp80)
REVERT: A  190 GLU cc_start: 0.8358 (tt0) cc_final: 0.7514 (tt0)
REVERT: A  220 LYS cc_start: 0.8555 (mmpt) cc_final: 0.8143 (mmpt)
REVERT: A  252 CYS cc_start: 0.8519 (t) cc_final: 0.8268 (p)
REVERT: A  265 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7339 (tm-30)
REVERT: A  291 LYS cc_start: 0.7503 (ttmm) cc_final: 0.7301 (ttmm)
REVERT: A  297 PHE cc_start: 0.7271 (m-80) cc_final: 0.7033 (m-80)
REVERT: A  299 MET cc_start: 0.7587 (mmp) cc_final: 0.6915 (mmt)
REVERT: A  314 MET cc_start: 0.6656 (ptm) cc_final: 0.6081 (ppp)
REVERT: A  322 LEU cc_start: 0.8240 (tp) cc_final: 0.7998 (tp)
REVERT: A  334 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7097 (tm-30)
REVERT: A  337 LYS cc_start: 0.8623 (mttp) cc_final: 0.8349 (ttmm)
REVERT: A  338 GLU cc_start: 0.7759 (mp0) cc_final: 0.6580 (mp0)
REVERT: A  359 HIS cc_start: 0.8225 (t70) cc_final: 0.7632 (t70)
REVERT: A  362 LYS cc_start: 0.9097 (mtmm) cc_final: 0.8749 (mtmm)
REVERT: A  387 MET cc_start: 0.7533 (ptp) cc_final: 0.7097 (ptp)
REVERT: A  388 MET cc_start: 0.6977 (ppp) cc_final: 0.6599 (ppp)
REVERT: A  404 ARG cc_start: 0.8718 (mmt180) cc_final: 0.8417 (mmm160)
REVERT: A  448 ASP cc_start: 0.8506 (t70) cc_final: 0.8270 (t70)
REVERT: B  358 PHE cc_start: 0.8746 (m-10) cc_final: 0.8477 (m-10)
REVERT: B  385 LEU cc_start: 0.8395 (pp) cc_final: 0.7703 (pp)
REVERT: B  387 ARG cc_start: 0.8689 (ptt-90) cc_final: 0.8408 (ptt-90)
REVERT: B  389 MET cc_start: 0.8129 (mtp) cc_final: 0.7857 (mtp)
REVERT: B  398 PHE cc_start: 0.8678 (t80) cc_final: 0.8437 (t80)
REVERT: B  414 LYS cc_start: 0.8346 (tppt) cc_final: 0.7901 (tppt)
REVERT: B  426 GLN cc_start: 0.7695 (mt0) cc_final: 0.7383 (mt0)
REVERT: B  427 ARG cc_start: 0.8649 (mmm160) cc_final: 0.8309 (mmm160)
REVERT: B  486 MET cc_start: 0.7758 (mpp) cc_final: 0.7188 (mpp)
REVERT: B  524 MET cc_start: 0.8643 (mtt) cc_final: 0.7998 (mmm)
REVERT: B  525 ILE cc_start: 0.8675 (mm) cc_final: 0.8408 (mm)
REVERT: B  526 LEU cc_start: 0.8803 (mm) cc_final: 0.8441 (mt)
REVERT: B  549 ASN cc_start: 0.8481 (m-40) cc_final: 0.7890 (t0)
REVERT: B  564 TYR cc_start: 0.7450 (m-10) cc_final: 0.7017 (m-10)
REVERT: B  626 GLN cc_start: 0.8660 (tp40) cc_final: 0.8420 (tp40)
REVERT: B  630 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.7891 (mm-40)
REVERT: B  636 GLN cc_start: 0.8327 (mm110) cc_final: 0.8120 (mm110)
REVERT: B  641 LEU cc_start: 0.8559 (tp) cc_final: 0.8051 (tp)
REVERT: B  653 LEU cc_start: 0.8146 (mt) cc_final: 0.7835 (mt)
REVERT: B  711 LEU cc_start: 0.8523 (tp) cc_final: 0.8164 (mm)
  outliers start: 2
  outliers final: 1
  residues processed: 254
  average time/residue: 0.0942
  time to fit residues: 31.5952
Evaluate side-chains
  242 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 240
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 81 optimal weight:    0.2980
   chunk 65 optimal weight:    0.4980
   chunk 118 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0050
   chunk 41 optimal weight:    0.2980
   chunk 39 optimal weight:    0.5980
   chunk 4 optimal weight:    0.3980
   chunk 31 optimal weight:    1.9990
   chunk 66 optimal weight:    0.1980
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.2194

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 GLN
A 258 GLN
** B 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 630 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.123721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.098701 restraints weight = 22311.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.101584 restraints weight = 15666.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.103767 restraints weight = 11793.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.105450 restraints weight = 9378.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.106703 restraints weight = 7726.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.3485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8159  Z= 0.133
  Angle     :  0.715   7.836  11146  Z= 0.347
  Chirality :  0.038   0.145   1413
  Planarity :  0.005   0.097   1469
  Dihedral  :  4.966  30.347   1264
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 11.12 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  3.83 %
    Favored  : 96.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.28), residues: 890
  helix:  0.50 (0.20), residues: 621
  sheet:  None (None), residues: 0
  loop : -4.42 (0.32), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 237 
 TYR   0.016   0.002   TYR B 498 
 PHE   0.031   0.003   PHE A  91 
 TRP   0.011   0.001   TRP A 343 
 HIS   0.004   0.001   HIS A 321 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8159)
  covalent geometry    : angle       0.71502 (11146)
  hydrogen bonds       : bond        0.03425 (  596)
  hydrogen bonds       : angle       4.60855 ( 1764)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 257
  time to evaluate  : 0.230 
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: A    8 VAL cc_start: 0.9013 (m) cc_final: 0.8796 (p)
REVERT: A   13 ARG cc_start: 0.8520 (mmt-90) cc_final: 0.8160 (mmt180)
REVERT: A   27 HIS cc_start: 0.8441 (m90) cc_final: 0.8105 (m90)
REVERT: A   75 LEU cc_start: 0.8995 (mt) cc_final: 0.8052 (mt)
REVERT: A  104 MET cc_start: 0.8611 (mmm) cc_final: 0.7966 (mmm)
REVERT: A  108 GLU cc_start: 0.8252 (pt0) cc_final: 0.7815 (pt0)
REVERT: A  118 MET cc_start: 0.7764 (tpt) cc_final: 0.7295 (tpt)
REVERT: A  133 LEU cc_start: 0.8301 (mp) cc_final: 0.8079 (mp)
REVERT: A  186 ARG cc_start: 0.8223 (ttp80) cc_final: 0.7795 (ttp80)
REVERT: A  190 GLU cc_start: 0.8360 (tt0) cc_final: 0.7564 (tt0)
REVERT: A  191 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7776 (mm-30)
REVERT: A  194 ARG cc_start: 0.8684 (mmt180) cc_final: 0.8255 (mmp80)
REVERT: A  197 GLN cc_start: 0.8260 (pp30) cc_final: 0.7702 (tp-100)
REVERT: A  220 LYS cc_start: 0.8624 (mmpt) cc_final: 0.8200 (mmpt)
REVERT: A  257 GLU cc_start: 0.7848 (pp20) cc_final: 0.7423 (pp20)
REVERT: A  265 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7392 (tm-30)
REVERT: A  291 LYS cc_start: 0.7481 (ttmm) cc_final: 0.7105 (ttmm)
REVERT: A  297 PHE cc_start: 0.7117 (m-80) cc_final: 0.6867 (m-80)
REVERT: A  299 MET cc_start: 0.7471 (mmp) cc_final: 0.6920 (mmt)
REVERT: A  334 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7173 (tm-30)
REVERT: A  359 HIS cc_start: 0.8240 (t70) cc_final: 0.7734 (t70)
REVERT: A  362 LYS cc_start: 0.9052 (mttp) cc_final: 0.8823 (mttp)
REVERT: A  373 GLU cc_start: 0.7677 (pm20) cc_final: 0.6735 (pt0)
REVERT: A  383 LEU cc_start: 0.8868 (tp) cc_final: 0.8556 (tp)
REVERT: A  387 MET cc_start: 0.7467 (ptp) cc_final: 0.7078 (ptp)
REVERT: A  388 MET cc_start: 0.6886 (ppp) cc_final: 0.6414 (ppp)
REVERT: A  404 ARG cc_start: 0.8683 (mmt180) cc_final: 0.8302 (mmm160)
REVERT: A  448 ASP cc_start: 0.8378 (t70) cc_final: 0.8146 (t70)
REVERT: B  353 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7936 (mmtm)
REVERT: B  358 PHE cc_start: 0.8695 (m-10) cc_final: 0.8473 (m-10)
REVERT: B  385 LEU cc_start: 0.8329 (pp) cc_final: 0.7402 (pp)
REVERT: B  389 MET cc_start: 0.8078 (mtp) cc_final: 0.7663 (mtp)
REVERT: B  414 LYS cc_start: 0.8194 (tppt) cc_final: 0.7806 (tppt)
REVERT: B  426 GLN cc_start: 0.7591 (mt0) cc_final: 0.7013 (mt0)
REVERT: B  427 ARG cc_start: 0.8546 (mmm160) cc_final: 0.8137 (mmm160)
REVERT: B  509 MET cc_start: 0.8989 (mtt) cc_final: 0.8594 (mmt)
REVERT: B  524 MET cc_start: 0.8775 (mtt) cc_final: 0.8160 (mmm)
REVERT: B  525 ILE cc_start: 0.8583 (mm) cc_final: 0.8312 (mm)
REVERT: B  526 LEU cc_start: 0.8747 (mm) cc_final: 0.8329 (mt)
REVERT: B  549 ASN cc_start: 0.8421 (m-40) cc_final: 0.7816 (t0)
REVERT: B  564 TYR cc_start: 0.7249 (m-10) cc_final: 0.7007 (m-10)
REVERT: B  626 GLN cc_start: 0.8622 (tp40) cc_final: 0.8396 (tp40)
REVERT: B  630 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7911 (mm-40)
REVERT: B  631 LEU cc_start: 0.9201 (mt) cc_final: 0.8989 (mm)
REVERT: B  641 LEU cc_start: 0.8419 (tp) cc_final: 0.7883 (tp)
REVERT: B  649 LEU cc_start: 0.8631 (mt) cc_final: 0.8366 (mt)
REVERT: B  653 LEU cc_start: 0.7947 (mt) cc_final: 0.7686 (mt)
REVERT: B  672 THR cc_start: 0.8904 (p) cc_final: 0.8574 (p)
REVERT: B  711 LEU cc_start: 0.8431 (tp) cc_final: 0.8105 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 257
  average time/residue: 0.0984
  time to fit residues: 33.2398
Evaluate side-chains
  247 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 246
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 79 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 116 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 258 GLN
** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 513 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.121471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.096957 restraints weight = 22660.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.099819 restraints weight = 15929.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.101978 restraints weight = 11989.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.103652 restraints weight = 9504.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.104933 restraints weight = 7829.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.3657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8159  Z= 0.161
  Angle     :  0.736   8.813  11146  Z= 0.360
  Chirality :  0.038   0.144   1413
  Planarity :  0.005   0.100   1469
  Dihedral  :  4.924  30.788   1264
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 12.58 %
    Favored  : 87.30 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  3.33 %
    Favored  : 96.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.28), residues: 890
  helix:  0.53 (0.20), residues: 624
  sheet:  None (None), residues: 0
  loop : -4.38 (0.33), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 237 
 TYR   0.024   0.001   TYR B 498 
 PHE   0.028   0.002   PHE B 417 
 TRP   0.006   0.001   TRP A  74 
 HIS   0.007   0.001   HIS A 351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8159)
  covalent geometry    : angle       0.73556 (11146)
  hydrogen bonds       : bond        0.03719 (  596)
  hydrogen bonds       : angle       4.64281 ( 1764)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 257
  time to evaluate  : 0.252 
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: A   13 ARG cc_start: 0.8448 (mmt-90) cc_final: 0.8088 (mmt180)
REVERT: A   27 HIS cc_start: 0.8490 (m90) cc_final: 0.8245 (m90)
REVERT: A   59 PHE cc_start: 0.7885 (t80) cc_final: 0.7625 (t80)
REVERT: A   75 LEU cc_start: 0.9005 (mt) cc_final: 0.8044 (mt)
REVERT: A   85 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7197 (tm-30)
REVERT: A  104 MET cc_start: 0.8748 (mmm) cc_final: 0.8147 (mmm)
REVERT: A  108 GLU cc_start: 0.8312 (pt0) cc_final: 0.7894 (pt0)
REVERT: A  118 MET cc_start: 0.7714 (tpt) cc_final: 0.7300 (tpt)
REVERT: A  130 GLU cc_start: 0.7772 (pm20) cc_final: 0.7217 (pm20)
REVERT: A  186 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7738 (tmm-80)
REVERT: A  190 GLU cc_start: 0.8382 (tt0) cc_final: 0.7785 (tt0)
REVERT: A  191 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7733 (mm-30)
REVERT: A  194 ARG cc_start: 0.8713 (mmt180) cc_final: 0.8334 (mmp80)
REVERT: A  220 LYS cc_start: 0.8674 (mmpt) cc_final: 0.8247 (mmpt)
REVERT: A  291 LYS cc_start: 0.7482 (ttmm) cc_final: 0.7150 (ttmm)
REVERT: A  297 PHE cc_start: 0.7267 (m-80) cc_final: 0.6951 (m-80)
REVERT: A  299 MET cc_start: 0.7433 (mmp) cc_final: 0.6931 (mmt)
REVERT: A  314 MET cc_start: 0.6240 (ppp) cc_final: 0.5788 (ppp)
REVERT: A  334 GLN cc_start: 0.7631 (tm-30) cc_final: 0.7085 (tm-30)
REVERT: A  338 GLU cc_start: 0.7800 (mp0) cc_final: 0.6991 (mp0)
REVERT: A  359 HIS cc_start: 0.8277 (t70) cc_final: 0.7795 (t70)
REVERT: A  380 ARG cc_start: 0.8524 (mpt180) cc_final: 0.8285 (mmt180)
REVERT: A  383 LEU cc_start: 0.8888 (tp) cc_final: 0.8564 (tp)
REVERT: A  387 MET cc_start: 0.7519 (ptp) cc_final: 0.7166 (ptp)
REVERT: A  388 MET cc_start: 0.6935 (ppp) cc_final: 0.6561 (ppp)
REVERT: A  403 ARG cc_start: 0.8509 (tpt170) cc_final: 0.8031 (tpp80)
REVERT: A  448 ASP cc_start: 0.8453 (t70) cc_final: 0.8213 (t70)
REVERT: B  358 PHE cc_start: 0.8754 (m-10) cc_final: 0.8483 (m-10)
REVERT: B  385 LEU cc_start: 0.8298 (pp) cc_final: 0.7291 (pp)
REVERT: B  389 MET cc_start: 0.8137 (mtp) cc_final: 0.7806 (mtp)
REVERT: B  414 LYS cc_start: 0.8337 (tppt) cc_final: 0.7871 (tppt)
REVERT: B  417 PHE cc_start: 0.6984 (t80) cc_final: 0.6776 (t80)
REVERT: B  426 GLN cc_start: 0.7658 (mt0) cc_final: 0.7164 (mt0)
REVERT: B  427 ARG cc_start: 0.8644 (mmm160) cc_final: 0.8235 (mmm160)
REVERT: B  486 MET cc_start: 0.7541 (mpp) cc_final: 0.6868 (mpp)
REVERT: B  509 MET cc_start: 0.8900 (mtt) cc_final: 0.8614 (mmt)
REVERT: B  524 MET cc_start: 0.8782 (mtt) cc_final: 0.8165 (mmm)
REVERT: B  525 ILE cc_start: 0.8652 (mm) cc_final: 0.8369 (mm)
REVERT: B  526 LEU cc_start: 0.8770 (mm) cc_final: 0.8380 (mt)
REVERT: B  549 ASN cc_start: 0.8481 (m-40) cc_final: 0.7878 (t0)
REVERT: B  626 GLN cc_start: 0.8651 (tp40) cc_final: 0.8440 (tp40)
REVERT: B  630 GLN cc_start: 0.8314 (tp-100) cc_final: 0.8056 (mm-40)
REVERT: B  636 GLN cc_start: 0.8393 (tp40) cc_final: 0.8149 (tp40)
REVERT: B  641 LEU cc_start: 0.8334 (tp) cc_final: 0.7806 (tp)
REVERT: B  649 LEU cc_start: 0.8638 (mt) cc_final: 0.8403 (mt)
REVERT: B  653 LEU cc_start: 0.8001 (mt) cc_final: 0.7779 (mt)
REVERT: B  672 THR cc_start: 0.8933 (p) cc_final: 0.8571 (p)
REVERT: B  676 MET cc_start: 0.7685 (ppp) cc_final: 0.7311 (ppp)
REVERT: B  711 LEU cc_start: 0.8447 (tp) cc_final: 0.8196 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 257
  average time/residue: 0.0915
  time to fit residues: 31.0538
Evaluate side-chains
  249 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 248
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   chunk 2 optimal weight:    0.1980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 258 GLN
B 379 HIS
B 513 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.121052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.096979 restraints weight = 22569.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.099858 restraints weight = 15755.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.101997 restraints weight = 11801.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.103652 restraints weight = 9303.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.104876 restraints weight = 7643.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.3830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8159  Z= 0.171
  Angle     :  0.742   7.943  11146  Z= 0.363
  Chirality :  0.038   0.185   1413
  Planarity :  0.005   0.107   1469
  Dihedral  :  5.005  32.466   1264
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 13.26 %
    Favored  : 86.63 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  2.33 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.28), residues: 890
  helix:  0.49 (0.20), residues: 624
  sheet:  None (None), residues: 0
  loop : -4.37 (0.33), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 519 
 TYR   0.025   0.001   TYR B 498 
 PHE   0.023   0.002   PHE A 297 
 TRP   0.008   0.001   TRP A 343 
 HIS   0.007   0.001   HIS B 714 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8159)
  covalent geometry    : angle       0.74166 (11146)
  hydrogen bonds       : bond        0.03763 (  596)
  hydrogen bonds       : angle       4.66486 ( 1764)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 252
  time to evaluate  : 0.273 
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: A   13 ARG cc_start: 0.8495 (mmt-90) cc_final: 0.8122 (mmt180)
REVERT: A   27 HIS cc_start: 0.8458 (m90) cc_final: 0.8130 (m90)
REVERT: A   59 PHE cc_start: 0.7927 (t80) cc_final: 0.7680 (t80)
REVERT: A   75 LEU cc_start: 0.8976 (mt) cc_final: 0.7992 (mt)
REVERT: A   85 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7307 (tm-30)
REVERT: A   93 GLU cc_start: 0.6790 (mp0) cc_final: 0.6585 (mp0)
REVERT: A  104 MET cc_start: 0.8683 (mmm) cc_final: 0.8298 (mmm)
REVERT: A  108 GLU cc_start: 0.8324 (pt0) cc_final: 0.7931 (pt0)
REVERT: A  118 MET cc_start: 0.7780 (tpt) cc_final: 0.7381 (tpt)
REVERT: A  130 GLU cc_start: 0.7795 (pm20) cc_final: 0.7233 (pm20)
REVERT: A  136 LEU cc_start: 0.7761 (mt) cc_final: 0.7490 (mt)
REVERT: A  186 ARG cc_start: 0.8317 (ttp80) cc_final: 0.7763 (tmm-80)
REVERT: A  190 GLU cc_start: 0.8446 (tt0) cc_final: 0.7740 (tt0)
REVERT: A  191 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7730 (mm-30)
REVERT: A  194 ARG cc_start: 0.8655 (mmt180) cc_final: 0.8246 (mmp80)
REVERT: A  220 LYS cc_start: 0.8695 (mmpt) cc_final: 0.8263 (mmpt)
REVERT: A  291 LYS cc_start: 0.7416 (ttmm) cc_final: 0.7127 (ttmm)
REVERT: A  297 PHE cc_start: 0.7200 (m-80) cc_final: 0.6922 (m-80)
REVERT: A  314 MET cc_start: 0.6328 (ppp) cc_final: 0.5878 (ppp)
REVERT: A  334 GLN cc_start: 0.7585 (tm-30) cc_final: 0.6893 (tm-30)
REVERT: A  337 LYS cc_start: 0.8644 (mttp) cc_final: 0.8442 (ttmm)
REVERT: A  338 GLU cc_start: 0.7865 (mp0) cc_final: 0.6651 (mp0)
REVERT: A  359 HIS cc_start: 0.8253 (t70) cc_final: 0.7790 (t70)
REVERT: A  373 GLU cc_start: 0.7661 (pm20) cc_final: 0.6748 (pt0)
REVERT: A  380 ARG cc_start: 0.8510 (mpt180) cc_final: 0.7937 (mpt180)
REVERT: A  383 LEU cc_start: 0.8900 (tp) cc_final: 0.8587 (tp)
REVERT: A  387 MET cc_start: 0.7528 (ptp) cc_final: 0.7201 (ptp)
REVERT: A  388 MET cc_start: 0.6993 (ppp) cc_final: 0.6610 (ppp)
REVERT: A  403 ARG cc_start: 0.8492 (tpt170) cc_final: 0.7961 (tpp80)
REVERT: A  404 ARG cc_start: 0.8700 (mmt180) cc_final: 0.8468 (mmt180)
REVERT: A  448 ASP cc_start: 0.8506 (t70) cc_final: 0.8216 (t70)
REVERT: B  358 PHE cc_start: 0.8750 (m-10) cc_final: 0.8482 (m-10)
REVERT: B  372 ASP cc_start: 0.9170 (m-30) cc_final: 0.8960 (m-30)
REVERT: B  385 LEU cc_start: 0.8293 (pp) cc_final: 0.7172 (pp)
REVERT: B  389 MET cc_start: 0.8216 (mtp) cc_final: 0.7821 (mtp)
REVERT: B  404 LEU cc_start: 0.8843 (tp) cc_final: 0.8608 (tt)
REVERT: B  414 LYS cc_start: 0.8414 (tppt) cc_final: 0.7962 (tppt)
REVERT: B  417 PHE cc_start: 0.6935 (t80) cc_final: 0.6622 (t80)
REVERT: B  426 GLN cc_start: 0.7656 (mt0) cc_final: 0.7103 (mt0)
REVERT: B  427 ARG cc_start: 0.8505 (mmm160) cc_final: 0.8245 (mmm160)
REVERT: B  509 MET cc_start: 0.8871 (mtt) cc_final: 0.8458 (mmm)
REVERT: B  519 ARG cc_start: 0.7654 (mtt90) cc_final: 0.7272 (mtt-85)
REVERT: B  524 MET cc_start: 0.8764 (mtt) cc_final: 0.8128 (mmm)
REVERT: B  525 ILE cc_start: 0.8695 (mm) cc_final: 0.8438 (mm)
REVERT: B  526 LEU cc_start: 0.8893 (mm) cc_final: 0.8506 (mt)
REVERT: B  549 ASN cc_start: 0.8478 (m-40) cc_final: 0.7875 (t0)
REVERT: B  623 ASN cc_start: 0.8942 (m110) cc_final: 0.8740 (m110)
REVERT: B  626 GLN cc_start: 0.8676 (tp40) cc_final: 0.8158 (tp40)
REVERT: B  636 GLN cc_start: 0.8447 (tp40) cc_final: 0.8216 (tp40)
REVERT: B  641 LEU cc_start: 0.8301 (tp) cc_final: 0.7762 (tp)
REVERT: B  649 LEU cc_start: 0.8616 (mt) cc_final: 0.8392 (mt)
REVERT: B  653 LEU cc_start: 0.8024 (mt) cc_final: 0.7758 (mt)
REVERT: B  676 MET cc_start: 0.7724 (ppp) cc_final: 0.7322 (ppp)
REVERT: B  693 GLN cc_start: 0.8352 (tp40) cc_final: 0.7652 (tp40)
REVERT: B  696 ASP cc_start: 0.8481 (t0) cc_final: 0.8273 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 252
  average time/residue: 0.0973
  time to fit residues: 32.0871
Evaluate side-chains
  242 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 241
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 67 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 258 GLN
** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 513 HIS
B 626 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.118066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.092305 restraints weight = 22290.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.095048 restraints weight = 16045.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.097129 restraints weight = 12373.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.098697 restraints weight = 10008.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.099922 restraints weight = 8432.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.3979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8159  Z= 0.183
  Angle     :  0.768   8.695  11146  Z= 0.375
  Chirality :  0.040   0.168   1413
  Planarity :  0.005   0.097   1469
  Dihedral  :  5.017  32.223   1264
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 12.81 %
    Favored  : 86.97 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  2.33 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.28), residues: 890
  helix:  0.42 (0.20), residues: 631
  sheet:  None (None), residues: 0
  loop : -4.41 (0.33), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B 554 
 TYR   0.023   0.001   TYR B 498 
 PHE   0.022   0.002   PHE A 297 
 TRP   0.015   0.002   TRP A 343 
 HIS   0.007   0.001   HIS A 351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 8159)
  covalent geometry    : angle       0.76798 (11146)
  hydrogen bonds       : bond        0.03919 (  596)
  hydrogen bonds       : angle       4.75026 ( 1764)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 250
  time to evaluate  : 0.270 
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   13 ARG cc_start: 0.8487 (mmt-90) cc_final: 0.8122 (mmt180)
REVERT: A   59 PHE cc_start: 0.7795 (t80) cc_final: 0.7494 (t80)
REVERT: A   83 LEU cc_start: 0.8186 (mt) cc_final: 0.7940 (mp)
REVERT: A   93 GLU cc_start: 0.6734 (mp0) cc_final: 0.6502 (mp0)
REVERT: A  104 MET cc_start: 0.8754 (mmm) cc_final: 0.8369 (mmm)
REVERT: A  108 GLU cc_start: 0.8299 (pt0) cc_final: 0.7909 (pt0)
REVERT: A  118 MET cc_start: 0.7746 (tpt) cc_final: 0.7336 (tpt)
REVERT: A  129 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7928 (mtt-85)
REVERT: A  130 GLU cc_start: 0.7864 (pm20) cc_final: 0.7190 (pm20)
REVERT: A  186 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7818 (tmm-80)
REVERT: A  190 GLU cc_start: 0.8476 (tt0) cc_final: 0.7642 (tt0)
REVERT: A  191 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7716 (mm-30)
REVERT: A  194 ARG cc_start: 0.8646 (mmt180) cc_final: 0.8270 (mmp80)
REVERT: A  220 LYS cc_start: 0.8680 (mmpt) cc_final: 0.8241 (mmpt)
REVERT: A  291 LYS cc_start: 0.7430 (ttmm) cc_final: 0.7167 (ttmm)
REVERT: A  297 PHE cc_start: 0.7231 (m-80) cc_final: 0.6949 (m-80)
REVERT: A  314 MET cc_start: 0.6338 (ppp) cc_final: 0.5943 (ppp)
REVERT: A  334 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7102 (tm-30)
REVERT: A  338 GLU cc_start: 0.7859 (mp0) cc_final: 0.6674 (mp0)
REVERT: A  359 HIS cc_start: 0.8243 (t70) cc_final: 0.7724 (t70)
REVERT: A  362 LYS cc_start: 0.9001 (mttm) cc_final: 0.8721 (mttm)
REVERT: A  380 ARG cc_start: 0.8487 (mpt180) cc_final: 0.8006 (mpt180)
REVERT: A  387 MET cc_start: 0.7474 (ptp) cc_final: 0.7207 (ptp)
REVERT: A  388 MET cc_start: 0.6995 (ppp) cc_final: 0.6619 (ppp)
REVERT: A  404 ARG cc_start: 0.8686 (mmt180) cc_final: 0.8440 (mmt180)
REVERT: A  448 ASP cc_start: 0.8507 (t70) cc_final: 0.8206 (t70)
REVERT: B  358 PHE cc_start: 0.8735 (m-10) cc_final: 0.8482 (m-10)
REVERT: B  372 ASP cc_start: 0.9167 (m-30) cc_final: 0.8956 (m-30)
REVERT: B  404 LEU cc_start: 0.8852 (tp) cc_final: 0.8584 (tt)
REVERT: B  414 LYS cc_start: 0.8373 (tppt) cc_final: 0.8000 (tppt)
REVERT: B  417 PHE cc_start: 0.6883 (t80) cc_final: 0.6436 (t80)
REVERT: B  427 ARG cc_start: 0.8489 (mmm160) cc_final: 0.8180 (mmm160)
REVERT: B  486 MET cc_start: 0.7584 (mpp) cc_final: 0.7089 (mpp)
REVERT: B  509 MET cc_start: 0.8857 (mtt) cc_final: 0.8445 (mmm)
REVERT: B  519 ARG cc_start: 0.7686 (mtt90) cc_final: 0.7215 (mtm-85)
REVERT: B  524 MET cc_start: 0.8693 (mtt) cc_final: 0.8067 (mmm)
REVERT: B  525 ILE cc_start: 0.8760 (mm) cc_final: 0.8543 (mm)
REVERT: B  526 LEU cc_start: 0.8906 (mm) cc_final: 0.8592 (mt)
REVERT: B  549 ASN cc_start: 0.8513 (m-40) cc_final: 0.7949 (t0)
REVERT: B  626 GLN cc_start: 0.8659 (tp-100) cc_final: 0.8436 (tp40)
REVERT: B  630 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8178 (mm-40)
REVERT: B  636 GLN cc_start: 0.8395 (tp40) cc_final: 0.8130 (tp40)
REVERT: B  641 LEU cc_start: 0.8379 (tp) cc_final: 0.7873 (tp)
REVERT: B  653 LEU cc_start: 0.8048 (mt) cc_final: 0.7803 (mt)
REVERT: B  672 THR cc_start: 0.8918 (p) cc_final: 0.8600 (p)
REVERT: B  676 MET cc_start: 0.7755 (ppp) cc_final: 0.7314 (ppp)
REVERT: B  693 GLN cc_start: 0.8412 (tp40) cc_final: 0.7702 (tp40)
REVERT: B  696 ASP cc_start: 0.8478 (t0) cc_final: 0.8263 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 250
  average time/residue: 0.0965
  time to fit residues: 31.4991
Evaluate side-chains
  238 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 237
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 61 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 111 optimal weight:    8.9990
   chunk 83 optimal weight:    0.0870
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
A 258 GLN
B 379 HIS
B 513 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.121243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.096937 restraints weight = 22360.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.099760 restraints weight = 15646.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.101844 restraints weight = 11782.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.103482 restraints weight = 9372.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.104754 restraints weight = 7763.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.4150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8159  Z= 0.167
  Angle     :  0.763   8.493  11146  Z= 0.370
  Chirality :  0.039   0.153   1413
  Planarity :  0.005   0.115   1469
  Dihedral  :  4.984  33.799   1264
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 12.47 %
    Favored  : 87.42 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  1.50 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.28), residues: 890
  helix:  0.53 (0.20), residues: 631
  sheet:  None (None), residues: 0
  loop : -4.38 (0.33), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 554 
 TYR   0.022   0.001   TYR B 498 
 PHE   0.022   0.002   PHE A 297 
 TRP   0.016   0.002   TRP A 343 
 HIS   0.006   0.001   HIS B 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8159)
  covalent geometry    : angle       0.76261 (11146)
  hydrogen bonds       : bond        0.03701 (  596)
  hydrogen bonds       : angle       4.63024 ( 1764)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 251
  time to evaluate  : 0.262 
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   13 ARG cc_start: 0.8498 (mmt-90) cc_final: 0.8132 (mmt180)
REVERT: A   27 HIS cc_start: 0.8453 (m90) cc_final: 0.8120 (m90)
REVERT: A   59 PHE cc_start: 0.7865 (t80) cc_final: 0.7577 (t80)
REVERT: A   83 LEU cc_start: 0.8174 (mt) cc_final: 0.7752 (mp)
REVERT: A   93 GLU cc_start: 0.6741 (mp0) cc_final: 0.6524 (mp0)
REVERT: A  104 MET cc_start: 0.8741 (mmm) cc_final: 0.8340 (mmm)
REVERT: A  108 GLU cc_start: 0.8293 (pt0) cc_final: 0.7904 (pt0)
REVERT: A  118 MET cc_start: 0.7718 (tpt) cc_final: 0.7302 (tpt)
REVERT: A  129 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7896 (mtt-85)
REVERT: A  149 PHE cc_start: 0.6499 (m-10) cc_final: 0.6128 (m-10)
REVERT: A  186 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7689 (tmm-80)
REVERT: A  190 GLU cc_start: 0.8484 (tt0) cc_final: 0.7618 (tt0)
REVERT: A  191 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7680 (mm-30)
REVERT: A  194 ARG cc_start: 0.8675 (mmt180) cc_final: 0.8216 (mmp80)
REVERT: A  220 LYS cc_start: 0.8686 (mmpt) cc_final: 0.8241 (mmpt)
REVERT: A  265 GLU cc_start: 0.7902 (pp20) cc_final: 0.7580 (tm-30)
REVERT: A  291 LYS cc_start: 0.7458 (ttmm) cc_final: 0.7172 (ttmm)
REVERT: A  297 PHE cc_start: 0.7252 (m-80) cc_final: 0.6886 (m-80)
REVERT: A  314 MET cc_start: 0.6382 (ppp) cc_final: 0.6023 (ppp)
REVERT: A  334 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7036 (tm-30)
REVERT: A  337 LYS cc_start: 0.8524 (mttp) cc_final: 0.8284 (ttmm)
REVERT: A  338 GLU cc_start: 0.7865 (mp0) cc_final: 0.6856 (mp0)
REVERT: A  358 ARG cc_start: 0.8308 (tpt170) cc_final: 0.7941 (tpt170)
REVERT: A  359 HIS cc_start: 0.8249 (t70) cc_final: 0.7750 (t70)
REVERT: A  362 LYS cc_start: 0.9060 (mttm) cc_final: 0.8752 (mttm)
REVERT: A  387 MET cc_start: 0.7520 (ptp) cc_final: 0.7212 (ptp)
REVERT: A  388 MET cc_start: 0.7008 (ppp) cc_final: 0.6625 (ppp)
REVERT: A  448 ASP cc_start: 0.8475 (t70) cc_final: 0.8183 (t70)
REVERT: B  358 PHE cc_start: 0.8743 (m-10) cc_final: 0.8482 (m-10)
REVERT: B  372 ASP cc_start: 0.9155 (m-30) cc_final: 0.8939 (m-30)
REVERT: B  380 SER cc_start: 0.8891 (t) cc_final: 0.8377 (m)
REVERT: B  404 LEU cc_start: 0.8875 (tp) cc_final: 0.8607 (tt)
REVERT: B  414 LYS cc_start: 0.8374 (tppt) cc_final: 0.7953 (tppt)
REVERT: B  417 PHE cc_start: 0.6887 (t80) cc_final: 0.6413 (t80)
REVERT: B  427 ARG cc_start: 0.8627 (mmm160) cc_final: 0.8172 (mmm160)
REVERT: B  486 MET cc_start: 0.7592 (mpp) cc_final: 0.7166 (mpp)
REVERT: B  497 TYR cc_start: 0.7738 (m-80) cc_final: 0.7486 (m-80)
REVERT: B  509 MET cc_start: 0.8854 (mtt) cc_final: 0.8609 (mmt)
REVERT: B  524 MET cc_start: 0.8717 (mtt) cc_final: 0.8110 (mmm)
REVERT: B  525 ILE cc_start: 0.8733 (mm) cc_final: 0.8406 (mm)
REVERT: B  526 LEU cc_start: 0.8810 (mm) cc_final: 0.8533 (mm)
REVERT: B  549 ASN cc_start: 0.8528 (m-40) cc_final: 0.7943 (t0)
REVERT: B  630 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8113 (mm-40)
REVERT: B  636 GLN cc_start: 0.8396 (tp40) cc_final: 0.8131 (tp40)
REVERT: B  641 LEU cc_start: 0.8369 (tp) cc_final: 0.7853 (tp)
REVERT: B  653 LEU cc_start: 0.8073 (mt) cc_final: 0.7780 (mt)
REVERT: B  672 THR cc_start: 0.8914 (p) cc_final: 0.8593 (p)
REVERT: B  676 MET cc_start: 0.7718 (ppp) cc_final: 0.7273 (ppp)
REVERT: B  696 ASP cc_start: 0.8503 (t0) cc_final: 0.8292 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 251
  average time/residue: 0.0976
  time to fit residues: 32.1301
Evaluate side-chains
  243 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 242
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 31 optimal weight:    0.0570
   chunk 0 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0970
   chunk 23 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.5696

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 258 GLN
B 513 HIS
B 626 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.121717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.096988 restraints weight = 22540.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.099809 restraints weight = 15854.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.101919 restraints weight = 12022.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.103557 restraints weight = 9613.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.104843 restraints weight = 7972.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.4303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8159  Z= 0.151
  Angle     :  0.763   9.302  11146  Z= 0.367
  Chirality :  0.039   0.145   1413
  Planarity :  0.005   0.113   1469
  Dihedral  :  4.907  33.141   1264
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 12.25 %
    Favored  : 87.64 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.50 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.28), residues: 890
  helix:  0.59 (0.20), residues: 625
  sheet:  None (None), residues: 0
  loop : -4.23 (0.33), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG B 554 
 TYR   0.019   0.001   TYR B 498 
 PHE   0.022   0.002   PHE A 297 
 TRP   0.014   0.002   TRP A 343 
 HIS   0.005   0.001   HIS A 351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8159)
  covalent geometry    : angle       0.76316 (11146)
  hydrogen bonds       : bond        0.03634 (  596)
  hydrogen bonds       : angle       4.55199 ( 1764)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 248
  time to evaluate  : 0.199 
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   13 ARG cc_start: 0.8472 (mmt-90) cc_final: 0.8109 (mmt180)
REVERT: A   27 HIS cc_start: 0.8454 (m90) cc_final: 0.8111 (m90)
REVERT: A   59 PHE cc_start: 0.7787 (t80) cc_final: 0.7486 (t80)
REVERT: A   93 GLU cc_start: 0.6757 (mp0) cc_final: 0.6507 (mp0)
REVERT: A  104 MET cc_start: 0.8764 (mmm) cc_final: 0.8375 (mmm)
REVERT: A  108 GLU cc_start: 0.8282 (pt0) cc_final: 0.7896 (pt0)
REVERT: A  118 MET cc_start: 0.7724 (tpt) cc_final: 0.7304 (tpt)
REVERT: A  129 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7828 (mtt-85)
REVERT: A  149 PHE cc_start: 0.6277 (m-10) cc_final: 0.5976 (m-10)
REVERT: A  186 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7670 (tmm-80)
REVERT: A  190 GLU cc_start: 0.8484 (tt0) cc_final: 0.7599 (tt0)
REVERT: A  191 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7668 (mm-30)
REVERT: A  194 ARG cc_start: 0.8677 (mmt180) cc_final: 0.8279 (mmp80)
REVERT: A  220 LYS cc_start: 0.8674 (mmpt) cc_final: 0.8235 (mmpt)
REVERT: A  265 GLU cc_start: 0.7922 (pp20) cc_final: 0.7548 (tm-30)
REVERT: A  291 LYS cc_start: 0.7438 (ttmm) cc_final: 0.7235 (ttmm)
REVERT: A  297 PHE cc_start: 0.7276 (m-80) cc_final: 0.6908 (m-80)
REVERT: A  314 MET cc_start: 0.6406 (ppp) cc_final: 0.6068 (ppp)
REVERT: A  359 HIS cc_start: 0.8277 (t70) cc_final: 0.7764 (t70)
REVERT: A  387 MET cc_start: 0.7517 (ptp) cc_final: 0.7187 (ptp)
REVERT: A  388 MET cc_start: 0.6996 (ppp) cc_final: 0.6609 (ppp)
REVERT: A  403 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.8014 (mmt90)
REVERT: A  448 ASP cc_start: 0.8432 (t70) cc_final: 0.8142 (t70)
REVERT: B  358 PHE cc_start: 0.8733 (m-10) cc_final: 0.8476 (m-10)
REVERT: B  372 ASP cc_start: 0.9168 (m-30) cc_final: 0.8944 (m-30)
REVERT: B  380 SER cc_start: 0.8875 (t) cc_final: 0.8366 (m)
REVERT: B  392 GLN cc_start: 0.8820 (mp10) cc_final: 0.8594 (mp10)
REVERT: B  404 LEU cc_start: 0.8845 (tp) cc_final: 0.8578 (tt)
REVERT: B  414 LYS cc_start: 0.8329 (tppt) cc_final: 0.7907 (tppt)
REVERT: B  417 PHE cc_start: 0.6902 (t80) cc_final: 0.6441 (t80)
REVERT: B  427 ARG cc_start: 0.8488 (mmm160) cc_final: 0.8144 (mmm160)
REVERT: B  486 MET cc_start: 0.7520 (mpp) cc_final: 0.6990 (mpp)
REVERT: B  497 TYR cc_start: 0.7711 (m-80) cc_final: 0.7501 (m-80)
REVERT: B  509 MET cc_start: 0.8819 (mtt) cc_final: 0.8602 (mmt)
REVERT: B  519 ARG cc_start: 0.7742 (mtt90) cc_final: 0.7105 (mtm-85)
REVERT: B  524 MET cc_start: 0.8750 (mtt) cc_final: 0.8092 (mmm)
REVERT: B  525 ILE cc_start: 0.8717 (mm) cc_final: 0.8495 (mm)
REVERT: B  526 LEU cc_start: 0.8865 (mm) cc_final: 0.8606 (mt)
REVERT: B  551 GLU cc_start: 0.8691 (mp0) cc_final: 0.8408 (mp0)
REVERT: B  630 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8011 (mm-40)
REVERT: B  636 GLN cc_start: 0.8296 (tp40) cc_final: 0.7993 (tp40)
REVERT: B  641 LEU cc_start: 0.8361 (tp) cc_final: 0.7866 (tp)
REVERT: B  653 LEU cc_start: 0.8074 (mt) cc_final: 0.7839 (mt)
REVERT: B  672 THR cc_start: 0.8909 (p) cc_final: 0.8586 (p)
REVERT: B  676 MET cc_start: 0.7708 (ppp) cc_final: 0.7225 (ppp)
REVERT: B  693 GLN cc_start: 0.8304 (tp40) cc_final: 0.7691 (tp40)
REVERT: B  696 ASP cc_start: 0.8483 (t0) cc_final: 0.8273 (t0)
REVERT: B  705 ASN cc_start: 0.8389 (t0) cc_final: 0.8187 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 248
  average time/residue: 0.0970
  time to fit residues: 31.2515
Evaluate side-chains
  244 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 243
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0670
   chunk 34 optimal weight:    0.0170
   chunk 63 optimal weight:    0.8980
   chunk 111 optimal weight:    8.9990
   chunk 85 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 99 optimal weight:    1.9990
   chunk 109 optimal weight:    4.9990
   overall best weight:    0.4756

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

Flipped N/Q/H residues before XYZ refinement:
A 258 GLN
B 513 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.120310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.094079 restraints weight = 21950.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.096806 restraints weight = 15810.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.098905 restraints weight = 12220.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.100503 restraints weight = 9925.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.101777 restraints weight = 8372.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
moved from start:          0.4494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8159  Z= 0.140
  Angle     :  0.750   8.180  11146  Z= 0.359
  Chirality :  0.038   0.150   1413
  Planarity :  0.005   0.111   1469
  Dihedral  :  4.840  32.657   1264
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 11.24 %
    Favored  : 88.65 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.00 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.28), residues: 890
  helix:  0.74 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop : -4.17 (0.33), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 554 
 TYR   0.017   0.001   TYR B 498 
 PHE   0.022   0.002   PHE A 297 
 TRP   0.011   0.002   TRP A 343 
 HIS   0.004   0.001   HIS A 351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8159)
  covalent geometry    : angle       0.75041 (11146)
  hydrogen bonds       : bond        0.03449 (  596)
  hydrogen bonds       : angle       4.43900 ( 1764)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 250
  time to evaluate  : 0.234 
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   13 ARG cc_start: 0.8543 (mmt-90) cc_final: 0.8152 (mmt180)
REVERT: A   27 HIS cc_start: 0.8450 (m90) cc_final: 0.8075 (m90)
REVERT: A   59 PHE cc_start: 0.7715 (t80) cc_final: 0.7419 (t80)
REVERT: A  104 MET cc_start: 0.8740 (mmm) cc_final: 0.8419 (mmm)
REVERT: A  108 GLU cc_start: 0.8272 (pt0) cc_final: 0.7870 (pt0)
REVERT: A  118 MET cc_start: 0.7749 (tpt) cc_final: 0.7334 (tpt)
REVERT: A  149 PHE cc_start: 0.6198 (m-10) cc_final: 0.5954 (m-10)
REVERT: A  186 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7784 (ttp80)
REVERT: A  190 GLU cc_start: 0.8499 (tt0) cc_final: 0.7502 (tt0)
REVERT: A  191 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7602 (mm-30)
REVERT: A  194 ARG cc_start: 0.8676 (mmt180) cc_final: 0.8019 (mmp80)
REVERT: A  220 LYS cc_start: 0.8709 (mmpt) cc_final: 0.8326 (mmpt)
REVERT: A  249 GLN cc_start: 0.7949 (mt0) cc_final: 0.7556 (mp10)
REVERT: A  265 GLU cc_start: 0.7913 (pp20) cc_final: 0.7396 (pp20)
REVERT: A  291 LYS cc_start: 0.7501 (ttmm) cc_final: 0.7267 (ttmm)
REVERT: A  297 PHE cc_start: 0.7236 (m-80) cc_final: 0.6866 (m-80)
REVERT: A  314 MET cc_start: 0.6400 (ppp) cc_final: 0.6053 (ppp)
REVERT: A  358 ARG cc_start: 0.8280 (tpt170) cc_final: 0.7900 (tpt170)
REVERT: A  359 HIS cc_start: 0.8278 (t70) cc_final: 0.7756 (t70)
REVERT: A  362 LYS cc_start: 0.8994 (mttm) cc_final: 0.8790 (mttm)
REVERT: A  387 MET cc_start: 0.7473 (ptp) cc_final: 0.7166 (ptp)
REVERT: A  388 MET cc_start: 0.6983 (ppp) cc_final: 0.6596 (ppp)
REVERT: A  403 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7615 (mmt90)
REVERT: A  448 ASP cc_start: 0.8456 (t70) cc_final: 0.8160 (t70)
REVERT: B  358 PHE cc_start: 0.8735 (m-10) cc_final: 0.8475 (m-10)
REVERT: B  372 ASP cc_start: 0.9143 (m-30) cc_final: 0.8895 (m-30)
REVERT: B  380 SER cc_start: 0.8847 (t) cc_final: 0.8353 (m)
REVERT: B  392 GLN cc_start: 0.8807 (mp10) cc_final: 0.8603 (mp10)
REVERT: B  414 LYS cc_start: 0.8340 (tppt) cc_final: 0.7917 (tppt)
REVERT: B  417 PHE cc_start: 0.6959 (t80) cc_final: 0.6433 (t80)
REVERT: B  426 GLN cc_start: 0.7623 (mt0) cc_final: 0.7107 (mt0)
REVERT: B  427 ARG cc_start: 0.8604 (mmm160) cc_final: 0.8097 (mmm160)
REVERT: B  486 MET cc_start: 0.7470 (mpp) cc_final: 0.7025 (mpp)
REVERT: B  519 ARG cc_start: 0.7604 (mtt90) cc_final: 0.7054 (mtm-85)
REVERT: B  524 MET cc_start: 0.8712 (mtt) cc_final: 0.8012 (mmm)
REVERT: B  526 LEU cc_start: 0.8862 (mm) cc_final: 0.8628 (mt)
REVERT: B  551 GLU cc_start: 0.8709 (mp0) cc_final: 0.8344 (mp0)
REVERT: B  629 ILE cc_start: 0.9055 (tt) cc_final: 0.8799 (tt)
REVERT: B  630 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8007 (mm-40)
REVERT: B  636 GLN cc_start: 0.8206 (tp40) cc_final: 0.7887 (tp40)
REVERT: B  641 LEU cc_start: 0.8320 (tp) cc_final: 0.7804 (tp)
REVERT: B  653 LEU cc_start: 0.8062 (mt) cc_final: 0.7839 (mt)
REVERT: B  672 THR cc_start: 0.8927 (p) cc_final: 0.8608 (p)
REVERT: B  676 MET cc_start: 0.7698 (ppp) cc_final: 0.7190 (ppp)
REVERT: B  693 GLN cc_start: 0.8321 (tp40) cc_final: 0.7684 (tp40)
REVERT: B  696 ASP cc_start: 0.8439 (t0) cc_final: 0.8222 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 250
  average time/residue: 0.1033
  time to fit residues: 33.4484
Evaluate side-chains
  240 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 239
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0070
   chunk 85 optimal weight:    0.6980
   chunk 18 optimal weight:    0.4980
   chunk 106 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 58 optimal weight:    7.9990
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 258 GLN
B 513 HIS
B 626 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.122284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.097540 restraints weight = 22401.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.100265 restraints weight = 15947.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.102335 restraints weight = 12171.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.103970 restraints weight = 9816.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.105263 restraints weight = 8173.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.4563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8159  Z= 0.148
  Angle     :  0.755   9.144  11146  Z= 0.363
  Chirality :  0.039   0.144   1413
  Planarity :  0.005   0.110   1469
  Dihedral  :  4.814  32.096   1264
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.25 %
    Favored  : 87.75 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.83 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.28), residues: 890
  helix:  0.74 (0.20), residues: 621
  sheet:  None (None), residues: 0
  loop : -4.18 (0.33), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 153 
 TYR   0.020   0.001   TYR B 498 
 PHE   0.022   0.002   PHE A 297 
 TRP   0.014   0.002   TRP A 343 
 HIS   0.005   0.001   HIS A 351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8159)
  covalent geometry    : angle       0.75457 (11146)
  hydrogen bonds       : bond        0.03487 (  596)
  hydrogen bonds       : angle       4.45540 ( 1764)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1605.20 seconds
wall clock time: 28 minutes 8.83 seconds (1688.83 seconds total)