Starting phenix.real_space_refine
on Fri Mar 14 01:29:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x1w_32951/03_2025/7x1w_32951.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x1w_32951/03_2025/7x1w_32951.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x1w_32951/03_2025/7x1w_32951.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x1w_32951/03_2025/7x1w_32951.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x1w_32951/03_2025/7x1w_32951.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x1w_32951/03_2025/7x1w_32951.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      44      5.16       5
     C    5967      2.51       5
     N    1641      2.21       5
     O    1657      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 102 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9315
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 579, 4624
          Classifications: {'peptide': 579}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 557}
          Chain breaks: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 4629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 580, 4629
          Classifications: {'peptide': 580}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 558}
          Chain breaks: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.99, per 1000 atoms: 0.75
  Number of scatterers: 9315
  At special positions: 0
  Unit cell: (80.51, 83.83, 135.29, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      44     16.00
     P       6     15.00
     O    1657      8.00
     N    1641      7.00
     C    5967      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.47
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2162

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      68.8% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 68 through 83
      removed outlier: 3.808A  pdb=" N   GLN A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 124
      removed outlier: 3.649A  pdb=" N   TYR A 110 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ARG A 113 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 140
    Processing helix  chain 'A' and resid 140 through 175
      removed outlier: 3.537A  pdb=" N   ARG A 152 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 186
      removed outlier: 4.086A  pdb=" N   SER A 184 " --> pdb=" O   TYR A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 236
      removed outlier: 3.819A  pdb=" N   ASP A 200 " --> pdb=" O   SER A 196 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL A 202 " --> pdb=" O   THR A 198 " (cutoff:3.500A)
      Proline residue:  A 218  - end of helix
      removed outlier: 3.649A  pdb=" N   TYR A 227 " --> pdb=" O   ALA A 223 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU A 230 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 254
    Processing helix  chain 'A' and resid 255 through 256
      No H-bonds generated for 'chain 'A' and resid 255 through 256'
    Processing helix  chain 'A' and resid 257 through 262
      removed outlier: 3.536A  pdb=" N   PHE A 261 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   SER A 262 " --> pdb=" O   ARG A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 289
      removed outlier: 4.425A  pdb=" N   GLU A 267 " --> pdb=" O   PRO A 263 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 296
    Processing helix  chain 'A' and resid 298 through 324
      removed outlier: 3.572A  pdb=" N   ALA A 304 " --> pdb=" O   GLU A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 337
    Processing helix  chain 'A' and resid 338 through 353
      removed outlier: 3.872A  pdb=" N   LEU A 345 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   MET A 346 " --> pdb=" O   SER A 342 " (cutoff:3.500A)
      Proline residue:  A 350  - end of helix
    Processing helix  chain 'A' and resid 373 through 431
      removed outlier: 3.926A  pdb=" N   SER A 379 " --> pdb=" O   GLU A 375 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLU A 380 " --> pdb=" O   GLU A 376 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   THR A 410 " --> pdb=" O   TYR A 406 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   GLU A 411 " --> pdb=" O   LYS A 407 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLY A 414 " --> pdb=" O   THR A 410 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   TYR A 415 " --> pdb=" O   GLU A 411 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLN A 430 " --> pdb=" O   PHE A 426 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG A 431 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 521
    Processing helix  chain 'A' and resid 552 through 556
    Processing helix  chain 'A' and resid 574 through 583
      removed outlier: 4.069A  pdb=" N   VAL A 583 " --> pdb=" O   ILE A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 590
      removed outlier: 4.273A  pdb=" N   LEU A 589 " --> pdb=" O   LEU A 585 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLN A 590 " --> pdb=" O   HIS A 586 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 585 through 590'
    Processing helix  chain 'A' and resid 606 through 622
      removed outlier: 4.252A  pdb=" N   GLN A 611 " --> pdb=" O   GLY A 607 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ARG A 612 " --> pdb=" O   GLY A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 651
      removed outlier: 3.542A  pdb=" N   LYS A 642 " --> pdb=" O   ASP A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 667
      removed outlier: 4.028A  pdb=" N   LYS A 665 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   HIS A 667 " --> pdb=" O   TRP A 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 83
      removed outlier: 3.712A  pdb=" N   LEU B  81 " --> pdb=" O   TRP B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 124
      removed outlier: 3.645A  pdb=" N   TYR B 110 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ARG B 113 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 140
    Processing helix  chain 'B' and resid 140 through 175
      removed outlier: 3.580A  pdb=" N   ARG B 152 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 186
      removed outlier: 4.049A  pdb=" N   SER B 184 " --> pdb=" O   TYR B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 197
    Processing helix  chain 'B' and resid 198 through 226
      removed outlier: 3.623A  pdb=" N   VAL B 202 " --> pdb=" O   THR B 198 " (cutoff:3.500A)
      Proline residue:  B 218  - end of helix
    Processing helix  chain 'B' and resid 226 through 236
      removed outlier: 3.640A  pdb=" N   LEU B 230 " --> pdb=" O   SER B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 260
    Processing helix  chain 'B' and resid 263 through 289
      removed outlier: 4.088A  pdb=" N   GLU B 267 " --> pdb=" O   PRO B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 297
    Processing helix  chain 'B' and resid 298 through 337
    Processing helix  chain 'B' and resid 338 through 354
      Proline residue:  B 350  - end of helix
    Processing helix  chain 'B' and resid 373 through 431
      removed outlier: 3.931A  pdb=" N   SER B 379 " --> pdb=" O   GLU B 375 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU B 380 " --> pdb=" O   GLU B 376 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLU B 400 " --> pdb=" O   ALA B 396 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ARG B 401 " --> pdb=" O   ASP B 397 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   GLU B 408 " --> pdb=" O   SER B 404 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   THR B 410 " --> pdb=" O   TYR B 406 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   GLU B 411 " --> pdb=" O   LYS B 407 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   GLY B 414 " --> pdb=" O   THR B 410 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   TYR B 415 " --> pdb=" O   GLU B 411 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLU B 427 " --> pdb=" O   PHE B 423 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLN B 430 " --> pdb=" O   PHE B 426 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ARG B 431 " --> pdb=" O   GLU B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 521
    Processing helix  chain 'B' and resid 572 through 583
      removed outlier: 4.051A  pdb=" N   VAL B 583 " --> pdb=" O   ILE B 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 590
      removed outlier: 4.231A  pdb=" N   LEU B 589 " --> pdb=" O   LEU B 585 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN B 590 " --> pdb=" O   HIS B 586 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 585 through 590'
    Processing helix  chain 'B' and resid 606 through 622
      removed outlier: 4.129A  pdb=" N   GLN B 611 " --> pdb=" O   GLY B 607 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ARG B 612 " --> pdb=" O   GLY B 608 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 636 through 651
      removed outlier: 3.855A  pdb=" N   LYS B 642 " --> pdb=" O   ASP B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 667
      removed outlier: 4.219A  pdb=" N   LYS B 665 " --> pdb=" O   SER B 662 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   HIS B 667 " --> pdb=" O   TRP B 664 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 469
    Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 482
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 542
    Processing sheet with id=AA4, first strand: chain 'B' and resid 466 through 469
    Processing sheet with id=AA5, first strand: chain 'B' and resid 481 through 482
      removed outlier: 6.659A  pdb=" N   ILE B 481 " --> pdb=" O   VAL B 489 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 539 through 540

    586 hydrogen bonds defined for protein.
    1716 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: 2.69

  Time building geometry restraints manager: 2.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3033
        1.34 -     1.46: 1597
        1.46 -     1.57: 4807
        1.57 -     1.69: 12
        1.69 -     1.81: 74
  Bond restraints: 9523
  Sorted by residual:
  bond pdb=" C2' ATP B 801 "
       pdb=" C3' ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.531  1.306  0.225 1.20e-02 6.94e+03 3.51e+02
  bond pdb=" C2' ATP A 801 "
       pdb=" C3' ATP A 801 "
    ideal  model  delta    sigma   weight residual
    1.531  1.307  0.224 1.20e-02 6.94e+03 3.50e+02
  bond pdb=" C4' ATP B 801 "
       pdb=" O4' ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.444  1.302  0.142 1.10e-02 8.26e+03 1.67e+02
  bond pdb=" C4' ATP A 801 "
       pdb=" O4' ATP A 801 "
    ideal  model  delta    sigma   weight residual
    1.444  1.302  0.142 1.10e-02 8.26e+03 1.67e+02
  bond pdb=" C6  ATP B 801 "
       pdb=" N6  ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.337  1.465 -0.128 1.10e-02 8.26e+03 1.35e+02
  ... (remaining 9518 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.89: 12764
        2.89 -     5.79: 116
        5.79 -     8.68: 18
        8.68 -    11.57: 5
       11.57 -    14.46: 4
  Bond angle restraints: 12907
  Sorted by residual:
  angle pdb=" PB  ATP A 801 "
        pdb=" O3B ATP A 801 "
        pdb=" PG  ATP A 801 "
      ideal   model   delta    sigma   weight residual
     139.87  125.41   14.46 1.00e+00 1.00e+00 2.09e+02
  angle pdb=" PB  ATP B 801 "
        pdb=" O3B ATP B 801 "
        pdb=" PG  ATP B 801 "
      ideal   model   delta    sigma   weight residual
     139.87  125.44   14.43 1.00e+00 1.00e+00 2.08e+02
  angle pdb=" PA  ATP B 801 "
        pdb=" O3A ATP B 801 "
        pdb=" PB  ATP B 801 "
      ideal   model   delta    sigma   weight residual
     136.83  124.21   12.62 1.00e+00 1.00e+00 1.59e+02
  angle pdb=" PA  ATP A 801 "
        pdb=" O3A ATP A 801 "
        pdb=" PB  ATP A 801 "
      ideal   model   delta    sigma   weight residual
     136.83  124.29   12.54 1.00e+00 1.00e+00 1.57e+02
  angle pdb=" C5  ATP B 801 "
        pdb=" C4  ATP B 801 "
        pdb=" N3  ATP B 801 "
      ideal   model   delta    sigma   weight residual
     126.80  117.87    8.93 1.00e+00 1.00e+00 7.98e+01
  ... (remaining 12902 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 5027
       17.73 -    35.46: 544
       35.46 -    53.19: 113
       53.19 -    70.91: 15
       70.91 -    88.64: 12
  Dihedral angle restraints: 5711
    sinusoidal: 2348
      harmonic: 3363
  Sorted by residual:
  dihedral pdb=" CA  LYS A 533 "
           pdb=" C   LYS A 533 "
           pdb=" N   PRO A 534 "
           pdb=" CA  PRO A 534 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.13   28.87     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  LYS B 533 "
           pdb=" C   LYS B 533 "
           pdb=" N   PRO B 534 "
           pdb=" CA  PRO B 534 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.13   27.87     0      5.00e+00 4.00e-02 3.11e+01
  dihedral pdb=" CA  SER A 572 "
           pdb=" C   SER A 572 "
           pdb=" N   GLU A 573 "
           pdb=" CA  GLU A 573 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.66   25.34     0      5.00e+00 4.00e-02 2.57e+01
  ... (remaining 5708 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1207
       0.054 -    0.107: 193
       0.107 -    0.161: 31
       0.161 -    0.214: 2
       0.214 -    0.268: 2
  Chirality restraints: 1435
  Sorted by residual:
  chirality pdb=" C2' ATP A 801 "
            pdb=" C1' ATP A 801 "
            pdb=" C3' ATP A 801 "
            pdb=" O2' ATP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.41   -0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" C2' ATP B 801 "
            pdb=" C1' ATP B 801 "
            pdb=" C3' ATP B 801 "
            pdb=" O2' ATP B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.41   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" C3' ATP B 801 "
            pdb=" C2' ATP B 801 "
            pdb=" C4' ATP B 801 "
            pdb=" O3' ATP B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 1432 not shown)

  Planarity restraints: 1625
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 479 "    0.030 5.00e-02 4.00e+02   4.49e-02 3.23e+00
        pdb=" N   PRO A 480 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 480 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 480 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 507 "   -0.027 5.00e-02 4.00e+02   4.16e-02 2.77e+00
        pdb=" N   PRO B 508 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 508 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 508 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 507 "   -0.027 5.00e-02 4.00e+02   4.08e-02 2.67e+00
        pdb=" N   PRO A 508 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 508 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 508 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1622 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 238
        2.71 -     3.26: 9413
        3.26 -     3.81: 14904
        3.81 -     4.35: 18596
        4.35 -     4.90: 32484
  Nonbonded interactions: 75635
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 506 "
            pdb=" OE1 GLN B 672 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" O   PRO B 508 "
            pdb=" NZ  LYS B 513 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" O   TYR B 547 "
            pdb=" NH2 ARG B 617 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   GLN B 472 "
            pdb=" OH  TYR B 625 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   TYR A 547 "
            pdb=" NH2 ARG A 617 "
     model   vdw
     2.295 3.120
  ... (remaining 75630 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 64 through 353 or resid 371 through 682 or resid 801))
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.940
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
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      :  0.007   0.225   9523  Z= 0.409
  Angle     :  0.764  14.464  12907  Z= 0.506
  Chirality :  0.042   0.268   1435
  Planarity :  0.004   0.045   1625
  Dihedral  : 15.415  88.644   3549
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.25), residues: 1147
  helix:  0.80 (0.20), residues: 746
  sheet: -2.70 (0.84), residues: 32
  loop : -3.15 (0.28), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 326 
 HIS   0.003   0.001   HIS A 669 
 PHE   0.026   0.001   PHE B 540 
 TYR   0.018   0.002   TYR B 541 
 ARG   0.004   0.000   ARG B 152 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A  466 GLN cc_start: 0.7903 (mt0) cc_final: 0.6817 (tt0)
REVERT: B  466 GLN cc_start: 0.7863 (mt0) cc_final: 0.6880 (tt0)
REVERT: B  498 GLU cc_start: 0.7794 (pt0) cc_final: 0.7468 (pt0)
REVERT: B  502 HIS cc_start: 0.8669 (m90) cc_final: 0.8351 (m170)
REVERT: B  524 TRP cc_start: 0.8488 (m-10) cc_final: 0.8163 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.2400
  time to fit residues: 36.2684
Evaluate side-chains
  90 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 87 optimal weight:    0.5980
   chunk 48 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 169 HIS
A 289 ASN
A 420 HIS
A 433 HIS
A 659 HIS
** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 289 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.171267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.128208 restraints weight = 9157.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 1.70
r_work: 0.3227 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.0985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9523  Z= 0.297
  Angle     :  0.612   8.307  12907  Z= 0.312
  Chirality :  0.041   0.149   1435
  Planarity :  0.004   0.044   1625
  Dihedral  :  7.605  74.405   1361
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  6.78 %
    Favored  : 92.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.25), residues: 1147
  helix:  0.94 (0.19), residues: 759
  sheet: -2.46 (0.68), residues: 48
  loop : -3.35 (0.29), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 326 
 HIS   0.005   0.001   HIS B 299 
 PHE   0.018   0.001   PHE B 540 
 TYR   0.016   0.002   TYR A 296 
 ARG   0.003   0.000   ARG B  69 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 1.196 
Fit side-chains
REVERT: A  615 MET cc_start: 0.8517 (mmm) cc_final: 0.8110 (mmt)
REVERT: B  200 ASP cc_start: 0.6673 (m-30) cc_final: 0.6390 (m-30)
REVERT: B  466 GLN cc_start: 0.7918 (mt0) cc_final: 0.6722 (tt0)
REVERT: B  498 GLU cc_start: 0.7992 (pt0) cc_final: 0.7611 (pt0)
  outliers start: 7
  outliers final: 5
  residues processed: 96
  average time/residue: 0.3262
  time to fit residues: 44.1782
Evaluate side-chains
  89 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  498 GLU
Chi-restraints excluded: chain A residue  588 ILE
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  670 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 93 optimal weight:    0.4980
   chunk 45 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 13 optimal weight:    0.4980
   chunk 41 optimal weight:    0.3980
   chunk 105 optimal weight:    0.0030
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.3590

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
B 420 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.175719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.132739 restraints weight = 9076.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.70
r_work: 0.3353 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9523  Z= 0.177
  Angle     :  0.530   8.659  12907  Z= 0.272
  Chirality :  0.038   0.146   1435
  Planarity :  0.004   0.045   1625
  Dihedral  :  6.381  69.644   1361
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  9.34 %
    Favored  : 89.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.26), residues: 1147
  helix:  1.33 (0.19), residues: 763
  sheet: -2.22 (0.72), residues: 46
  loop : -3.30 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 326 
 HIS   0.003   0.001   HIS A 669 
 PHE   0.012   0.001   PHE B 540 
 TYR   0.017   0.001   TYR A 296 
 ARG   0.003   0.000   ARG B  69 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A  186 MET cc_start: 0.8200 (mtt) cc_final: 0.7806 (mtt)
REVERT: A  411 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7365 (tt0)
REVERT: A  618 MET cc_start: 0.8159 (tmm) cc_final: 0.7777 (ttt)
REVERT: B  200 ASP cc_start: 0.6638 (m-30) cc_final: 0.6382 (m-30)
REVERT: B  466 GLN cc_start: 0.7874 (mt0) cc_final: 0.6726 (tt0)
REVERT: B  498 GLU cc_start: 0.7912 (pt0) cc_final: 0.7607 (pt0)
REVERT: B  502 HIS cc_start: 0.8790 (m90) cc_final: 0.8584 (m170)
  outliers start: 10
  outliers final: 3
  residues processed: 103
  average time/residue: 0.1990
  time to fit residues: 29.8556
Evaluate side-chains
  86 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  498 GLU
Chi-restraints excluded: chain B residue  429 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 90 optimal weight:    0.3980
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 102 optimal weight:    0.2980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.172775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.129261 restraints weight = 9070.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.69
r_work: 0.3325 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9523  Z= 0.227
  Angle     :  0.549  10.632  12907  Z= 0.279
  Chirality :  0.040   0.259   1435
  Planarity :  0.004   0.044   1625
  Dihedral  :  6.043  64.586   1361
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 11.40 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.26), residues: 1147
  helix:  1.40 (0.19), residues: 765
  sheet: -2.32 (0.72), residues: 48
  loop : -3.24 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 326 
 HIS   0.006   0.001   HIS B 621 
 PHE   0.011   0.001   PHE B 540 
 TYR   0.015   0.001   TYR A 296 
 ARG   0.002   0.000   ARG A 381 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 1.192 
Fit side-chains
REVERT: A  163 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7868 (ttt180)
REVERT: A  177 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7479 (mt0)
REVERT: A  200 ASP cc_start: 0.6686 (m-30) cc_final: 0.6438 (m-30)
REVERT: A  411 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7679 (tm-30)
REVERT: A  615 MET cc_start: 0.8135 (mmm) cc_final: 0.7916 (mmt)
REVERT: A  618 MET cc_start: 0.8192 (tmm) cc_final: 0.7745 (ttt)
REVERT: B   73 GLN cc_start: 0.7178 (tt0) cc_final: 0.6977 (mt0)
REVERT: B  466 GLN cc_start: 0.7853 (mt0) cc_final: 0.6708 (tt0)
REVERT: B  498 GLU cc_start: 0.7874 (pt0) cc_final: 0.7635 (pt0)
REVERT: B  501 MET cc_start: 0.8760 (mmm) cc_final: 0.8495 (mmt)
REVERT: B  615 MET cc_start: 0.8444 (mmm) cc_final: 0.8018 (mmp)
  outliers start: 22
  outliers final: 12
  residues processed: 106
  average time/residue: 0.2361
  time to fit residues: 36.4171
Evaluate side-chains
  96 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  498 GLU
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  582 VAL
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  657 ILE
Chi-restraints excluded: chain B residue  670 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 111 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   chunk 89 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 112 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.177873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.138266 restraints weight = 8992.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 1.61
r_work: 0.3355 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9523  Z= 0.247
  Angle     :  0.556   9.201  12907  Z= 0.282
  Chirality :  0.040   0.222   1435
  Planarity :  0.004   0.044   1625
  Dihedral  :  5.878  63.812   1361
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 12.73 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.26), residues: 1147
  helix:  1.43 (0.19), residues: 763
  sheet: -2.31 (0.71), residues: 48
  loop : -3.15 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 326 
 HIS   0.004   0.001   HIS A 669 
 PHE   0.010   0.001   PHE B 540 
 TYR   0.017   0.001   TYR A 296 
 ARG   0.002   0.000   ARG B 324 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 1.022 
Fit side-chains
REVERT: A  163 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7827 (ttt180)
REVERT: A  177 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.6525 (mm-40)
REVERT: A  178 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8103 (mt0)
REVERT: A  411 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7572 (tm-30)
REVERT: B  200 ASP cc_start: 0.6696 (m-30) cc_final: 0.6475 (m-30)
REVERT: B  466 GLN cc_start: 0.7933 (mt0) cc_final: 0.6806 (tt0)
REVERT: B  498 GLU cc_start: 0.7865 (pt0) cc_final: 0.7503 (pt0)
REVERT: B  615 MET cc_start: 0.8438 (mmm) cc_final: 0.8085 (mmm)
  outliers start: 23
  outliers final: 15
  residues processed: 105
  average time/residue: 0.2433
  time to fit residues: 35.6808
Evaluate side-chains
  98 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  588 ILE
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  540 PHE
Chi-restraints excluded: chain B residue  582 VAL
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  657 ILE
Chi-restraints excluded: chain B residue  670 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0970
   chunk 32 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 106 optimal weight:    0.5980
   chunk 110 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.170309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.126475 restraints weight = 9123.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 1.69
r_work: 0.3293 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9523  Z= 0.299
  Angle     :  0.579   7.999  12907  Z= 0.294
  Chirality :  0.041   0.205   1435
  Planarity :  0.004   0.044   1625
  Dihedral  :  5.948  63.556   1361
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.76 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.25), residues: 1147
  helix:  1.35 (0.19), residues: 763
  sheet: -2.32 (0.70), residues: 48
  loop : -3.12 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 326 
 HIS   0.005   0.001   HIS B 299 
 PHE   0.009   0.001   PHE A 265 
 TYR   0.014   0.002   TYR A 296 
 ARG   0.002   0.000   ARG B 324 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.994 
Fit side-chains
REVERT: A  163 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7853 (ttt180)
REVERT: A  177 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.6706 (mm-40)
REVERT: A  178 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8070 (mt0)
REVERT: B  200 ASP cc_start: 0.6676 (m-30) cc_final: 0.6421 (m-30)
REVERT: B  217 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8054 (ptpt)
REVERT: B  466 GLN cc_start: 0.7908 (mt0) cc_final: 0.6757 (tt0)
REVERT: B  498 GLU cc_start: 0.7902 (pt0) cc_final: 0.7534 (pt0)
REVERT: B  615 MET cc_start: 0.8414 (mmm) cc_final: 0.8023 (mmm)
  outliers start: 25
  outliers final: 14
  residues processed: 107
  average time/residue: 0.2305
  time to fit residues: 34.3179
Evaluate side-chains
  101 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  588 ILE
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  582 VAL
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  657 ILE
Chi-restraints excluded: chain B residue  670 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 85 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.169455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.127882 restraints weight = 9172.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 1.72
r_work: 0.3332 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9523  Z= 0.278
  Angle     :  0.567   7.605  12907  Z= 0.288
  Chirality :  0.041   0.183   1435
  Planarity :  0.004   0.044   1625
  Dihedral  :  5.902  63.833   1361
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.27 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.25), residues: 1147
  helix:  1.35 (0.19), residues: 765
  sheet: -2.32 (0.70), residues: 48
  loop : -3.08 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 326 
 HIS   0.004   0.001   HIS B 299 
 PHE   0.009   0.001   PHE A 265 
 TYR   0.014   0.001   TYR A 296 
 ARG   0.002   0.000   ARG B 324 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 87
  time to evaluate  : 1.461 
Fit side-chains
REVERT: A  163 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7859 (ttt180)
REVERT: A  177 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.6717 (mm-40)
REVERT: A  178 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8072 (mt0)
REVERT: B  200 ASP cc_start: 0.6724 (m-30) cc_final: 0.6475 (m-30)
REVERT: B  217 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8081 (ptpt)
REVERT: B  466 GLN cc_start: 0.7926 (mt0) cc_final: 0.6778 (tt0)
REVERT: B  498 GLU cc_start: 0.7890 (pt0) cc_final: 0.7522 (pt0)
REVERT: B  615 MET cc_start: 0.8367 (mmm) cc_final: 0.7959 (mmm)
  outliers start: 27
  outliers final: 19
  residues processed: 109
  average time/residue: 0.2811
  time to fit residues: 43.9658
Evaluate side-chains
  105 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  588 ILE
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  152 ARG
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain B residue  375 GLU
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  582 VAL
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  657 ILE
Chi-restraints excluded: chain B residue  670 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 84 optimal weight:    0.1980
   chunk 49 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.170145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.128375 restraints weight = 9249.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.71
r_work: 0.3240 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9523  Z= 0.279
  Angle     :  0.569   7.488  12907  Z= 0.289
  Chirality :  0.041   0.174   1435
  Planarity :  0.004   0.043   1625
  Dihedral  :  5.880  63.396   1361
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.48 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.25), residues: 1147
  helix:  1.34 (0.19), residues: 765
  sheet: -2.28 (0.71), residues: 48
  loop : -3.06 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 326 
 HIS   0.005   0.001   HIS A 669 
 PHE   0.009   0.001   PHE A 265 
 TYR   0.014   0.002   TYR A 296 
 ARG   0.002   0.000   ARG B 324 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 87
  time to evaluate  : 1.365 
Fit side-chains
REVERT: A  163 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7866 (ttt180)
REVERT: A  177 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.6741 (mm-40)
REVERT: A  178 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8086 (mt0)
REVERT: B  200 ASP cc_start: 0.6745 (m-30) cc_final: 0.6483 (m-30)
REVERT: B  217 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8065 (ptpt)
REVERT: B  466 GLN cc_start: 0.7925 (mt0) cc_final: 0.6753 (tt0)
REVERT: B  498 GLU cc_start: 0.7892 (pt0) cc_final: 0.7536 (pt0)
REVERT: B  615 MET cc_start: 0.8440 (mmm) cc_final: 0.8048 (mmm)
  outliers start: 27
  outliers final: 22
  residues processed: 107
  average time/residue: 0.2669
  time to fit residues: 40.8942
Evaluate side-chains
  107 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  588 ILE
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  152 ARG
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  335 MET
Chi-restraints excluded: chain B residue  375 GLU
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  582 VAL
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  588 ILE
Chi-restraints excluded: chain B residue  657 ILE
Chi-restraints excluded: chain B residue  670 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 102 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 69 optimal weight:    0.4980
   chunk 57 optimal weight:    4.9990
   chunk 106 optimal weight:    0.1980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.172288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.128081 restraints weight = 9092.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 1.72
r_work: 0.3351 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9523  Z= 0.227
  Angle     :  0.545   7.645  12907  Z= 0.277
  Chirality :  0.040   0.172   1435
  Planarity :  0.004   0.043   1625
  Dihedral  :  5.689  62.653   1361
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.68 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.26), residues: 1147
  helix:  1.50 (0.19), residues: 765
  sheet: -2.03 (0.76), residues: 44
  loop : -3.02 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 326 
 HIS   0.004   0.001   HIS A 669 
 PHE   0.007   0.001   PHE A 385 
 TYR   0.014   0.001   TYR A 296 
 ARG   0.002   0.000   ARG A 381 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A  163 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7806 (ttt180)
REVERT: A  177 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.6578 (mm-40)
REVERT: A  178 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8048 (mt0)
REVERT: B   73 GLN cc_start: 0.7229 (tt0) cc_final: 0.7029 (mt0)
REVERT: B  200 ASP cc_start: 0.6653 (m-30) cc_final: 0.6394 (m-30)
REVERT: B  411 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7857 (tm-30)
REVERT: B  466 GLN cc_start: 0.7911 (mt0) cc_final: 0.6762 (tt0)
REVERT: B  498 GLU cc_start: 0.7841 (pt0) cc_final: 0.7491 (pt0)
REVERT: B  502 HIS cc_start: 0.8835 (m90) cc_final: 0.8630 (m170)
REVERT: B  615 MET cc_start: 0.8428 (mmm) cc_final: 0.8019 (mmm)
  outliers start: 27
  outliers final: 20
  residues processed: 112
  average time/residue: 0.2208
  time to fit residues: 34.9107
Evaluate side-chains
  107 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  588 ILE
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  152 ARG
Chi-restraints excluded: chain B residue  375 GLU
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  582 VAL
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  588 ILE
Chi-restraints excluded: chain B residue  657 ILE
Chi-restraints excluded: chain B residue  670 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 111 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 83 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0470
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
B 169 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.172638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.128289 restraints weight = 9155.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 1.73
r_work: 0.3243 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9523  Z= 0.233
  Angle     :  0.556   7.559  12907  Z= 0.281
  Chirality :  0.040   0.165   1435
  Planarity :  0.004   0.043   1625
  Dihedral  :  5.623  61.827   1361
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 14.99 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.26), residues: 1147
  helix:  1.52 (0.19), residues: 763
  sheet: -1.98 (0.77), residues: 44
  loop : -3.01 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 326 
 HIS   0.004   0.001   HIS A 621 
 PHE   0.007   0.001   PHE A 385 
 TYR   0.014   0.001   TYR A 296 
 ARG   0.002   0.000   ARG A 554 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.932 
Fit side-chains
REVERT: A  163 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7805 (ttt180)
REVERT: A  177 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.6540 (mm-40)
REVERT: A  178 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.8065 (mt0)
REVERT: B  200 ASP cc_start: 0.6624 (m-30) cc_final: 0.6354 (m-30)
REVERT: B  466 GLN cc_start: 0.7861 (mt0) cc_final: 0.6691 (tt0)
REVERT: B  498 GLU cc_start: 0.7816 (pt0) cc_final: 0.7460 (pt0)
REVERT: B  615 MET cc_start: 0.8400 (mmm) cc_final: 0.7999 (mmm)
  outliers start: 23
  outliers final: 20
  residues processed: 104
  average time/residue: 0.2224
  time to fit residues: 32.5676
Evaluate side-chains
  106 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 83
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  588 ILE
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  152 ARG
Chi-restraints excluded: chain B residue  335 MET
Chi-restraints excluded: chain B residue  375 GLU
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  582 VAL
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  588 ILE
Chi-restraints excluded: chain B residue  657 ILE
Chi-restraints excluded: chain B residue  670 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 108 optimal weight:    0.6980
   chunk 84 optimal weight:    0.3980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 169 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.177106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.136235 restraints weight = 9062.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 1.68
r_work: 0.3305 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9523  Z= 0.276
  Angle     :  0.576   7.422  12907  Z= 0.292
  Chirality :  0.041   0.157   1435
  Planarity :  0.004   0.043   1625
  Dihedral  :  5.706  61.768   1361
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.99 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.26), residues: 1147
  helix:  1.41 (0.19), residues: 763
  sheet: -2.20 (0.75), residues: 46
  loop : -2.97 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 326 
 HIS   0.004   0.001   HIS B 299 
 PHE   0.008   0.001   PHE A 265 
 TYR   0.018   0.002   TYR B 415 
 ARG   0.002   0.000   ARG B 324 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5121.04 seconds
wall clock time: 91 minutes 44.85 seconds (5504.85 seconds total)