Starting phenix.real_space_refine
on Thu Feb 13 22:01:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x1w_32951/02_2025/7x1w_32951.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x1w_32951/02_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_32951/02_2025/7x1w_32951.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x1w_32951/02_2025/7x1w_32951.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x1w_32951/02_2025/7x1w_32951.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x1w_32951/02_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): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.56, per 1000 atoms: 0.81
  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: 2.68
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.78
  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: 2.63

  Time building geometry restraints manager: 2.95 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:             4.520
  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:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.180
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.030
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.580
-------------------------------------------------------------------------------
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  : 0.965 
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: 0.2581
  time to fit residues: 38.8186
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  : 0.974 
-------------------------------------------------------------------------------
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 = 0.171266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.128208 restraints weight = 9157.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 1.70
r_work: 0.3227 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
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  : 0.997 
Fit side-chains
REVERT: A  615 MET cc_start: 0.8513 (mmm) cc_final: 0.8105 (mmt)
REVERT: B  200 ASP cc_start: 0.6670 (m-30) cc_final: 0.6385 (m-30)
REVERT: B  466 GLN cc_start: 0.7914 (mt0) cc_final: 0.6715 (tt0)
REVERT: B  498 GLU cc_start: 0.7989 (pt0) cc_final: 0.7609 (pt0)
  outliers start: 7
  outliers final: 5
  residues processed: 96
  average time/residue: 0.2506
  time to fit residues: 33.0604
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  : 1.099 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 93 optimal weight:    0.0870
   chunk 45 optimal weight:    0.2980
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 105 optimal weight:    0.0670
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.3296

-------------------------------------------------------------------------------
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 = 0.3929 r_free = 0.3929 target = 0.176618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.133606 restraints weight = 9063.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 1.70
r_work: 0.3362 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.1304

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= 0.172
  Angle     :  0.526   8.692  12907  Z= 0.269
  Chirality :  0.038   0.146   1435
  Planarity :  0.004   0.044   1625
  Dihedral  :  6.235  69.459   1361
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  9.03 %
    Favored  : 89.84 %
  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: -0.10 (0.26), residues: 1147
  helix:  1.38 (0.19), residues: 763
  sheet: -2.18 (0.75), residues: 44
  loop : -3.27 (0.30), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 326 
 HIS   0.003   0.001   HIS A 299 
 PHE   0.010   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
  110 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 1.064 
Fit side-chains
REVERT: A  186 MET cc_start: 0.8185 (mtt) cc_final: 0.7788 (mtt)
REVERT: A  411 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7313 (tt0)
REVERT: A  618 MET cc_start: 0.8158 (tmm) cc_final: 0.7777 (ttt)
REVERT: B  200 ASP cc_start: 0.6619 (m-30) cc_final: 0.6368 (m-30)
REVERT: B  466 GLN cc_start: 0.7859 (mt0) cc_final: 0.6695 (tt0)
REVERT: B  498 GLU cc_start: 0.7920 (pt0) cc_final: 0.7627 (pt0)
  outliers start: 11
  outliers final: 4
  residues processed: 107
  average time/residue: 0.1978
  time to fit residues: 31.1911
Evaluate side-chains
  90 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  498 GLU
Chi-restraints excluded: chain A residue  657 ILE
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:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0000
   chunk 3 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0470
   overall best weight:    0.4482

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
** B 502 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 = 0.4008 r_free = 0.4008 target = 0.183100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.145229 restraints weight = 8858.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 1.58
r_work: 0.3324 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9523  Z= 0.190
  Angle     :  0.532   9.794  12907  Z= 0.271
  Chirality :  0.039   0.241   1435
  Planarity :  0.004   0.041   1625
  Dihedral  :  5.858  63.299   1361
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 11.29 %
    Favored  : 86.76 %
  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:  0.10 (0.26), residues: 1147
  helix:  1.54 (0.19), residues: 761
  sheet: -2.12 (0.75), residues: 46
  loop : -3.19 (0.30), residues: 340

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   0.009   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: 19
    poor density    : 92
  time to evaluate  : 1.034 
Fit side-chains
REVERT: A  200 ASP cc_start: 0.6665 (m-30) cc_final: 0.6447 (m-30)
REVERT: A  411 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7688 (tm-30)
REVERT: A  615 MET cc_start: 0.8094 (mmm) cc_final: 0.7867 (mmt)
REVERT: A  618 MET cc_start: 0.8168 (tmm) cc_final: 0.7741 (ttt)
REVERT: B  466 GLN cc_start: 0.7857 (mt0) cc_final: 0.6735 (tt0)
REVERT: B  498 GLU cc_start: 0.7860 (pt0) cc_final: 0.7612 (pt0)
REVERT: B  615 MET cc_start: 0.8448 (mmm) cc_final: 0.8013 (mmp)
  outliers start: 19
  outliers final: 12
  residues processed: 108
  average time/residue: 0.2399
  time to fit residues: 35.7396
Evaluate side-chains
  95 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
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 B residue  325 LEU
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:    2.9990
   chunk 111 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0050
   chunk 2 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.7798

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
B  73 GLN
** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.174216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.130602 restraints weight = 9093.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.71
r_work: 0.3235 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.1515

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= 0.266
  Angle     :  0.570   9.380  12907  Z= 0.289
  Chirality :  0.041   0.229   1435
  Planarity :  0.004   0.045   1625
  Dihedral  :  5.863  63.210   1361
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 12.53 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.25), residues: 1147
  helix:  1.38 (0.19), residues: 763
  sheet: -2.28 (0.71), residues: 48
  loop : -3.14 (0.30), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 326 
 HIS   0.004   0.001   HIS B 299 
 PHE   0.010   0.001   PHE B 540 
 TYR   0.016   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
  110 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A  178 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8092 (mt0)
REVERT: A  411 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7733 (tm-30)
REVERT: B  200 ASP cc_start: 0.6704 (m-30) cc_final: 0.6480 (m-30)
REVERT: B  466 GLN cc_start: 0.7905 (mt0) cc_final: 0.6746 (tt0)
REVERT: B  498 GLU cc_start: 0.7767 (pt0) cc_final: 0.7440 (pt0)
REVERT: B  615 MET cc_start: 0.8425 (mmm) cc_final: 0.8008 (mmm)
  outliers start: 23
  outliers final: 16
  residues processed: 106
  average time/residue: 0.2569
  time to fit residues: 37.1054
Evaluate side-chains
  98 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  325 LEU
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  503 LEU
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:    0.6980
   chunk 28 optimal weight:    0.2980
   chunk 54 optimal weight:    0.6980
   chunk 69 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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**
** B 502 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 = 0.3864 r_free = 0.3864 target = 0.170550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.128768 restraints weight = 9117.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.68
r_work: 0.3252 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1581

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= 0.255
  Angle     :  0.560   8.066  12907  Z= 0.283
  Chirality :  0.040   0.208   1435
  Planarity :  0.004   0.044   1625
  Dihedral  :  5.806  62.688   1361
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.17 %
    Favored  : 83.57 %
  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:  0.02 (0.25), residues: 1147
  helix:  1.41 (0.19), residues: 765
  sheet: -2.24 (0.71), residues: 48
  loop : -3.09 (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   0.008   0.001   PHE B 265 
 TYR   0.014   0.001   TYR A 296 
 ARG   0.002   0.000   ARG B 308 

*********************** 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
  105 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 1.114 
Fit side-chains
REVERT: A  411 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7665 (tm-30)
REVERT: B  200 ASP cc_start: 0.6746 (m-30) cc_final: 0.6506 (m-30)
REVERT: B  466 GLN cc_start: 0.7939 (mt0) cc_final: 0.6782 (tt0)
REVERT: B  498 GLU cc_start: 0.7898 (pt0) cc_final: 0.7560 (pt0)
REVERT: B  615 MET cc_start: 0.8495 (mmm) cc_final: 0.8121 (mmm)
  outliers start: 22
  outliers final: 17
  residues processed: 100
  average time/residue: 0.2639
  time to fit residues: 36.9465
Evaluate side-chains
  97 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
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  325 LEU
Chi-restraints excluded: chain B residue  375 GLU
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  503 LEU
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:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0040
   chunk 73 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0770
   chunk 60 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.4350

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

Flipped N/Q/H residues before XYZ refinement:
** B 502 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 = 0.3877 r_free = 0.3877 target = 0.172274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.128636 restraints weight = 9139.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.68
r_work: 0.3271 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9523  Z= 0.187
  Angle     :  0.523   7.280  12907  Z= 0.265
  Chirality :  0.039   0.198   1435
  Planarity :  0.004   0.043   1625
  Dihedral  :  5.506  60.777   1361
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.37 %
    Favored  : 83.47 %
  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:  0.30 (0.26), residues: 1147
  helix:  1.64 (0.19), residues: 764
  sheet: -1.93 (0.78), residues: 44
  loop : -3.04 (0.30), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 326 
 HIS   0.004   0.001   HIS B 621 
 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 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
  109 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A  411 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7551 (tm-30)
REVERT: A  618 MET cc_start: 0.8219 (tmm) cc_final: 0.7848 (ttt)
REVERT: B  200 ASP cc_start: 0.6606 (m-30) cc_final: 0.6353 (m-30)
REVERT: B  376 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7433 (tt0)
REVERT: B  466 GLN cc_start: 0.7863 (mt0) cc_final: 0.6718 (tt0)
REVERT: B  498 GLU cc_start: 0.7836 (pt0) cc_final: 0.7553 (pt0)
REVERT: B  615 MET cc_start: 0.8468 (mmm) cc_final: 0.8069 (mmm)
  outliers start: 21
  outliers final: 15
  residues processed: 105
  average time/residue: 0.2290
  time to fit residues: 33.7658
Evaluate side-chains
  97 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
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  657 ILE
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  375 GLU
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  503 LEU
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:    3.9990
   chunk 110 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0770
   chunk 34 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0770
   chunk 63 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 102 optimal weight:    0.7980
   overall best weight:    0.5096

-------------------------------------------------------------------------------
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**
** B 502 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 = 0.3853 r_free = 0.3853 target = 0.170524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.128947 restraints weight = 9256.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 1.73
r_work: 0.3359 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9523  Z= 0.210
  Angle     :  0.535   7.045  12907  Z= 0.271
  Chirality :  0.039   0.177   1435
  Planarity :  0.004   0.043   1625
  Dihedral  :  5.452  60.181   1361
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.17 %
    Favored  : 83.78 %
  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:  0.33 (0.26), residues: 1147
  helix:  1.66 (0.19), residues: 763
  sheet: -1.89 (0.79), residues: 44
  loop : -2.99 (0.30), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 326 
 HIS   0.006   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 381 

*********************** 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
  107 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 1.011 
Fit side-chains
REVERT: A  411 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7678 (tm-30)
REVERT: A  618 MET cc_start: 0.8270 (tmm) cc_final: 0.7911 (ttt)
REVERT: B  200 ASP cc_start: 0.6678 (m-30) cc_final: 0.6428 (m-30)
REVERT: B  376 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7500 (tt0)
REVERT: B  466 GLN cc_start: 0.7928 (mt0) cc_final: 0.6823 (tt0)
REVERT: B  498 GLU cc_start: 0.7838 (pt0) cc_final: 0.7493 (pt0)
REVERT: B  501 MET cc_start: 0.8593 (mmm) cc_final: 0.8323 (mmt)
REVERT: B  615 MET cc_start: 0.8478 (mmm) cc_final: 0.8007 (mmm)
  outliers start: 20
  outliers final: 19
  residues processed: 102
  average time/residue: 0.2323
  time to fit residues: 33.0403
Evaluate side-chains
  102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
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  657 ILE
Chi-restraints excluded: chain B residue  123 VAL
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  503 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0770
   chunk 1 optimal weight:    0.8980
   chunk 102 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   chunk 57 optimal weight:    4.9990
   chunk 106 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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**
** B 502 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 = 0.3894 r_free = 0.3894 target = 0.173239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.129034 restraints weight = 9083.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.72
r_work: 0.3234 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9523  Z= 0.231
  Angle     :  0.546   6.934  12907  Z= 0.276
  Chirality :  0.040   0.167   1435
  Planarity :  0.004   0.043   1625
  Dihedral  :  5.473  59.970   1361
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.58 %
    Favored  : 83.26 %
  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:  0.28 (0.26), residues: 1147
  helix:  1.61 (0.19), residues: 763
  sheet: -1.94 (0.76), residues: 46
  loop : -3.00 (0.30), 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 621 
 PHE   0.007   0.001   PHE A 385 
 TYR   0.013   0.001   TYR A 296 
 ARG   0.002   0.000   ARG B 324 

*********************** 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
  104 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 1.030 
Fit side-chains
REVERT: A  411 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7657 (tm-30)
REVERT: A  618 MET cc_start: 0.8197 (tmm) cc_final: 0.7879 (ttt)
REVERT: B  200 ASP cc_start: 0.6626 (m-30) cc_final: 0.6367 (m-30)
REVERT: B  376 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7434 (tt0)
REVERT: B  466 GLN cc_start: 0.7867 (mt0) cc_final: 0.6727 (tt0)
REVERT: B  498 GLU cc_start: 0.7799 (pt0) cc_final: 0.7434 (pt0)
REVERT: B  501 MET cc_start: 0.8575 (mmm) cc_final: 0.8295 (mmt)
  outliers start: 21
  outliers final: 20
  residues processed: 99
  average time/residue: 0.2303
  time to fit residues: 32.3893
Evaluate side-chains
  99 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  347 VAL
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  657 ILE
Chi-restraints excluded: chain B residue  123 VAL
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  503 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 83 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0970
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
B  73 GLN
** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 502 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 = 0.3884 r_free = 0.3884 target = 0.172622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.130798 restraints weight = 9159.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 1.66
r_work: 0.3373 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1802

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= 0.224
  Angle     :  0.545   6.976  12907  Z= 0.276
  Chirality :  0.040   0.163   1435
  Planarity :  0.004   0.042   1625
  Dihedral  :  5.449  59.608   1361
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.27 %
    Favored  : 83.26 %
  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:  0.28 (0.26), residues: 1147
  helix:  1.60 (0.19), residues: 763
  sheet: -1.91 (0.76), residues: 46
  loop : -2.96 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 326 
 HIS   0.003   0.001   HIS B 299 
 PHE   0.007   0.001   PHE A 385 
 TYR   0.013   0.001   TYR A 296 
 ARG   0.002   0.000   ARG A 381 

********************** 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
  108 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 1.061 
Fit side-chains
REVERT: A  618 MET cc_start: 0.8269 (tmm) cc_final: 0.7927 (ttt)
REVERT: B  187 ASP cc_start: 0.7857 (m-30) cc_final: 0.7641 (m-30)
REVERT: B  200 ASP cc_start: 0.6727 (m-30) cc_final: 0.6476 (m-30)
REVERT: B  376 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7505 (tt0)
REVERT: B  466 GLN cc_start: 0.7933 (mt0) cc_final: 0.6833 (tt0)
REVERT: B  498 GLU cc_start: 0.7846 (pt0) cc_final: 0.7520 (pt0)
REVERT: B  501 MET cc_start: 0.8609 (mmm) cc_final: 0.8339 (mmt)
  outliers start: 24
  outliers final: 23
  residues processed: 102
  average time/residue: 0.2330
  time to fit residues: 33.2701
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  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  347 VAL
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  657 ILE
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  152 ARG
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  503 LEU
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:    0.5980
   chunk 72 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 95 optimal weight:    0.2980
   chunk 108 optimal weight:    0.6980
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B  73 GLN
B 169 HIS
** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.170156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.125323 restraints weight = 9191.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.75
r_work: 0.3278 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1817

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= 0.237
  Angle     :  0.552   6.912  12907  Z= 0.280
  Chirality :  0.040   0.158   1435
  Planarity :  0.004   0.042   1625
  Dihedral  :  5.462  59.528   1361
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 14.48 %
    Favored  : 82.85 %
  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:  0.25 (0.26), residues: 1147
  helix:  1.56 (0.19), residues: 763
  sheet: -1.92 (0.76), residues: 46
  loop : -2.94 (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   0.007   0.001   PHE B  71 
 TYR   0.023   0.001   TYR A 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: 4699.41 seconds
wall clock time: 84 minutes 16.86 seconds (5056.86 seconds total)