Starting phenix.real_space_refine
on Wed Feb  4 17:21:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9e61_47541/02_2026/9e61_47541.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9e61_47541/02_2026/9e61_47541.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9e61_47541/02_2026/9e61_47541.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9e61_47541/02_2026/9e61_47541.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9e61_47541/02_2026/9e61_47541.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9e61_47541/02_2026/9e61_47541.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.005
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       2      5.49       5
     S      42      5.16       5
     C    7955      2.51       5
     N    1915      2.21       5
     O    2109      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 178 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12023
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 726, 5963
          Classifications: {'peptide': 726}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 689}
    Chain: "B"
      Number of atoms: 5979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 728, 5979
          Classifications: {'peptide': 728}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 691}
    Chain: "A"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 41
          Unusual residues: {'CPL': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'CPL:plan-4': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "B"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'CPL': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'CPL:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 2.47, per 1000 atoms: 0.21
  Number of scatterers: 12023
  At special positions: 0
  Unit cell: (100.188, 115.92, 133.308, 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      42     16.00
     P       2     15.00
     O    2109      8.00
     N    1915      7.00
     C    7955      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 501.8 milliseconds
  

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2768

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 4 sheets defined
      56.3% alpha, 8.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 48 through 69
      removed outlier: 3.719A  pdb=" N   TYR A  52 " --> pdb=" O   PRO A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 94
      removed outlier: 4.016A  pdb=" N   LYS A  86 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 116
    Processing helix  chain 'A' and resid 137 through 163
      removed outlier: 3.918A  pdb=" N   VAL A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      Proline residue:  A 154  - end of helix
    Processing helix  chain 'A' and resid 166 through 179
      removed outlier: 3.800A  pdb=" N   VAL A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 189
      removed outlier: 3.767A  pdb=" N   LEU A 189 " --> pdb=" O   THR A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 217
    Processing helix  chain 'A' and resid 220 through 241
    Processing helix  chain 'A' and resid 244 through 264
    Processing helix  chain 'A' and resid 265 through 268
    Processing helix  chain 'A' and resid 270 through 286
    Processing helix  chain 'A' and resid 286 through 304
      removed outlier: 3.604A  pdb=" N   PHE A 297 " --> pdb=" O   TYR A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 314
    Processing helix  chain 'A' and resid 315 through 320
    Processing helix  chain 'A' and resid 325 through 330
      removed outlier: 3.638A  pdb=" N   ASP A 330 " --> pdb=" O   PRO A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 383
      No H-bonds generated for 'chain 'A' and resid 381 through 383'
    Processing helix  chain 'A' and resid 440 through 444
    Processing helix  chain 'A' and resid 447 through 451
    Processing helix  chain 'A' and resid 459 through 463
    Processing helix  chain 'A' and resid 494 through 498
    Processing helix  chain 'A' and resid 511 through 514
    Processing helix  chain 'A' and resid 525 through 530
    Processing helix  chain 'A' and resid 540 through 558
    Processing helix  chain 'A' and resid 568 through 572
    Processing helix  chain 'A' and resid 596 through 623
    Processing helix  chain 'A' and resid 629 through 638
    Processing helix  chain 'A' and resid 638 through 652
    Processing helix  chain 'A' and resid 653 through 657
    Processing helix  chain 'A' and resid 662 through 665
    Processing helix  chain 'A' and resid 666 through 685
      removed outlier: 3.551A  pdb=" N   LEU A 675 " --> pdb=" O   LEU A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 739
      Proline residue:  A 735  - end of helix
    Processing helix  chain 'A' and resid 744 through 750
    Processing helix  chain 'B' and resid 37 through 42
    Processing helix  chain 'B' and resid 48 through 69
      removed outlier: 3.721A  pdb=" N   TYR B  52 " --> pdb=" O   PRO B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 94
      removed outlier: 4.016A  pdb=" N   LYS B  86 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 116
    Processing helix  chain 'B' and resid 137 through 163
      removed outlier: 3.916A  pdb=" N   VAL B 153 " --> pdb=" O   GLY B 149 " (cutoff:3.500A)
      Proline residue:  B 154  - end of helix
    Processing helix  chain 'B' and resid 166 through 179
      removed outlier: 3.799A  pdb=" N   VAL B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 189
      removed outlier: 3.767A  pdb=" N   LEU B 189 " --> pdb=" O   THR B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 217
    Processing helix  chain 'B' and resid 220 through 241
    Processing helix  chain 'B' and resid 244 through 264
    Processing helix  chain 'B' and resid 265 through 268
    Processing helix  chain 'B' and resid 270 through 286
    Processing helix  chain 'B' and resid 286 through 304
      removed outlier: 3.604A  pdb=" N   PHE B 297 " --> pdb=" O   TYR B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 314
    Processing helix  chain 'B' and resid 315 through 320
    Processing helix  chain 'B' and resid 325 through 331
      removed outlier: 3.811A  pdb=" N   ASP B 330 " --> pdb=" O   LEU B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 383
      No H-bonds generated for 'chain 'B' and resid 381 through 383'
    Processing helix  chain 'B' and resid 440 through 444
    Processing helix  chain 'B' and resid 447 through 451
    Processing helix  chain 'B' and resid 459 through 463
    Processing helix  chain 'B' and resid 494 through 498
    Processing helix  chain 'B' and resid 511 through 514
    Processing helix  chain 'B' and resid 525 through 530
    Processing helix  chain 'B' and resid 540 through 557
    Processing helix  chain 'B' and resid 568 through 572
    Processing helix  chain 'B' and resid 596 through 623
    Processing helix  chain 'B' and resid 629 through 638
    Processing helix  chain 'B' and resid 638 through 652
    Processing helix  chain 'B' and resid 653 through 657
    Processing helix  chain 'B' and resid 662 through 665
    Processing helix  chain 'B' and resid 666 through 685
      removed outlier: 3.552A  pdb=" N   LEU B 675 " --> pdb=" O   LEU B 671 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 711 through 739
      Proline residue:  B 735  - end of helix
    Processing helix  chain 'B' and resid 744 through 750
    Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 344
      removed outlier: 13.272A  pdb=" N   ILE A 340 " --> pdb=" O   SER A 353 " (cutoff:3.500A)
      removed outlier: 9.963A  pdb=" N   SER A 353 " --> pdb=" O   ILE A 340 " (cutoff:3.500A)
      removed outlier: 5.336A  pdb=" N   ILE A 342 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   HIS A 354 " --> pdb=" O   GLN A 373 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   GLN A 373 " --> pdb=" O   HIS A 354 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 372 through 377
    current: chain 'A' and resid 407 through 412
      removed outlier: 13.285A  pdb=" N   ILE A 408 " --> pdb=" O   ALA A 421 " (cutoff:3.500A)
      removed outlier: 10.046A  pdb=" N   ALA A 421 " --> pdb=" O   ILE A 408 " (cutoff:3.500A)
      removed outlier: 5.493A  pdb=" N   LEU A 410 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR A 417 " --> pdb=" O   HIS A 412 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   LEU A 420 " --> pdb=" O   VAL A 438 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   VAL A 438 " --> pdb=" O   LEU A 420 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   HIS A 422 " --> pdb=" O   THR A 436 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   THR A 436 " --> pdb=" O   HIS A 422 " (cutoff:3.500A)
      removed outlier: 5.732A  pdb=" N   VAL A 424 " --> pdb=" O   GLU A 434 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 433 through 439
    current: chain 'A' and resid 473 through 478
      removed outlier: 13.816A  pdb=" N   PHE A 474 " --> pdb=" O   THR A 487 " (cutoff:3.500A)
      removed outlier: 10.440A  pdb=" N   THR A 487 " --> pdb=" O   PHE A 474 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   LEU A 476 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 579 through 584
      removed outlier: 6.363A  pdb=" N   ILE A 591 " --> pdb=" O   PHE A 581 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   THR A 583 " --> pdb=" O   LYS A 589 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   LYS A 589 " --> pdb=" O   THR A 583 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 339 through 344
      removed outlier: 13.271A  pdb=" N   ILE B 340 " --> pdb=" O   SER B 353 " (cutoff:3.500A)
      removed outlier: 9.965A  pdb=" N   SER B 353 " --> pdb=" O   ILE B 340 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   ILE B 342 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   HIS B 354 " --> pdb=" O   GLN B 373 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   GLN B 373 " --> pdb=" O   HIS B 354 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 372 through 377
    current: chain 'B' and resid 407 through 412
      removed outlier: 13.285A  pdb=" N   ILE B 408 " --> pdb=" O   ALA B 421 " (cutoff:3.500A)
      removed outlier: 10.047A  pdb=" N   ALA B 421 " --> pdb=" O   ILE B 408 " (cutoff:3.500A)
      removed outlier: 5.493A  pdb=" N   LEU B 410 " --> pdb=" O   LEU B 419 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   THR B 417 " --> pdb=" O   HIS B 412 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   LEU B 420 " --> pdb=" O   VAL B 438 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   VAL B 438 " --> pdb=" O   LEU B 420 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   HIS B 422 " --> pdb=" O   THR B 436 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   THR B 436 " --> pdb=" O   HIS B 422 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   VAL B 424 " --> pdb=" O   GLU B 434 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 433 through 439
    current: chain 'B' and resid 473 through 478
      removed outlier: 13.818A  pdb=" N   PHE B 474 " --> pdb=" O   THR B 487 " (cutoff:3.500A)
      removed outlier: 10.440A  pdb=" N   THR B 487 " --> pdb=" O   PHE B 474 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   LEU B 476 " --> pdb=" O   LEU B 485 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 579 through 584
      removed outlier: 6.363A  pdb=" N   ILE B 591 " --> pdb=" O   PHE B 581 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   THR B 583 " --> pdb=" O   LYS B 589 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   LYS B 589 " --> pdb=" O   THR B 583 " (cutoff:3.500A)

    579 hydrogen bonds defined for protein.
    1620 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.52

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2122
        1.33 -     1.45: 3518
        1.45 -     1.57: 6721
        1.57 -     1.70: 4
        1.70 -     1.82: 64
  Bond restraints: 12429
  Sorted by residual:
  bond pdb=" CE1 HIS B 563 "
       pdb=" NE2 HIS B 563 "
    ideal  model  delta    sigma   weight residual
    1.321  1.362 -0.041 1.00e-02 1.00e+04 1.64e+01
  bond pdb=" CE1 HIS A 563 "
       pdb=" NE2 HIS A 563 "
    ideal  model  delta    sigma   weight residual
    1.321  1.361 -0.040 1.00e-02 1.00e+04 1.58e+01
  bond pdb=" CZ  ARG A 409 "
       pdb=" NH2 ARG A 409 "
    ideal  model  delta    sigma   weight residual
    1.330  1.286  0.044 1.30e-02 5.92e+03 1.14e+01
  bond pdb=" N   SER A 331 "
       pdb=" CA  SER A 331 "
    ideal  model  delta    sigma   weight residual
    1.454  1.495 -0.041 1.23e-02 6.61e+03 1.13e+01
  bond pdb=" CZ  ARG B 409 "
       pdb=" NH2 ARG B 409 "
    ideal  model  delta    sigma   weight residual
    1.330  1.287  0.043 1.30e-02 5.92e+03 1.07e+01
  ... (remaining 12424 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 13163
        1.91 -     3.82: 3383
        3.82 -     5.73: 356
        5.73 -     7.64: 21
        7.64 -     9.55: 8
  Bond angle restraints: 16931
  Sorted by residual:
  angle pdb=" OD1 ASN A 629 "
        pdb=" CG  ASN A 629 "
        pdb=" ND2 ASN A 629 "
      ideal   model   delta    sigma   weight residual
     122.60  116.53    6.07 1.00e+00 1.00e+00 3.68e+01
  angle pdb=" OD1 ASN B 629 "
        pdb=" CG  ASN B 629 "
        pdb=" ND2 ASN B 629 "
      ideal   model   delta    sigma   weight residual
     122.60  116.54    6.06 1.00e+00 1.00e+00 3.68e+01
  angle pdb=" OE1 GLN A 373 "
        pdb=" CD  GLN A 373 "
        pdb=" NE2 GLN A 373 "
      ideal   model   delta    sigma   weight residual
     122.60  116.82    5.78 1.00e+00 1.00e+00 3.35e+01
  angle pdb=" OE1 GLN B 373 "
        pdb=" CD  GLN B 373 "
        pdb=" NE2 GLN B 373 "
      ideal   model   delta    sigma   weight residual
     122.60  116.91    5.69 1.00e+00 1.00e+00 3.24e+01
  angle pdb=" C   THR A 152 "
        pdb=" N   VAL A 153 "
        pdb=" CA  VAL A 153 "
      ideal   model   delta    sigma   weight residual
     120.33  124.69   -4.36 8.00e-01 1.56e+00 2.97e+01
  ... (remaining 16926 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.25: 6991
       33.25 -    66.50: 134
       66.50 -    99.74: 7
       99.74 -   132.99: 1
      132.99 -   166.24: 4
  Dihedral angle restraints: 7137
    sinusoidal: 2841
      harmonic: 4296
  Sorted by residual:
  dihedral pdb=" N   CPL A 801 "
           pdb=" C4  CPL A 801 "
           pdb=" C5  CPL A 801 "
           pdb=" O4P CPL A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.08   95.16 -166.24     1      3.00e+01 1.11e-03 2.10e+01
  dihedral pdb=" C33 CPL A 801 "
           pdb=" C31 CPL A 801 "
           pdb=" C32 CPL A 801 "
           pdb=" O2  CPL A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.65  -28.11 -160.24     1      3.00e+01 1.11e-03 2.07e+01
  dihedral pdb=" O2  CPL A 801 "
           pdb=" C1  CPL A 801 "
           pdb=" C2  CPL A 801 "
           pdb=" O3P CPL A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -50.82   88.52 -139.34     1      3.00e+01 1.11e-03 1.88e+01
  ... (remaining 7134 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1046
       0.066 -    0.131: 539
       0.131 -    0.197: 178
       0.197 -    0.263: 42
       0.263 -    0.328: 6
  Chirality restraints: 1811
  Sorted by residual:
  chirality pdb=" CA  THR A 187 "
            pdb=" N   THR A 187 "
            pdb=" C   THR A 187 "
            pdb=" CB  THR A 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.20    0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" CA  THR B 187 "
            pdb=" N   THR B 187 "
            pdb=" C   THR B 187 "
            pdb=" CB  THR B 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.20    0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" CA  ASN A 164 "
            pdb=" N   ASN A 164 "
            pdb=" C   ASN A 164 "
            pdb=" CB  ASN A 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.33 2.00e-01 2.50e+01 2.64e+00
  ... (remaining 1808 not shown)

  Planarity restraints: 2107
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C38 CPL A 801 "    0.065 2.00e-02 2.50e+03   1.23e-01 1.51e+02
        pdb=" C39 CPL A 801 "   -0.161 2.00e-02 2.50e+03
        pdb=" C40 CPL A 801 "    0.161 2.00e-02 2.50e+03
        pdb=" C41 CPL A 801 "   -0.065 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 242 "    0.082 2.00e-02 2.50e+03   5.43e-02 5.89e+01
        pdb=" CG  TYR B 242 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 242 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 242 "   -0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 242 "   -0.035 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 242 "   -0.048 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 242 "   -0.023 2.00e-02 2.50e+03
        pdb=" OH  TYR B 242 "    0.100 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 242 "   -0.081 2.00e-02 2.50e+03   5.40e-02 5.84e+01
        pdb=" CG  TYR A 242 "    0.003 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 242 "    0.045 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 242 "    0.026 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 242 "    0.035 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 242 "    0.048 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 242 "    0.023 2.00e-02 2.50e+03
        pdb=" OH  TYR A 242 "   -0.100 2.00e-02 2.50e+03
  ... (remaining 2104 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 982
        2.78 -     3.31: 12616
        3.31 -     3.84: 20790
        3.84 -     4.37: 26193
        4.37 -     4.90: 42516
  Nonbonded interactions: 103097
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 326 "
            pdb=" CG2 VAL A 329 "
     model   vdw
     2.254 3.460
  nonbonded pdb=" O   PRO B 326 "
            pdb=" CG1 VAL B 329 "
     model   vdw
     2.326 3.460
  nonbonded pdb=" CD2 HIS A 622 "
            pdb=" CD2 LEU B 263 "
     model   vdw
     2.433 3.680
  nonbonded pdb=" O   SER A 328 "
            pdb=" OG  SER A 331 "
     model   vdw
     2.469 3.040
  nonbonded pdb=" O   SER A 560 "
            pdb=" OG  SER A 561 "
     model   vdw
     2.492 3.040
  ... (remaining 103092 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' and (resid 37 through 762 or (resid 801 and (name N or name C1 or nam \ 
e C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ 
 name C18 or name C19 or name C2 or name C3 or name C31 or name C32 or name C33  \ 
or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name  \ 
C4 or name C40 or name C41 or name C42 or name C5 or name C6 or name C7 or name  \ 
C8 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name \ 
 O3P or name O4P or name P ))))
  selection = (chain 'B' and (resid 37 through 762 or (resid 801 and (name N or name C1 or nam \ 
e C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ 
 name C18 or name C19 or name C2 or name C3 or name C31 or name C32 or name C33  \ 
or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name  \ 
C4 or name C40 or name C41 or name C42 or name C5 or name C6 or name C7 or name  \ 
C8 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name \ 
 O3P or name O4P or name P ))))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.490
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
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      :  0.013   0.045  12429  Z= 0.742
  Angle     :  1.604   9.555  16931  Z= 1.085
  Chirality :  0.086   0.328   1811
  Planarity :  0.014   0.145   2107
  Dihedral  : 13.102 166.239   4369
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.38 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.16 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.21), residues: 1450
  helix:  0.42 (0.18), residues: 708
  sheet: -1.06 (0.53), residues: 84
  loop :  0.22 (0.24), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.002   ARG A 409 
 TYR   0.100   0.016   TYR B 242 
 PHE   0.052   0.011   PHE B 455 
 TRP   0.080   0.017   TRP B 486 
 HIS   0.020   0.007   HIS B 478 

Details of bonding type rmsd
  covalent geometry    : bond        0.01306 (12429)
  covalent geometry    : angle       1.60426 (16931)
  hydrogen bonds       : bond        0.15529 (  579)
  hydrogen bonds       : angle       6.32902 ( 1620)

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

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

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 336
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 THR cc_start: 0.8660 (m) cc_final: 0.8261 (p)
REVERT: A  223 TRP cc_start: 0.8996 (t60) cc_final: 0.8312 (t60)
REVERT: A  246 MET cc_start: 0.8472 (mmt) cc_final: 0.7633 (mmt)
REVERT: A  544 LYS cc_start: 0.8844 (tttt) cc_final: 0.8323 (mtmt)
REVERT: A  634 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8045 (tt0)
REVERT: A  695 LYS cc_start: 0.8080 (mttt) cc_final: 0.7774 (mttm)
REVERT: A  719 LEU cc_start: 0.9114 (mt) cc_final: 0.8796 (mt)
REVERT: B   40 TRP cc_start: 0.8317 (t-100) cc_final: 0.7949 (t-100)
REVERT: B   99 ASP cc_start: 0.8227 (t0) cc_final: 0.7949 (t70)
REVERT: B  131 TYR cc_start: 0.7907 (m-80) cc_final: 0.7425 (m-10)
REVERT: B  519 ASP cc_start: 0.8566 (t70) cc_final: 0.8036 (t0)
REVERT: B  552 MET cc_start: 0.8845 (mtt) cc_final: 0.8444 (mtt)
REVERT: B  719 LEU cc_start: 0.8857 (mt) cc_final: 0.8482 (mt)
REVERT: B  738 TYR cc_start: 0.8928 (m-80) cc_final: 0.8722 (m-80)
REVERT: B  752 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7810 (mt-10)
REVERT: B  756 ILE cc_start: 0.7554 (mt) cc_final: 0.7290 (mt)
REVERT: B  758 LEU cc_start: 0.8062 (mt) cc_final: 0.7782 (mp)
  outliers start: 1
  outliers final: 0
  residues processed: 336
  average time/residue: 0.0875
  time to fit residues: 44.0188
Evaluate side-chains
  154 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.4980
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.6988

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

Flipped N/Q/H residues before XYZ refinement:
A 405 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 GLN
B 261 GLN
B 335 ASN
B 385 GLN
** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 603 GLN
B 660 GLN
B 670 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.128702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.101518 restraints weight = 23976.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.104350 restraints weight = 11680.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.106106 restraints weight = 7374.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.107397 restraints weight = 5541.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.108125 restraints weight = 4550.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12429  Z= 0.146
  Angle     :  0.564   7.024  16931  Z= 0.301
  Chirality :  0.045   0.153   1811
  Planarity :  0.005   0.047   2107
  Dihedral  : 10.064 150.757   1643
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  7.88 %
    Favored  : 89.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.22), residues: 1450
  helix:  1.82 (0.19), residues: 713
  sheet: -1.23 (0.51), residues: 94
  loop :  0.60 (0.25), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 188 
 TYR   0.023   0.002   TYR A 715 
 PHE   0.020   0.002   PHE B 553 
 TRP   0.016   0.001   TRP A 223 
 HIS   0.009   0.001   HIS A 664 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (12429)
  covalent geometry    : angle       0.56392 (16931)
  hydrogen bonds       : bond        0.04865 (  579)
  hydrogen bonds       : angle       4.37032 ( 1620)

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

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

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 174
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 PHE cc_start: 0.9034 (t80) cc_final: 0.8610 (t80)
REVERT: A  246 MET cc_start: 0.8590 (mmt) cc_final: 0.7921 (mmt)
REVERT: A  539 LEU cc_start: 0.8548 (tp) cc_final: 0.8194 (tp)
REVERT: A  544 LYS cc_start: 0.8597 (tttt) cc_final: 0.8171 (mttt)
REVERT: A  634 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8484 (tt0)
REVERT: A  695 LYS cc_start: 0.8332 (mttt) cc_final: 0.7967 (mttm)
REVERT: B   99 ASP cc_start: 0.8443 (t0) cc_final: 0.8005 (t70)
REVERT: B  193 ASP cc_start: 0.7308 (m-30) cc_final: 0.6923 (t70)
REVERT: B  198 ILE cc_start: 0.9057 (tp) cc_final: 0.8790 (tp)
REVERT: B  199 SER cc_start: 0.9474 (m) cc_final: 0.9025 (t)
REVERT: B  314 MET cc_start: 0.7685 (mmt) cc_final: 0.7253 (mmt)
REVERT: B  318 PHE cc_start: 0.8666 (t80) cc_final: 0.8318 (t80)
REVERT: B  519 ASP cc_start: 0.8731 (t70) cc_final: 0.8310 (t0)
REVERT: B  552 MET cc_start: 0.9084 (mtt) cc_final: 0.8499 (mtt)
REVERT: B  646 SER cc_start: 0.8859 (m) cc_final: 0.8415 (t)
REVERT: B  719 LEU cc_start: 0.8924 (mt) cc_final: 0.8561 (mt)
REVERT: B  752 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7457 (mt-10)
  outliers start: 29
  outliers final: 17
  residues processed: 194
  average time/residue: 0.0848
  time to fit residues: 25.3661
Evaluate side-chains
  151 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  422 HIS
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  526 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 141 optimal weight:    0.9990
   chunk 114 optimal weight:    7.9990
   chunk 33 optimal weight:   40.0000
   chunk 96 optimal weight:    8.9990
   chunk 123 optimal weight:   10.0000
   chunk 142 optimal weight:    0.3980
   chunk 79 optimal weight:    5.9990
   chunk 124 optimal weight:   20.0000
   chunk 54 optimal weight:    5.9990
   chunk 108 optimal weight:   20.0000
   chunk 80 optimal weight:   10.0000
   overall best weight:    4.2788

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

Flipped N/Q/H residues before XYZ refinement:
A 345 GLN
A 405 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 549 GLN
A 660 GLN
A 670 HIS
A 759 ASN
B 372 GLN
B 422 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.118499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.091514 restraints weight = 24962.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.094039 restraints weight = 12799.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.095683 restraints weight = 8326.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.096697 restraints weight = 6327.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.097420 restraints weight = 5327.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.3964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  12429  Z= 0.232
  Angle     :  0.632   9.739  16931  Z= 0.330
  Chirality :  0.047   0.240   1811
  Planarity :  0.005   0.047   2107
  Dihedral  :  9.333 133.285   1643
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.10 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  :  9.20 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.22), residues: 1450
  helix:  1.57 (0.19), residues: 719
  sheet: -1.34 (0.49), residues: 101
  loop :  0.39 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 281 
 TYR   0.020   0.002   TYR A 207 
 PHE   0.028   0.002   PHE B 477 
 TRP   0.025   0.002   TRP B  40 
 HIS   0.006   0.002   HIS A 670 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 (12429)
  covalent geometry    : angle       0.63193 (16931)
  hydrogen bonds       : bond        0.05283 (  579)
  hydrogen bonds       : angle       4.63878 ( 1620)

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

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

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 141
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 TRP cc_start: 0.8517 (t-100) cc_final: 0.8234 (t-100)
REVERT: A  388 VAL cc_start: 0.8332 (t) cc_final: 0.8053 (m)
REVERT: A  521 ILE cc_start: 0.7865 (mm) cc_final: 0.7624 (mm)
REVERT: A  544 LYS cc_start: 0.8730 (tttt) cc_final: 0.8230 (ttmt)
REVERT: A  634 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8583 (tt0)
REVERT: A  695 LYS cc_start: 0.8443 (mttt) cc_final: 0.8207 (mttm)
REVERT: B   62 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8996 (tt)
REVERT: B   91 TYR cc_start: 0.8551 (m-80) cc_final: 0.8025 (m-80)
REVERT: B  156 MET cc_start: 0.8877 (tpp) cc_final: 0.8570 (mmp)
REVERT: B  249 SER cc_start: 0.9123 (m) cc_final: 0.8876 (p)
REVERT: B  519 ASP cc_start: 0.8827 (t70) cc_final: 0.8478 (t0)
REVERT: B  587 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8141 (mt-10)
REVERT: B  591 ILE cc_start: 0.9179 (mt) cc_final: 0.8914 (mm)
  outliers start: 37
  outliers final: 27
  residues processed: 171
  average time/residue: 0.0825
  time to fit residues: 21.8925
Evaluate side-chains
  149 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  422 HIS
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  677 SER
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  422 HIS
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  526 GLU
Chi-restraints excluded: chain B residue  622 HIS
Chi-restraints excluded: chain B residue  684 ILE
Chi-restraints excluded: chain B residue  743 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 105 optimal weight:   30.0000
   chunk 123 optimal weight:    3.9990
   chunk 37 optimal weight:    9.9990
   chunk 140 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9990
   chunk 95 optimal weight:   10.0000
   chunk 70 optimal weight:    0.0670
   chunk 81 optimal weight:    3.9990
   chunk 137 optimal weight:    0.0470
   overall best weight:    1.2222

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

Flipped N/Q/H residues before XYZ refinement:
** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 405 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 277 HIS
B 379 HIS
B 422 HIS
** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.121920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.095350 restraints weight = 24361.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.097974 restraints weight = 12207.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.099628 restraints weight = 7820.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.100776 restraints weight = 5894.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.101489 restraints weight = 4889.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.4189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12429  Z= 0.115
  Angle     :  0.491   8.411  16931  Z= 0.260
  Chirality :  0.042   0.129   1811
  Planarity :  0.004   0.043   2107
  Dihedral  :  8.920 129.102   1643
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.14 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 10.36 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.22), residues: 1450
  helix:  1.81 (0.19), residues: 727
  sheet: -1.33 (0.50), residues: 94
  loop :  0.45 (0.25), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 621 
 TYR   0.013   0.001   TYR A 207 
 PHE   0.032   0.001   PHE A 157 
 TRP   0.019   0.001   TRP B  40 
 HIS   0.010   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (12429)
  covalent geometry    : angle       0.49073 (16931)
  hydrogen bonds       : bond        0.04339 (  579)
  hydrogen bonds       : angle       4.14000 ( 1620)

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

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

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 TRP cc_start: 0.8478 (t-100) cc_final: 0.8199 (t-100)
REVERT: A   64 PHE cc_start: 0.9076 (t80) cc_final: 0.8742 (t80)
REVERT: A   91 TYR cc_start: 0.8737 (m-80) cc_final: 0.7593 (t80)
REVERT: A  544 LYS cc_start: 0.8670 (tttt) cc_final: 0.8159 (ttmt)
REVERT: A  634 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8497 (tt0)
REVERT: A  635 LYS cc_start: 0.8337 (mttt) cc_final: 0.8112 (mttt)
REVERT: A  695 LYS cc_start: 0.8426 (mttt) cc_final: 0.8096 (mttm)
REVERT: B   91 TYR cc_start: 0.8406 (m-80) cc_final: 0.8203 (m-80)
REVERT: B   93 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8286 (mt-10)
REVERT: B   99 ASP cc_start: 0.8688 (t0) cc_final: 0.8330 (t70)
REVERT: B  156 MET cc_start: 0.8782 (tpp) cc_final: 0.8512 (mmt)
REVERT: B  474 PHE cc_start: 0.7230 (p90) cc_final: 0.6668 (p90)
REVERT: B  519 ASP cc_start: 0.8907 (t70) cc_final: 0.8607 (t0)
REVERT: B  587 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8080 (mt-10)
REVERT: B  752 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8146 (mt-10)
  outliers start: 33
  outliers final: 23
  residues processed: 166
  average time/residue: 0.0749
  time to fit residues: 19.3941
Evaluate side-chains
  141 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  248 TYR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  422 HIS
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  422 HIS
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  526 GLU
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  622 HIS
Chi-restraints excluded: chain B residue  684 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 31 optimal weight:   30.0000
   chunk 45 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0770
   chunk 114 optimal weight:    9.9990
   chunk 95 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 47 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 142 optimal weight:    0.9990
   overall best weight:    1.4146

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

Flipped N/Q/H residues before XYZ refinement:
** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 405 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 360 GLN
B 379 HIS
B 422 HIS
** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.122039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.095493 restraints weight = 24256.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.098059 restraints weight = 12281.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.099777 restraints weight = 7916.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.100865 restraints weight = 5949.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.101565 restraints weight = 4945.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.4418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12429  Z= 0.116
  Angle     :  0.492   7.285  16931  Z= 0.255
  Chirality :  0.042   0.136   1811
  Planarity :  0.004   0.041   2107
  Dihedral  :  8.677 126.234   1643
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.62 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 11.59 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.22), residues: 1450
  helix:  1.81 (0.19), residues: 728
  sheet: -1.26 (0.52), residues: 93
  loop :  0.52 (0.25), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 621 
 TYR   0.014   0.001   TYR B 418 
 PHE   0.029   0.001   PHE A 157 
 TRP   0.022   0.001   TRP B  40 
 HIS   0.009   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (12429)
  covalent geometry    : angle       0.49234 (16931)
  hydrogen bonds       : bond        0.04166 (  579)
  hydrogen bonds       : angle       4.07261 ( 1620)

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

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

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 TRP cc_start: 0.8535 (t-100) cc_final: 0.8222 (t-100)
REVERT: A   64 PHE cc_start: 0.9092 (t80) cc_final: 0.8723 (t80)
REVERT: A   91 TYR cc_start: 0.8714 (m-80) cc_final: 0.7540 (t80)
REVERT: A  544 LYS cc_start: 0.8670 (tttt) cc_final: 0.8197 (ttmt)
REVERT: A  634 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8436 (tt0)
REVERT: A  635 LYS cc_start: 0.8385 (mttt) cc_final: 0.8167 (mttt)
REVERT: A  695 LYS cc_start: 0.8361 (mttt) cc_final: 0.8039 (mttm)
REVERT: B   93 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8283 (mt-10)
REVERT: B   99 ASP cc_start: 0.8716 (t0) cc_final: 0.8385 (t70)
REVERT: B  156 MET cc_start: 0.8735 (tpp) cc_final: 0.8456 (mmt)
REVERT: B  193 ASP cc_start: 0.7052 (m-30) cc_final: 0.6549 (t70)
REVERT: B  474 PHE cc_start: 0.7279 (p90) cc_final: 0.6696 (p90)
REVERT: B  646 SER cc_start: 0.8844 (m) cc_final: 0.8461 (t)
REVERT: B  752 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8108 (mt-10)
  outliers start: 31
  outliers final: 26
  residues processed: 155
  average time/residue: 0.0724
  time to fit residues: 17.6496
Evaluate side-chains
  156 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  248 TYR
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  422 HIS
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  368 SER
Chi-restraints excluded: chain B residue  422 HIS
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  526 GLU
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain B residue  622 HIS
Chi-restraints excluded: chain B residue  684 ILE
Chi-restraints excluded: chain B residue  743 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 126 optimal weight:    5.9990
   chunk 129 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 122 optimal weight:    6.9990
   chunk 115 optimal weight:    5.9990
   chunk 110 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 75 optimal weight:    2.9990
   chunk 108 optimal weight:    0.7980
   chunk 54 optimal weight:    6.9990
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 405 ASN
A 406 GLN
** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 379 HIS
B 385 GLN
B 422 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.117044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.090816 restraints weight = 24899.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.093164 restraints weight = 13084.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.094714 restraints weight = 8623.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.095754 restraints weight = 6609.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.096384 restraints weight = 5552.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.4889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  12429  Z= 0.217
  Angle     :  0.566   7.293  16931  Z= 0.293
  Chirality :  0.044   0.140   1811
  Planarity :  0.004   0.042   2107
  Dihedral  :  8.454 119.485   1643
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.52 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 11.75 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.22), residues: 1450
  helix:  1.62 (0.19), residues: 725
  sheet: -1.33 (0.51), residues: 98
  loop :  0.34 (0.25), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 621 
 TYR   0.017   0.002   TYR A  73 
 PHE   0.029   0.002   PHE A 157 
 TRP   0.038   0.002   TRP B  40 
 HIS   0.009   0.001   HIS B 422 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 (12429)
  covalent geometry    : angle       0.56575 (16931)
  hydrogen bonds       : bond        0.04648 (  579)
  hydrogen bonds       : angle       4.33453 ( 1620)

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

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

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 122
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TRP cc_start: 0.8668 (t-100) cc_final: 0.8238 (t-100)
REVERT: A  544 LYS cc_start: 0.8711 (tttt) cc_final: 0.8263 (ttmt)
REVERT: A  603 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7789 (mm-40)
REVERT: A  634 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8465 (tt0)
REVERT: A  635 LYS cc_start: 0.8517 (mttt) cc_final: 0.7957 (mttt)
REVERT: B   62 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9104 (tt)
REVERT: B   93 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8333 (mt-10)
REVERT: B   99 ASP cc_start: 0.8850 (t0) cc_final: 0.8445 (t70)
REVERT: B  156 MET cc_start: 0.8704 (tpp) cc_final: 0.8454 (mmt)
REVERT: B  181 THR cc_start: 0.9158 (p) cc_final: 0.8928 (m)
REVERT: B  193 ASP cc_start: 0.7236 (m-30) cc_final: 0.6690 (t70)
REVERT: B  246 MET cc_start: 0.8330 (mmm) cc_final: 0.7959 (mmt)
REVERT: B  539 LEU cc_start: 0.9092 (mm) cc_final: 0.8832 (mm)
REVERT: B  752 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8002 (mt-10)
  outliers start: 40
  outliers final: 30
  residues processed: 150
  average time/residue: 0.0795
  time to fit residues: 18.9196
Evaluate side-chains
  150 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  248 TYR
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  422 HIS
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  235 SER
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  368 SER
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  526 GLU
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  622 HIS
Chi-restraints excluded: chain B residue  684 ILE
Chi-restraints excluded: chain B residue  698 ASP
Chi-restraints excluded: chain B residue  743 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 123 optimal weight:    6.9990
   chunk 74 optimal weight:    9.9990
   chunk 81 optimal weight:    9.9990
   chunk 55 optimal weight:    8.9990
   chunk 23 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 277 HIS
** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 405 ASN
A 432 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 379 HIS
B 422 HIS
** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.119024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.093076 restraints weight = 24660.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.095488 restraints weight = 12860.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.097081 restraints weight = 8435.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.098092 restraints weight = 6436.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.098722 restraints weight = 5399.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.5121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12429  Z= 0.144
  Angle     :  0.500   6.791  16931  Z= 0.261
  Chirality :  0.042   0.130   1811
  Planarity :  0.004   0.043   2107
  Dihedral  :  7.918 118.278   1643
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.03 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 11.82 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.22), residues: 1450
  helix:  1.71 (0.19), residues: 725
  sheet: -1.21 (0.51), residues: 98
  loop :  0.34 (0.25), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 621 
 TYR   0.013   0.001   TYR A 207 
 PHE   0.033   0.001   PHE A 157 
 TRP   0.035   0.001   TRP B  40 
 HIS   0.008   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (12429)
  covalent geometry    : angle       0.50007 (16931)
  hydrogen bonds       : bond        0.04327 (  579)
  hydrogen bonds       : angle       4.14204 ( 1620)

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

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

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 127
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TRP cc_start: 0.8646 (t-100) cc_final: 0.8343 (t-100)
REVERT: A   64 PHE cc_start: 0.9123 (t80) cc_final: 0.8756 (t80)
REVERT: A  544 LYS cc_start: 0.8647 (tttt) cc_final: 0.8226 (ttmt)
REVERT: A  603 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7272 (mm-40)
REVERT: A  634 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8492 (tt0)
REVERT: B   93 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8325 (mt-10)
REVERT: B  118 TYR cc_start: 0.8870 (t80) cc_final: 0.8667 (t80)
REVERT: B  156 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8475 (mmt)
REVERT: B  193 ASP cc_start: 0.7089 (m-30) cc_final: 0.6582 (t70)
REVERT: B  246 MET cc_start: 0.8157 (mmm) cc_final: 0.7904 (mmt)
REVERT: B  539 LEU cc_start: 0.9075 (mm) cc_final: 0.8776 (mm)
REVERT: B  634 GLU cc_start: 0.8325 (tp30) cc_final: 0.8083 (tp30)
REVERT: B  752 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8133 (mt-10)
  outliers start: 41
  outliers final: 30
  residues processed: 157
  average time/residue: 0.0801
  time to fit residues: 19.8950
Evaluate side-chains
  150 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  248 TYR
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  422 HIS
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  677 SER
Chi-restraints excluded: chain A residue  684 ILE
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain B residue   40 TRP
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  156 MET
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  526 GLU
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  622 HIS
Chi-restraints excluded: chain B residue  743 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 99 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 115 optimal weight:    6.9990
   chunk 31 optimal weight:   30.0000
   chunk 82 optimal weight:    9.9990
   chunk 138 optimal weight:    4.9990
   chunk 139 optimal weight:    3.9990
   chunk 120 optimal weight:   20.0000
   chunk 6 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 40 optimal weight:   20.0000
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 405 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 379 HIS
** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.118842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.092966 restraints weight = 24654.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.095368 restraints weight = 12835.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.096860 restraints weight = 8404.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.097920 restraints weight = 6459.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.098603 restraints weight = 5416.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.5339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12429  Z= 0.143
  Angle     :  0.511   7.089  16931  Z= 0.265
  Chirality :  0.042   0.132   1811
  Planarity :  0.004   0.044   2107
  Dihedral  :  7.712 116.094   1643
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.24 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 12.44 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.22), residues: 1450
  helix:  1.67 (0.19), residues: 726
  sheet: -1.25 (0.49), residues: 109
  loop :  0.36 (0.25), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 621 
 TYR   0.022   0.001   TYR A  73 
 PHE   0.037   0.001   PHE A 157 
 TRP   0.058   0.002   TRP B  40 
 HIS   0.008   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (12429)
  covalent geometry    : angle       0.51107 (16931)
  hydrogen bonds       : bond        0.04329 (  579)
  hydrogen bonds       : angle       4.12221 ( 1620)

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

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

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 119
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TRP cc_start: 0.8476 (t-100) cc_final: 0.8263 (t-100)
REVERT: A   64 PHE cc_start: 0.9126 (t80) cc_final: 0.8727 (t80)
REVERT: A   91 TYR cc_start: 0.8789 (m-80) cc_final: 0.7846 (t80)
REVERT: A  544 LYS cc_start: 0.8644 (tttt) cc_final: 0.8219 (ttmt)
REVERT: A  603 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7321 (mm-40)
REVERT: A  634 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8509 (tt0)
REVERT: B   93 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8345 (mt-10)
REVERT: B  193 ASP cc_start: 0.7053 (m-30) cc_final: 0.6488 (t70)
REVERT: B  329 VAL cc_start: 0.7706 (m) cc_final: 0.7442 (m)
REVERT: B  539 LEU cc_start: 0.9087 (mm) cc_final: 0.8699 (mp)
REVERT: B  752 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8108 (mt-10)
  outliers start: 38
  outliers final: 28
  residues processed: 148
  average time/residue: 0.0799
  time to fit residues: 18.8829
Evaluate side-chains
  141 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  248 TYR
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  422 HIS
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  677 SER
Chi-restraints excluded: chain A residue  684 ILE
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  526 GLU
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  622 HIS
Chi-restraints excluded: chain B residue  743 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 27 optimal weight:   20.0000
   chunk 69 optimal weight:    2.9990
   chunk 70 optimal weight:    0.2980
   chunk 23 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 110 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0570
   chunk 131 optimal weight:   10.0000
   chunk 121 optimal weight:   10.0000
   chunk 116 optimal weight:   10.0000
   overall best weight:    2.4704

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

Flipped N/Q/H residues before XYZ refinement:
** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 405 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 379 HIS
** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.118778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.092970 restraints weight = 24572.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.095365 restraints weight = 12836.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.096922 restraints weight = 8451.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.097953 restraints weight = 6465.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.098537 restraints weight = 5444.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.5493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12429  Z= 0.147
  Angle     :  0.519   8.557  16931  Z= 0.269
  Chirality :  0.043   0.176   1811
  Planarity :  0.004   0.044   2107
  Dihedral  :  7.577 115.011   1643
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.97 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.14 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.22), residues: 1450
  helix:  1.66 (0.19), residues: 727
  sheet: -1.28 (0.50), residues: 109
  loop :  0.33 (0.25), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 621 
 TYR   0.017   0.001   TYR A  73 
 PHE   0.044   0.001   PHE A 157 
 TRP   0.048   0.001   TRP B  40 
 HIS   0.008   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (12429)
  covalent geometry    : angle       0.51935 (16931)
  hydrogen bonds       : bond        0.04334 (  579)
  hydrogen bonds       : angle       4.12684 ( 1620)

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

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

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 120
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 PHE cc_start: 0.9131 (t80) cc_final: 0.8736 (t80)
REVERT: A   91 TYR cc_start: 0.8761 (m-80) cc_final: 0.7755 (t80)
REVERT: A  246 MET cc_start: 0.8825 (mmp) cc_final: 0.8007 (mmt)
REVERT: A  439 THR cc_start: 0.7005 (OUTLIER) cc_final: 0.6739 (p)
REVERT: A  544 LYS cc_start: 0.8644 (tttt) cc_final: 0.8227 (ttmt)
REVERT: A  603 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7363 (mm-40)
REVERT: B   62 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8906 (tt)
REVERT: B   93 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8356 (mt-10)
REVERT: B  115 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9035 (mp)
REVERT: B  143 SER cc_start: 0.9401 (m) cc_final: 0.9115 (p)
REVERT: B  148 LEU cc_start: 0.9017 (mm) cc_final: 0.8689 (tp)
REVERT: B  193 ASP cc_start: 0.7039 (m-30) cc_final: 0.6541 (t70)
REVERT: B  246 MET cc_start: 0.8594 (mmm) cc_final: 0.8121 (mmt)
REVERT: B  329 VAL cc_start: 0.7717 (m) cc_final: 0.7441 (m)
REVERT: B  539 LEU cc_start: 0.9108 (mm) cc_final: 0.8750 (mp)
REVERT: B  752 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8112 (mt-10)
  outliers start: 34
  outliers final: 29
  residues processed: 147
  average time/residue: 0.0891
  time to fit residues: 20.5549
Evaluate side-chains
  146 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  248 TYR
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  422 HIS
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  677 SER
Chi-restraints excluded: chain A residue  684 ILE
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain B residue   40 TRP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  526 GLU
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  622 HIS
Chi-restraints excluded: chain B residue  743 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 97 optimal weight:    0.8980
   chunk 81 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 44 optimal weight:   30.0000
   chunk 102 optimal weight:   20.0000
   chunk 100 optimal weight:    9.9990
   chunk 94 optimal weight:    0.5980
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 405 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 603 GLN ** 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 = 0.3640 r_free = 0.3640 target = 0.120042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.095261 restraints weight = 24878.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.097718 restraints weight = 13174.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.098361 restraints weight = 7498.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.098638 restraints weight = 6944.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.098863 restraints weight = 6353.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.5623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12429  Z= 0.129
  Angle     :  0.512   8.623  16931  Z= 0.265
  Chirality :  0.042   0.127   1811
  Planarity :  0.004   0.045   2107
  Dihedral  :  7.390 113.725   1643
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.10 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 13.21 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.27 (0.22), residues: 1450
  helix:  1.65 (0.19), residues: 728
  sheet: -1.12 (0.55), residues: 98
  loop :  0.34 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 621 
 TYR   0.016   0.001   TYR A  73 
 PHE   0.042   0.001   PHE A 157 
 TRP   0.045   0.001   TRP B  40 
 HIS   0.008   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (12429)
  covalent geometry    : angle       0.51219 (16931)
  hydrogen bonds       : bond        0.04191 (  579)
  hydrogen bonds       : angle       4.09205 ( 1620)

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

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

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2900 Ramachandran restraints generated.
    1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 118
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 PHE cc_start: 0.9109 (t80) cc_final: 0.8728 (t80)
REVERT: A   91 TYR cc_start: 0.8744 (m-80) cc_final: 0.7804 (t80)
REVERT: A  186 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8182 (mm-30)
REVERT: A  246 MET cc_start: 0.8775 (mmp) cc_final: 0.7994 (mmt)
REVERT: A  439 THR cc_start: 0.7145 (OUTLIER) cc_final: 0.6876 (p)
REVERT: A  544 LYS cc_start: 0.8618 (tttt) cc_final: 0.8213 (ttmt)
REVERT: A  603 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7422 (mm-40)
REVERT: A  634 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8557 (tt0)
REVERT: B   62 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8896 (tt)
REVERT: B   99 ASP cc_start: 0.8927 (t70) cc_final: 0.8621 (t70)
REVERT: B  115 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9132 (mp)
REVERT: B  143 SER cc_start: 0.9403 (m) cc_final: 0.9109 (p)
REVERT: B  148 LEU cc_start: 0.9010 (mm) cc_final: 0.8694 (tp)
REVERT: B  193 ASP cc_start: 0.6979 (m-30) cc_final: 0.6508 (t70)
REVERT: B  329 VAL cc_start: 0.7692 (m) cc_final: 0.7419 (m)
REVERT: B  539 LEU cc_start: 0.9109 (mm) cc_final: 0.8774 (mp)
REVERT: B  752 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8117 (mt-10)
  outliers start: 36
  outliers final: 29
  residues processed: 145
  average time/residue: 0.0783
  time to fit residues: 18.0954
Evaluate side-chains
  145 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  248 TYR
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  422 HIS
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  594 ILE
Chi-restraints excluded: chain A residue  677 SER
Chi-restraints excluded: chain A residue  684 ILE
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  526 GLU
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  622 HIS
Chi-restraints excluded: chain B residue  743 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 83 optimal weight:    9.9990
   chunk 116 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 132 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 123 optimal weight:    9.9990
   chunk 26 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0040
   chunk 20 optimal weight:    1.9990
   chunk 141 optimal weight:    7.9990
   chunk 115 optimal weight:    6.9990
   overall best weight:    1.8996

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

Flipped N/Q/H residues before XYZ refinement:
A 352 HIS
A 383 ASN
A 405 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.120297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.095662 restraints weight = 24791.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.097461 restraints weight = 14164.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.098443 restraints weight = 9288.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.098604 restraints weight = 7561.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.099466 restraints weight = 6765.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.5740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12429  Z= 0.128
  Angle     :  0.513   8.715  16931  Z= 0.266
  Chirality :  0.042   0.127   1811
  Planarity :  0.004   0.044   2107
  Dihedral  :  7.240 113.148   1643
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.97 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.68 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.22), residues: 1450
  helix:  1.67 (0.19), residues: 727
  sheet: -1.09 (0.55), residues: 98
  loop :  0.32 (0.25), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 621 
 TYR   0.015   0.001   TYR A  73 
 PHE   0.039   0.001   PHE A 157 
 TRP   0.048   0.001   TRP B  40 
 HIS   0.008   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (12429)
  covalent geometry    : angle       0.51257 (16931)
  hydrogen bonds       : bond        0.04164 (  579)
  hydrogen bonds       : angle       4.07642 ( 1620)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1577.12 seconds
wall clock time: 28 minutes 17.41 seconds (1697.41 seconds total)