Starting phenix.real_space_refine
on Sat Aug 23 09:46:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8toi_41453/08_2025/8toi_41453.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8toi_41453/08_2025/8toi_41453.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8toi_41453/08_2025/8toi_41453.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8toi_41453/08_2025/8toi_41453.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8toi_41453/08_2025/8toi_41453.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8toi_41453/08_2025/8toi_41453.map"
  }
  resolution = 2.64
  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=   0.057 sd=   0.508
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: 6
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     P      34      5.49       5
     S      40      5.16       5
     C    7502      2.51       5
     N    1724      2.21       5
     O    2110      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11414
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 649, 5160
          Classifications: {'peptide': 649}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 28, 'TRANS': 620}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 106
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 66
    Chain: "A"
      Number of atoms: 547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 547
          Unusual residues: {' CA': 2, 'PGW': 18}
          Classifications: {'undetermined': 20}
          Link IDs: {None: 19}
          Unresolved non-hydrogen bonds: 373
          Unresolved non-hydrogen angles: 394
          Unresolved non-hydrogen dihedrals: 425
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'PGW:plan-3': 9}
          Unresolved non-hydrogen planarities: 27
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.96, per 1000 atoms: 0.35
  Number of scatterers: 11414
  At special positions: 0
  Unit cell: (91.575, 137.775, 106.425, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      4     19.99
     S      40     16.00
     P      34     15.00
     O    2110      8.00
     N    1724      7.00
     C    7502      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: 0.97
  Conformation dependent library (CDL) restraints added in 373.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2460

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 4 sheets defined
      73.3% alpha, 2.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 47
      removed outlier: 3.644A  pdb=" N   GLY A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 90
      removed outlier: 3.618A  pdb=" N   PHE A  76 " --> pdb=" O   SER A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 107
      removed outlier: 3.833A  pdb=" N   LEU A 105 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN A 106 " --> pdb=" O   GLN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 125
    Processing helix  chain 'A' and resid 126 through 130
      removed outlier: 3.552A  pdb=" N   GLU A 129 " --> pdb=" O   PRO A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 165
    Processing helix  chain 'A' and resid 170 through 182
      removed outlier: 3.813A  pdb=" N   ILE A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 199
      removed outlier: 3.549A  pdb=" N   ALA A 186 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 217 through 246
    Processing helix  chain 'A' and resid 250 through 254
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.578A  pdb=" N   ARG A 284 " --> pdb=" O   PRO A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 320
    Processing helix  chain 'A' and resid 330 through 358
      Proline residue:  A 341  - end of helix
    Processing helix  chain 'A' and resid 362 through 392
      removed outlier: 6.230A  pdb=" N   ALA A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 413
      removed outlier: 3.627A  pdb=" N   LEU A 404 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   THR A 413 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 453
      removed outlier: 3.793A  pdb=" N   ASN A 435 " --> pdb=" O   ALA A 431 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   THR A 443 " --> pdb=" O   TYR A 439 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   PHE A 449 " --> pdb=" O   GLN A 445 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLU A 452 " --> pdb=" O   ASN A 448 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL A 453 " --> pdb=" O   PHE A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 466
    Processing helix  chain 'A' and resid 477 through 481
      removed outlier: 3.584A  pdb=" N   GLU A 480 " --> pdb=" O   GLU A 477 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   GLU A 481 " --> pdb=" O   ASP A 478 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 477 through 481'
    Processing helix  chain 'A' and resid 482 through 493
    Processing helix  chain 'A' and resid 499 through 518
      removed outlier: 4.318A  pdb=" N   ASP A 503 " --> pdb=" O   ASP A 499 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER A 518 " --> pdb=" O   VAL A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 545
      removed outlier: 3.987A  pdb=" N   ARG A 537 " --> pdb=" O   TRP A 533 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ALA A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 585
      removed outlier: 3.705A  pdb=" N   GLY A 572 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   SER A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ALA A 578 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER A 584 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ASN A 585 " --> pdb=" O   TYR A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 625
      removed outlier: 3.506A  pdb=" N   LEU A 602 " --> pdb=" O   LYS A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 642
    Processing helix  chain 'A' and resid 667 through 685
    Processing helix  chain 'A' and resid 689 through 694
    Processing helix  chain 'A' and resid 701 through 716
      removed outlier: 3.653A  pdb=" N   ILE A 705 " --> pdb=" O   MET A 701 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU A 716 " --> pdb=" O   ILE A 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 47
      removed outlier: 3.644A  pdb=" N   GLY B  39 " --> pdb=" O   GLU B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 90
      removed outlier: 3.618A  pdb=" N   PHE B  76 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 107
      removed outlier: 3.834A  pdb=" N   LEU B 105 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN B 106 " --> pdb=" O   GLN B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 125
    Processing helix  chain 'B' and resid 126 through 130
      removed outlier: 3.552A  pdb=" N   GLU B 129 " --> pdb=" O   PRO B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 165
    Processing helix  chain 'B' and resid 170 through 182
      removed outlier: 3.813A  pdb=" N   ILE B 174 " --> pdb=" O   GLU B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 199
      removed outlier: 3.549A  pdb=" N   ALA B 186 " --> pdb=" O   GLY B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 212
    Processing helix  chain 'B' and resid 217 through 246
    Processing helix  chain 'B' and resid 250 through 254
    Processing helix  chain 'B' and resid 280 through 289
      removed outlier: 3.578A  pdb=" N   ARG B 284 " --> pdb=" O   PRO B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 320
    Processing helix  chain 'B' and resid 330 through 358
      Proline residue:  B 341  - end of helix
    Processing helix  chain 'B' and resid 362 through 392
      removed outlier: 6.230A  pdb=" N   ALA B 385 " --> pdb=" O   THR B 381 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   LEU B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 413
      removed outlier: 3.627A  pdb=" N   LEU B 404 " --> pdb=" O   LEU B 400 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   THR B 413 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 453
      removed outlier: 3.793A  pdb=" N   ASN B 435 " --> pdb=" O   ALA B 431 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   THR B 443 " --> pdb=" O   TYR B 439 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   PHE B 449 " --> pdb=" O   GLN B 445 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLU B 452 " --> pdb=" O   ASN B 448 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL B 453 " --> pdb=" O   PHE B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 466
    Processing helix  chain 'B' and resid 477 through 481
      removed outlier: 3.584A  pdb=" N   GLU B 480 " --> pdb=" O   GLU B 477 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   GLU B 481 " --> pdb=" O   ASP B 478 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 477 through 481'
    Processing helix  chain 'B' and resid 482 through 493
    Processing helix  chain 'B' and resid 499 through 518
      removed outlier: 4.317A  pdb=" N   ASP B 503 " --> pdb=" O   ASP B 499 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER B 518 " --> pdb=" O   VAL B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 545
      removed outlier: 3.986A  pdb=" N   ARG B 537 " --> pdb=" O   TRP B 533 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ALA B 540 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 585
      removed outlier: 3.705A  pdb=" N   GLY B 572 " --> pdb=" O   LEU B 568 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   SER B 577 " --> pdb=" O   SER B 573 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ALA B 578 " --> pdb=" O   ILE B 574 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER B 584 " --> pdb=" O   VAL B 580 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ASN B 585 " --> pdb=" O   TYR B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 625
      removed outlier: 3.506A  pdb=" N   LEU B 602 " --> pdb=" O   LYS B 598 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 629 through 642
    Processing helix  chain 'B' and resid 667 through 685
    Processing helix  chain 'B' and resid 689 through 694
    Processing helix  chain 'B' and resid 701 through 716
      removed outlier: 3.653A  pdb=" N   ILE B 705 " --> pdb=" O   MET B 701 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU B 716 " --> pdb=" O   ILE B 712 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268
      removed outlier: 3.784A  pdb=" N   HIS A 265 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56
    Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 268
      removed outlier: 3.784A  pdb=" N   HIS B 265 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)

    694 hydrogen bonds defined for protein.
    2046 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: 1.38

  Time building geometry restraints manager: 1.26 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1722
        1.31 -     1.44: 3226
        1.44 -     1.57: 6564
        1.57 -     1.70: 68
        1.70 -     1.83: 66
  Bond restraints: 11646
  Sorted by residual:
  bond pdb=" C1  PGW A 820 "
       pdb=" O01 PGW A 820 "
    ideal  model  delta    sigma   weight residual
    1.332  1.428 -0.096 2.00e-02 2.50e+03 2.31e+01
  bond pdb=" C1  PGW A 809 "
       pdb=" O01 PGW A 809 "
    ideal  model  delta    sigma   weight residual
    1.332  1.428 -0.096 2.00e-02 2.50e+03 2.30e+01
  bond pdb=" C1  PGW B 820 "
       pdb=" O01 PGW B 820 "
    ideal  model  delta    sigma   weight residual
    1.332  1.428 -0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" C1  PGW B 809 "
       pdb=" O01 PGW B 809 "
    ideal  model  delta    sigma   weight residual
    1.332  1.428 -0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" C1  PGW A 817 "
       pdb=" O01 PGW A 817 "
    ideal  model  delta    sigma   weight residual
    1.332  1.427 -0.095 2.00e-02 2.50e+03 2.24e+01
  ... (remaining 11641 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.90: 15536
        9.90 -    19.80: 78
       19.80 -    29.70: 2
       29.70 -    39.60: 0
       39.60 -    49.50: 6
  Bond angle restraints: 15622
  Sorted by residual:
  angle pdb=" C2  PGW A 805 "
        pdb=" C1  PGW A 805 "
        pdb=" O01 PGW A 805 "
      ideal   model   delta    sigma   weight residual
     110.92  160.42  -49.50 3.00e+00 1.11e-01 2.72e+02
  angle pdb=" C2  PGW B 805 "
        pdb=" C1  PGW B 805 "
        pdb=" O01 PGW B 805 "
      ideal   model   delta    sigma   weight residual
     110.92  160.38  -49.46 3.00e+00 1.11e-01 2.72e+02
  angle pdb=" C2  PGW B 805 "
        pdb=" C1  PGW B 805 "
        pdb=" O02 PGW B 805 "
      ideal   model   delta    sigma   weight residual
     125.44   80.14   45.30 3.00e+00 1.11e-01 2.28e+02
  angle pdb=" C2  PGW A 805 "
        pdb=" C1  PGW A 805 "
        pdb=" O02 PGW A 805 "
      ideal   model   delta    sigma   weight residual
     125.44   80.21   45.23 3.00e+00 1.11e-01 2.27e+02
  angle pdb=" O01 PGW A 805 "
        pdb=" C1  PGW A 805 "
        pdb=" O02 PGW A 805 "
      ideal   model   delta    sigma   weight residual
     123.63   80.21   43.42 3.00e+00 1.11e-01 2.09e+02
  ... (remaining 15617 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.20: 6550
       33.20 -    66.41: 400
       66.41 -    99.61: 58
       99.61 -   132.82: 20
      132.82 -   166.02: 28
  Dihedral angle restraints: 7056
    sinusoidal: 3268
      harmonic: 3788
  Sorted by residual:
  dihedral pdb=" CA  ILE A 101 "
           pdb=" C   ILE A 101 "
           pdb=" N   ALA A 102 "
           pdb=" CA  ALA A 102 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.57  -23.43     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  ILE B 101 "
           pdb=" C   ILE B 101 "
           pdb=" N   ALA B 102 "
           pdb=" CA  ALA B 102 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.58  -23.42     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" O01 PGW B 815 "
           pdb=" C01 PGW B 815 "
           pdb=" C02 PGW B 815 "
           pdb=" O03 PGW B 815 "
      ideal   model   delta sinusoidal    sigma   weight residual
      59.30 -106.72  166.02     1      3.00e+01 1.11e-03 2.10e+01
  ... (remaining 7053 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1242
       0.054 -    0.109: 292
       0.109 -    0.163: 74
       0.163 -    0.217: 20
       0.217 -    0.272: 4
  Chirality restraints: 1632
  Sorted by residual:
  chirality pdb=" CA  THR A 340 "
            pdb=" N   THR A 340 "
            pdb=" C   THR A 340 "
            pdb=" CB  THR A 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CA  THR B 340 "
            pdb=" N   THR B 340 "
            pdb=" C   THR B 340 "
            pdb=" CB  THR B 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CB  VAL B 111 "
            pdb=" CA  VAL B 111 "
            pdb=" CG1 VAL B 111 "
            pdb=" CG2 VAL B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.68e+00
  ... (remaining 1629 not shown)

  Planarity restraints: 1914
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 396 "    0.014 2.00e-02 2.50e+03   1.86e-02 6.03e+00
        pdb=" CG  PHE B 396 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 396 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 396 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 396 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 396 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 396 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 396 "   -0.014 2.00e-02 2.50e+03   1.85e-02 5.98e+00
        pdb=" CG  PHE A 396 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 396 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 396 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 396 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 396 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 396 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 134 "   -0.012 2.00e-02 2.50e+03   2.38e-02 5.65e+00
        pdb=" C   VAL B 134 "    0.041 2.00e-02 2.50e+03
        pdb=" O   VAL B 134 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   THR B 135 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1911 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 3412
        2.83 -     3.35: 10087
        3.35 -     3.87: 18858
        3.87 -     4.38: 21109
        4.38 -     4.90: 36789
  Nonbonded interactions: 90255
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 188 "
            pdb=" OD2 ASP A 539 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" OH  TYR B 188 "
            pdb=" OD2 ASP B 539 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   TRP B 570 "
            pdb=" OG  SER B 573 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" O   TRP A 570 "
            pdb=" OG  SER A 573 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" OE2 GLU B 358 "
            pdb=" OH  TYR B 360 "
     model   vdw
     2.360 3.040
  ... (remaining 90250 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.580
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  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:5.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
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      :  0.010   0.096  11646  Z= 0.469
  Angle     :  1.856  49.496  15622  Z= 0.718
  Chirality :  0.054   0.272   1632
  Planarity :  0.006   0.053   1914
  Dihedral  : 24.382 166.024   4596
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.60 (0.20), residues: 1274
  helix: -0.55 (0.15), residues: 888
  sheet: -1.94 (0.77), residues: 44
  loop : -1.97 (0.30), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 537 
 TYR   0.017   0.002   TYR B 457 
 PHE   0.043   0.002   PHE B 396 
 TRP   0.032   0.002   TRP A 141 
 HIS   0.004   0.001   HIS B 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00950 (11646)
  covalent geometry    : angle       1.85630 (15622)
  hydrogen bonds       : bond        0.14143 (  694)
  hydrogen bonds       : angle       6.47489 ( 2046)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  320 TYR cc_start: 0.8068 (t80) cc_final: 0.7754 (t80)
REVERT: B   55 GLU cc_start: 0.7866 (tp30) cc_final: 0.6878 (mm-30)
REVERT: B  320 TYR cc_start: 0.8143 (t80) cc_final: 0.7800 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.5560
  time to fit residues: 99.0800
Evaluate side-chains
  131 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
A 153 HIS
A 265 HIS
A 310 ASN
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 366 HIS
A 696 GLN
A 698 GLN
B  79 GLN
B 153 HIS
B 265 HIS
B 310 ASN
B 366 HIS
B 696 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.128385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.092264 restraints weight = 16317.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.01
r_work: 0.3104 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11646  Z= 0.140
  Angle     :  1.073  46.372  15622  Z= 0.418
  Chirality :  0.040   0.158   1632
  Planarity :  0.004   0.045   1914
  Dihedral  : 26.204 160.863   2250
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  9.33 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.46 (0.23), residues: 1274
  helix:  1.14 (0.17), residues: 892
  sheet: -1.52 (0.81), residues: 44
  loop : -1.64 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 537 
 TYR   0.014   0.001   TYR A 188 
 PHE   0.024   0.001   PHE A 406 
 TRP   0.014   0.001   TRP B 235 
 HIS   0.003   0.001   HIS B 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (11646)
  covalent geometry    : angle       1.07274 (15622)
  hydrogen bonds       : bond        0.04266 (  694)
  hydrogen bonds       : angle       3.88578 ( 2046)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8857 (pt0) cc_final: 0.8448 (pm20)
REVERT: A  320 TYR cc_start: 0.7915 (t80) cc_final: 0.7556 (t80)
REVERT: A  326 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7294 (pp30)
REVERT: A  484 GLU cc_start: 0.8618 (mp0) cc_final: 0.8413 (tm-30)
REVERT: B  268 GLU cc_start: 0.8838 (pt0) cc_final: 0.8460 (pm20)
REVERT: B  320 TYR cc_start: 0.7995 (t80) cc_final: 0.7599 (t80)
REVERT: B  326 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7563 (pp30)
REVERT: B  484 GLU cc_start: 0.8670 (mp0) cc_final: 0.8464 (tm-30)
  outliers start: 19
  outliers final: 5
  residues processed: 142
  average time/residue: 0.4602
  time to fit residues: 71.0232
Evaluate side-chains
  136 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 129
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  326 GLN
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  326 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 58 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 117 optimal weight:    0.6980
   chunk 125 optimal weight:   20.0000
   chunk 10 optimal weight:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 479 HIS
A 510 GLN
A 531 ASN
A 696 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 479 HIS
B 696 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.128521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.092512 restraints weight = 16401.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.02
r_work: 0.3100 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11646  Z= 0.122
  Angle     :  1.043  46.268  15622  Z= 0.401
  Chirality :  0.039   0.154   1632
  Planarity :  0.004   0.042   1914
  Dihedral  : 24.511 164.555   2250
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 11.01 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.16 (0.23), residues: 1274
  helix:  1.70 (0.17), residues: 900
  sheet: -1.16 (0.87), residues: 44
  loop : -1.59 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 697 
 TYR   0.015   0.001   TYR A  26 
 PHE   0.012   0.001   PHE A 396 
 TRP   0.014   0.001   TRP B 235 
 HIS   0.003   0.001   HIS B 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (11646)
  covalent geometry    : angle       1.04348 (15622)
  hydrogen bonds       : bond        0.03945 (  694)
  hydrogen bonds       : angle       3.61469 ( 2046)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 140
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7704 (tm-30)
REVERT: A  268 GLU cc_start: 0.8862 (pt0) cc_final: 0.8414 (pm20)
REVERT: A  320 TYR cc_start: 0.7820 (t80) cc_final: 0.7379 (t80)
REVERT: A  326 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7541 (pp30)
REVERT: A  352 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8141 (mt-10)
REVERT: A  400 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6681 (pp)
REVERT: A  633 GLN cc_start: 0.8578 (tt0) cc_final: 0.8353 (tt0)
REVERT: B   33 ARG cc_start: 0.8496 (ttp80) cc_final: 0.8285 (ttp80)
REVERT: B  320 TYR cc_start: 0.7846 (t80) cc_final: 0.7386 (t80)
REVERT: B  326 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7548 (pp30)
REVERT: B  400 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6702 (pp)
  outliers start: 32
  outliers final: 6
  residues processed: 152
  average time/residue: 0.4704
  time to fit residues: 77.8802
Evaluate side-chains
  147 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  326 GLN
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  269 ASP
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  326 GLN
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  627 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 51 optimal weight:    0.0010
   chunk 79 optimal weight:    4.9990
   chunk 120 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 123 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0040
   chunk 48 optimal weight:    0.8980
   chunk 102 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    1.3802

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

Flipped N/Q/H residues before XYZ refinement:
A  25 HIS
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 479 HIS
A 641 GLN
A 696 GLN
B  25 HIS
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 510 GLN
B 531 ASN
B 641 GLN
B 696 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.126162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.089549 restraints weight = 16440.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.02
r_work: 0.3055 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  11646  Z= 0.167
  Angle     :  1.053  46.193  15622  Z= 0.408
  Chirality :  0.041   0.157   1632
  Planarity :  0.004   0.040   1914
  Dihedral  : 23.708 165.778   2250
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 12.69 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.45 (0.24), residues: 1274
  helix:  1.95 (0.17), residues: 892
  sheet: -0.93 (0.89), residues: 44
  loop : -1.54 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 697 
 TYR   0.016   0.002   TYR A  26 
 PHE   0.024   0.001   PHE B 406 
 TRP   0.015   0.001   TRP A 235 
 HIS   0.004   0.001   HIS A 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (11646)
  covalent geometry    : angle       1.05255 (15622)
  hydrogen bonds       : bond        0.04198 (  694)
  hydrogen bonds       : angle       3.56880 ( 2046)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 135
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7693 (tm-30)
REVERT: A  268 GLU cc_start: 0.8848 (pt0) cc_final: 0.8373 (pm20)
REVERT: A  320 TYR cc_start: 0.7993 (t80) cc_final: 0.7511 (t80)
REVERT: A  326 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7649 (pp30)
REVERT: A  400 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6844 (pp)
REVERT: B  268 GLU cc_start: 0.8824 (pt0) cc_final: 0.8348 (pm20)
REVERT: B  320 TYR cc_start: 0.8009 (t80) cc_final: 0.7462 (t80)
REVERT: B  326 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7643 (pp30)
REVERT: B  400 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6883 (pp)
  outliers start: 31
  outliers final: 3
  residues processed: 148
  average time/residue: 0.4884
  time to fit residues: 78.6583
Evaluate side-chains
  136 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  326 GLN
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  326 GLN
Chi-restraints excluded: chain B residue  400 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 93 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 124 optimal weight:    5.9990
   chunk 109 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 ASN
A 696 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 696 GLN
** B 698 GLN ** 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 = 0.3808 r_free = 0.3808 target = 0.127636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.091371 restraints weight = 16434.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.01
r_work: 0.3090 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11646  Z= 0.124
  Angle     :  1.047  46.264  15622  Z= 0.403
  Chirality :  0.040   0.152   1632
  Planarity :  0.003   0.036   1914
  Dihedral  : 22.949 166.972   2250
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 13.53 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.68 (0.24), residues: 1274
  helix:  2.07 (0.17), residues: 904
  sheet: -0.96 (0.89), residues: 44
  loop : -1.37 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 697 
 TYR   0.015   0.001   TYR A  26 
 PHE   0.030   0.001   PHE A 406 
 TRP   0.015   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (11646)
  covalent geometry    : angle       1.04671 (15622)
  hydrogen bonds       : bond        0.03838 (  694)
  hydrogen bonds       : angle       3.46639 ( 2046)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 136
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8838 (pt0) cc_final: 0.8369 (pm20)
REVERT: A  320 TYR cc_start: 0.7846 (t80) cc_final: 0.7329 (t80)
REVERT: A  326 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7642 (pp30)
REVERT: A  484 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7894 (tm-30)
REVERT: B  268 GLU cc_start: 0.8815 (pt0) cc_final: 0.8324 (pm20)
REVERT: B  282 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8328 (tpp)
REVERT: B  320 TYR cc_start: 0.7816 (t80) cc_final: 0.7237 (t80)
REVERT: B  326 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7628 (pp30)
REVERT: B  400 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6866 (pp)
REVERT: B  484 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7914 (tm-30)
  outliers start: 33
  outliers final: 11
  residues processed: 149
  average time/residue: 0.4621
  time to fit residues: 74.8241
Evaluate side-chains
  145 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  326 GLN
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  269 ASP
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  326 GLN
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  507 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 120 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 113 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 123 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 479 HIS
A 696 GLN
B 310 ASN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 696 GLN
B 698 GLN
B 714 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.126966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.090282 restraints weight = 16503.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.02
r_work: 0.3069 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11646  Z= 0.141
  Angle     :  1.057  46.141  15622  Z= 0.408
  Chirality :  0.041   0.156   1632
  Planarity :  0.004   0.039   1914
  Dihedral  : 22.374 166.488   2250
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 14.65 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.73 (0.24), residues: 1274
  helix:  2.14 (0.17), residues: 898
  sheet: -1.02 (0.88), residues: 44
  loop : -1.41 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  33 
 TYR   0.015   0.001   TYR A  26 
 PHE   0.029   0.001   PHE B 406 
 TRP   0.015   0.001   TRP A 235 
 HIS   0.004   0.001   HIS A 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (11646)
  covalent geometry    : angle       1.05707 (15622)
  hydrogen bonds       : bond        0.03941 (  694)
  hydrogen bonds       : angle       3.45700 ( 2046)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8840 (pt0) cc_final: 0.8363 (pm20)
REVERT: A  320 TYR cc_start: 0.7968 (t80) cc_final: 0.7375 (t80)
REVERT: A  326 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7672 (pp30)
REVERT: A  701 MET cc_start: 0.7870 (tpp) cc_final: 0.7384 (tpt)
REVERT: A  703 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7541 (pm20)
REVERT: B  268 GLU cc_start: 0.8845 (pt0) cc_final: 0.8327 (pm20)
REVERT: B  282 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8329 (tpp)
REVERT: B  320 TYR cc_start: 0.7922 (t80) cc_final: 0.7350 (t80)
REVERT: B  326 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7629 (pp30)
REVERT: B  701 MET cc_start: 0.7978 (tpp) cc_final: 0.7655 (tpt)
  outliers start: 30
  outliers final: 10
  residues processed: 147
  average time/residue: 0.4918
  time to fit residues: 78.4285
Evaluate side-chains
  145 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  326 GLN
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain A residue  703 GLU
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  326 GLN
Chi-restraints excluded: chain B residue  507 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 94 optimal weight:    0.0000
   chunk 16 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 99 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 44 optimal weight:    9.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 479 HIS
A 666 HIS
A 696 GLN
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 427 GLN
B 429 ASN
B 666 HIS
B 696 GLN
B 698 GLN
B 714 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.126642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.090109 restraints weight = 16450.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.00
r_work: 0.3069 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11646  Z= 0.146
  Angle     :  1.062  46.127  15622  Z= 0.411
  Chirality :  0.041   0.153   1632
  Planarity :  0.004   0.034   1914
  Dihedral  : 21.878 165.741   2250
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.18 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.24), residues: 1274
  helix:  2.18 (0.17), residues: 898
  sheet: -1.00 (0.88), residues: 44
  loop : -1.34 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  33 
 TYR   0.015   0.001   TYR B  26 
 PHE   0.032   0.001   PHE A 406 
 TRP   0.016   0.001   TRP B 141 
 HIS   0.003   0.001   HIS A 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (11646)
  covalent geometry    : angle       1.06195 (15622)
  hydrogen bonds       : bond        0.03958 (  694)
  hydrogen bonds       : angle       3.45437 ( 2046)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 132
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8862 (pt0) cc_final: 0.8368 (pm20)
REVERT: A  320 TYR cc_start: 0.7879 (t80) cc_final: 0.7183 (t80)
REVERT: A  326 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7683 (pp30)
REVERT: A  701 MET cc_start: 0.7823 (tpp) cc_final: 0.7532 (tpt)
REVERT: B  268 GLU cc_start: 0.8859 (pt0) cc_final: 0.8328 (pm20)
REVERT: B  282 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8342 (tpp)
REVERT: B  320 TYR cc_start: 0.7878 (t80) cc_final: 0.7269 (t80)
REVERT: B  701 MET cc_start: 0.7976 (tpp) cc_final: 0.7673 (tpt)
REVERT: B  703 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7551 (pm20)
  outliers start: 32
  outliers final: 8
  residues processed: 143
  average time/residue: 0.5267
  time to fit residues: 81.6484
Evaluate side-chains
  141 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  326 GLN
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  507 MET
Chi-restraints excluded: chain B residue  703 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 64 optimal weight:    4.9990
   chunk 101 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0770
   chunk 125 optimal weight:   20.0000
   chunk 88 optimal weight:    1.9990
   chunk 44 optimal weight:    8.9990
   chunk 96 optimal weight:    4.9990
   overall best weight:    1.7544

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 479 HIS
A 696 GLN
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 696 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.124891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.088083 restraints weight = 16314.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.98
r_work: 0.3034 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  11646  Z= 0.202
  Angle     :  1.084  46.171  15622  Z= 0.426
  Chirality :  0.042   0.156   1632
  Planarity :  0.004   0.038   1914
  Dihedral  : 21.523 163.964   2250
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.58 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.72 (0.24), residues: 1274
  helix:  2.11 (0.17), residues: 898
  sheet: -1.04 (0.88), residues: 44
  loop : -1.34 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  33 
 TYR   0.017   0.002   TYR A  26 
 PHE   0.034   0.001   PHE B 406 
 TRP   0.022   0.002   TRP B 141 
 HIS   0.003   0.001   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 (11646)
  covalent geometry    : angle       1.08375 (15622)
  hydrogen bonds       : bond        0.04366 (  694)
  hydrogen bonds       : angle       3.53599 ( 2046)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.442 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8830 (pt0) cc_final: 0.8357 (pm20)
REVERT: A  320 TYR cc_start: 0.8095 (t80) cc_final: 0.7540 (t80)
REVERT: A  701 MET cc_start: 0.7860 (tpp) cc_final: 0.7634 (tpt)
REVERT: B  268 GLU cc_start: 0.8809 (pt0) cc_final: 0.8304 (pm20)
REVERT: B  320 TYR cc_start: 0.8088 (t80) cc_final: 0.7381 (t80)
REVERT: B  325 LYS cc_start: 0.8592 (tppt) cc_final: 0.8227 (tppt)
REVERT: B  701 MET cc_start: 0.7966 (tpp) cc_final: 0.7740 (tpt)
REVERT: B  703 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7596 (pm20)
  outliers start: 22
  outliers final: 8
  residues processed: 139
  average time/residue: 0.6177
  time to fit residues: 92.6218
Evaluate side-chains
  141 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  507 MET
Chi-restraints excluded: chain B residue  703 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 118 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 59 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 427 GLN
B 696 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.126917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.090564 restraints weight = 16258.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.99
r_work: 0.3081 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11646  Z= 0.134
  Angle     :  1.070  46.246  15622  Z= 0.417
  Chirality :  0.041   0.150   1632
  Planarity :  0.003   0.034   1914
  Dihedral  : 20.774 164.132   2250
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 16.42 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.82 (0.24), residues: 1274
  helix:  2.10 (0.17), residues: 910
  sheet: -1.00 (0.86), residues: 48
  loop : -1.14 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  33 
 TYR   0.015   0.001   TYR A  26 
 PHE   0.035   0.001   PHE A 406 
 TRP   0.024   0.001   TRP A 141 
 HIS   0.003   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (11646)
  covalent geometry    : angle       1.07026 (15622)
  hydrogen bonds       : bond        0.03855 (  694)
  hydrogen bonds       : angle       3.45504 ( 2046)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8848 (pt0) cc_final: 0.8369 (pm20)
REVERT: A  320 TYR cc_start: 0.7931 (t80) cc_final: 0.6661 (t80)
REVERT: A  325 LYS cc_start: 0.8554 (tppt) cc_final: 0.8003 (tppt)
REVERT: A  327 TYR cc_start: 0.8185 (m-10) cc_final: 0.7856 (m-10)
REVERT: B  268 GLU cc_start: 0.8821 (pt0) cc_final: 0.8312 (pm20)
REVERT: B  282 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8316 (tpp)
REVERT: B  320 TYR cc_start: 0.8014 (t80) cc_final: 0.6949 (t80)
REVERT: B  325 LYS cc_start: 0.8558 (tppt) cc_final: 0.8017 (tppt)
REVERT: B  437 MET cc_start: 0.8937 (tpt) cc_final: 0.8387 (tpt)
REVERT: B  703 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7534 (pm20)
  outliers start: 16
  outliers final: 5
  residues processed: 139
  average time/residue: 0.6116
  time to fit residues: 92.0759
Evaluate side-chains
  141 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 134
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  507 MET
Chi-restraints excluded: chain B residue  703 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 126 optimal weight:    0.9980
   chunk 11 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 7 optimal weight:    7.9990
   chunk 125 optimal weight:    6.9990
   chunk 77 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 429 ASN
A 696 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 429 ASN
B 696 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.127027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.090725 restraints weight = 16364.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.00
r_work: 0.3082 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11646  Z= 0.133
  Angle     :  1.067  46.223  15622  Z= 0.416
  Chirality :  0.041   0.151   1632
  Planarity :  0.004   0.033   1914
  Dihedral  : 20.143 163.999   2250
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 17.54 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.85 (0.24), residues: 1274
  helix:  2.12 (0.17), residues: 912
  sheet: -0.92 (0.87), residues: 48
  loop : -1.14 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  33 
 TYR   0.015   0.001   TYR A 457 
 PHE   0.038   0.001   PHE B 406 
 TRP   0.017   0.001   TRP A 235 
 HIS   0.003   0.001   HIS A 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (11646)
  covalent geometry    : angle       1.06706 (15622)
  hydrogen bonds       : bond        0.03824 (  694)
  hydrogen bonds       : angle       3.43663 ( 2046)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8838 (pt0) cc_final: 0.8359 (pm20)
REVERT: A  282 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8319 (tpp)
REVERT: A  320 TYR cc_start: 0.8011 (t80) cc_final: 0.7061 (t80)
REVERT: A  325 LYS cc_start: 0.8436 (tppt) cc_final: 0.8085 (tppt)
REVERT: A  327 TYR cc_start: 0.8109 (m-10) cc_final: 0.7754 (m-10)
REVERT: B  268 GLU cc_start: 0.8844 (pt0) cc_final: 0.8325 (pm20)
REVERT: B  282 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8323 (tpp)
REVERT: B  320 TYR cc_start: 0.7924 (t80) cc_final: 0.6980 (t80)
REVERT: B  325 LYS cc_start: 0.8422 (tppt) cc_final: 0.7943 (tppt)
REVERT: B  437 MET cc_start: 0.8925 (tpt) cc_final: 0.8368 (tpt)
REVERT: B  703 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7596 (pm20)
  outliers start: 11
  outliers final: 3
  residues processed: 141
  average time/residue: 0.6018
  time to fit residues: 92.0868
Evaluate side-chains
  140 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 134
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  507 MET
Chi-restraints excluded: chain B residue  703 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 94 optimal weight:    0.4980
   chunk 90 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 124 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 112 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 GLN
B 326 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 427 GLN
B 696 GLN
** B 698 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 = 0.3806 r_free = 0.3806 target = 0.127206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.090786 restraints weight = 16364.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.00
r_work: 0.3078 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11646  Z= 0.135
  Angle     :  1.079  46.175  15622  Z= 0.421
  Chirality :  0.041   0.150   1632
  Planarity :  0.004   0.034   1914
  Dihedral  : 19.804 163.717   2250
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 17.07 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.89 (0.24), residues: 1274
  helix:  2.14 (0.17), residues: 912
  sheet: -0.91 (0.87), residues: 48
  loop : -1.11 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  33 
 TYR   0.016   0.001   TYR A 457 
 PHE   0.038   0.001   PHE A 406 
 TRP   0.017   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (11646)
  covalent geometry    : angle       1.07886 (15622)
  hydrogen bonds       : bond        0.03811 (  694)
  hydrogen bonds       : angle       3.43152 ( 2046)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4058.13 seconds
wall clock time: 69 minutes 39.12 seconds (4179.12 seconds total)