Starting phenix.real_space_refine
on Tue Jul 29 10:37:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8toi_41453/07_2025/8toi_41453.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8toi_41453/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8toi_41453/07_2025/8toi_41453.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8toi_41453/07_2025/8toi_41453.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8toi_41453/07_2025/8toi_41453.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8toi_41453/07_2025/8toi_41453.cif"
  }
  resolution = 2.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.057 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1}
          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: 12.22, per 1000 atoms: 1.07
  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: 2.94
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 1.09
  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: 3.41

  Time building geometry restraints manager: 3.43 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: 0.05
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:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     33.570
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.660
-------------------------------------------------------------------------------
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 : 2.95
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.032   0.002   TRP A 141 
 HIS   0.004   0.001   HIS B 366 
 PHE   0.043   0.002   PHE B 396 
 TYR   0.017   0.002   TYR B 457 
 ARG   0.003   0.000   ARG B 537 

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

*********************** 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  : 1.303 
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: 0.7066 (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: 1.3392
  time to fit residues: 239.2806
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  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 116 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 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 = 0.3823 r_free = 0.3823 target = 0.128635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.092646 restraints weight = 16201.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.01
r_work: 0.3111 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11646  Z= 0.133
  Angle     :  1.070  46.300  15622  Z= 0.417
  Chirality :  0.040   0.159   1632
  Planarity :  0.004   0.044   1914
  Dihedral  : 26.313 160.955   2250
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  9.33 %
    Favored  : 89.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.23), residues: 1274
  helix:  1.09 (0.17), residues: 892
  sheet: -1.55 (0.81), residues: 44
  loop : -1.65 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 235 
 HIS   0.003   0.001   HIS B 479 
 PHE   0.022   0.001   PHE A 406 
 TYR   0.013   0.001   TYR A 188 
 ARG   0.003   0.000   ARG A 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04392 (  694)
  hydrogen bonds       : angle       3.95492 ( 2046)
  covalent geometry    : bond        0.00304 (11646)
  covalent geometry    : angle       1.06958 (15622)

*********************** 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
  152 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 1.141 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8864 (pt0) cc_final: 0.8453 (pm20)
REVERT: A  320 TYR cc_start: 0.7906 (t80) cc_final: 0.7559 (t80)
REVERT: A  326 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7291 (pp30)
REVERT: A  484 GLU cc_start: 0.8619 (mp0) cc_final: 0.8409 (tm-30)
REVERT: B  320 TYR cc_start: 0.7986 (t80) cc_final: 0.7604 (t80)
REVERT: B  326 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7553 (pp30)
  outliers start: 17
  outliers final: 6
  residues processed: 138
  average time/residue: 1.1933
  time to fit residues: 180.3759
Evaluate side-chains
  135 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
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 A residue  707 ILE
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 27 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 125 optimal weight:   20.0000
   chunk 117 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 510 GLN
A 531 ASN
A 696 GLN
B  25 HIS
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 510 GLN
B 531 ASN
B 696 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.125844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.089433 restraints weight = 16461.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.01
r_work: 0.3045 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.2037

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= 0.186
  Angle     :  1.067  46.218  15622  Z= 0.418
  Chirality :  0.042   0.158   1632
  Planarity :  0.004   0.036   1914
  Dihedral  : 24.732 163.545   2250
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 11.57 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.24), residues: 1274
  helix:  1.70 (0.17), residues: 890
  sheet: -1.11 (0.87), residues: 44
  loop : -1.67 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 235 
 HIS   0.005   0.001   HIS A 479 
 PHE   0.012   0.001   PHE A 396 
 TYR   0.018   0.002   TYR B  26 
 ARG   0.006   0.000   ARG B 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04439 (  694)
  hydrogen bonds       : angle       3.70091 ( 2046)
  covalent geometry    : bond        0.00440 (11646)
  covalent geometry    : angle       1.06743 (15622)

*********************** 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
  174 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 141
  time to evaluate  : 1.193 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.8552 (ttp80) cc_final: 0.8351 (ttp80)
REVERT: A   35 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7717 (tm-30)
REVERT: A  268 GLU cc_start: 0.8897 (pt0) cc_final: 0.8416 (pm20)
REVERT: A  320 TYR cc_start: 0.7920 (t80) cc_final: 0.7511 (t80)
REVERT: A  326 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7615 (pp30)
REVERT: A  352 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8181 (mt-10)
REVERT: A  400 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6823 (pp)
REVERT: B   33 ARG cc_start: 0.8520 (ttp80) cc_final: 0.8299 (ttp80)
REVERT: B  268 GLU cc_start: 0.8878 (pt0) cc_final: 0.8412 (pm20)
REVERT: B  320 TYR cc_start: 0.7976 (t80) cc_final: 0.7490 (t80)
REVERT: B  326 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7604 (pp30)
REVERT: B  400 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6851 (pp)
  outliers start: 33
  outliers final: 6
  residues processed: 154
  average time/residue: 1.1559
  time to fit residues: 194.0900
Evaluate side-chains
  144 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue  153 HIS
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 A residue  627 LEU
Chi-restraints excluded: chain B residue  153 HIS
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 22 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 108 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0980
   chunk 86 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 121 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   chunk 102 optimal weight:    0.6980
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 641 GLN
A 696 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 641 GLN
B 696 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.125723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.089283 restraints weight = 16354.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 2.00
r_work: 0.3045 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11646  Z= 0.165
  Angle     :  1.053  46.243  15622  Z= 0.409
  Chirality :  0.041   0.159   1632
  Planarity :  0.004   0.037   1914
  Dihedral  : 23.706 165.803   2250
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 12.78 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.24), residues: 1274
  helix:  1.90 (0.17), residues: 892
  sheet: -1.03 (0.88), residues: 44
  loop : -1.54 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 235 
 HIS   0.004   0.001   HIS A 366 
 PHE   0.026   0.001   PHE A 406 
 TYR   0.017   0.002   TYR B  26 
 ARG   0.007   0.000   ARG A 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04191 (  694)
  hydrogen bonds       : angle       3.59841 ( 2046)
  covalent geometry    : bond        0.00389 (11646)
  covalent geometry    : angle       1.05266 (15622)

*********************** 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: 34
    poor density    : 132
  time to evaluate  : 1.159 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8870 (pt0) cc_final: 0.8371 (pm20)
REVERT: A  320 TYR cc_start: 0.7953 (t80) cc_final: 0.7469 (t80)
REVERT: A  400 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6791 (pp)
REVERT: A  484 GLU cc_start: 0.8627 (mp0) cc_final: 0.8425 (tm-30)
REVERT: B  268 GLU cc_start: 0.8850 (pt0) cc_final: 0.8352 (pm20)
REVERT: B  320 TYR cc_start: 0.7994 (t80) cc_final: 0.7541 (t80)
REVERT: B  400 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6805 (pp)
REVERT: B  484 GLU cc_start: 0.8617 (mp0) cc_final: 0.8413 (tm-30)
  outliers start: 34
  outliers final: 4
  residues processed: 144
  average time/residue: 1.0965
  time to fit residues: 173.2858
Evaluate side-chains
  136 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 130
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  507 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    8.9990
   chunk 72 optimal weight:    8.9990
   chunk 104 optimal weight:    5.9990
   chunk 105 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 60 optimal weight:   20.0000
   chunk 93 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 114 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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 666 HIS
A 696 GLN
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 ASN
B 479 HIS
B 666 HIS
B 696 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.124234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.087514 restraints weight = 16337.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.98
r_work: 0.3019 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  11646  Z= 0.223
  Angle     :  1.080  46.137  15622  Z= 0.424
  Chirality :  0.043   0.157   1632
  Planarity :  0.004   0.035   1914
  Dihedral  : 23.207 165.324   2250
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 13.34 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.24), residues: 1274
  helix:  1.90 (0.17), residues: 898
  sheet: -1.08 (0.89), residues: 44
  loop : -1.56 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 235 
 HIS   0.004   0.001   HIS A 611 
 PHE   0.011   0.001   PHE B 608 
 TYR   0.018   0.002   TYR B  26 
 ARG   0.004   0.000   ARG A 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04530 (  694)
  hydrogen bonds       : angle       3.63349 ( 2046)
  covalent geometry    : bond        0.00537 (11646)
  covalent geometry    : angle       1.08037 (15622)

*********************** 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
  176 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 133
  time to evaluate  : 1.310 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.8579 (ttp80) cc_final: 0.8344 (ttp80)
REVERT: A  268 GLU cc_start: 0.8840 (pt0) cc_final: 0.8344 (pm20)
REVERT: A  320 TYR cc_start: 0.8031 (t80) cc_final: 0.7276 (t80)
REVERT: A  325 LYS cc_start: 0.8675 (tppt) cc_final: 0.8292 (tppt)
REVERT: A  400 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6987 (pp)
REVERT: A  484 GLU cc_start: 0.8621 (mp0) cc_final: 0.8380 (tm-30)
REVERT: B   33 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8316 (ttp80)
REVERT: B  268 GLU cc_start: 0.8826 (pt0) cc_final: 0.8339 (pm20)
REVERT: B  320 TYR cc_start: 0.8075 (t80) cc_final: 0.7275 (t80)
REVERT: B  325 LYS cc_start: 0.8681 (tppt) cc_final: 0.8321 (tppt)
REVERT: B  400 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.7043 (pp)
  outliers start: 43
  outliers final: 13
  residues processed: 150
  average time/residue: 1.2766
  time to fit residues: 207.7120
Evaluate side-chains
  144 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
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  400 LEU
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  491 GLU
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain A residue  546 SER
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  400 LEU
Chi-restraints excluded: chain B residue  458 ILE
Chi-restraints excluded: chain B residue  507 MET
Chi-restraints excluded: chain B residue  546 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0980
   chunk 23 optimal weight:    4.9990
   chunk 102 optimal weight:    0.6980
   chunk 103 optimal weight:    4.9990
   chunk 66 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9980
   chunk 111 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 696 GLN
B 715 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.127360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.090993 restraints weight = 16413.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.00
r_work: 0.3076 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2596

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= 0.115
  Angle     :  1.053  46.330  15622  Z= 0.406
  Chirality :  0.040   0.151   1632
  Planarity :  0.003   0.033   1914
  Dihedral  : 22.357 166.572   2250
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.83 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.24), residues: 1274
  helix:  2.02 (0.17), residues: 910
  sheet: -1.03 (0.90), residues: 44
  loop : -1.42 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 141 
 HIS   0.003   0.001   HIS B 366 
 PHE   0.028   0.001   PHE A 406 
 TYR   0.015   0.001   TYR A  26 
 ARG   0.003   0.000   ARG A 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03773 (  694)
  hydrogen bonds       : angle       3.47414 ( 2046)
  covalent geometry    : bond        0.00258 (11646)
  covalent geometry    : angle       1.05292 (15622)

*********************** 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
  158 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 1.418 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8843 (pt0) cc_final: 0.8311 (pm20)
REVERT: A  282 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8283 (tpp)
REVERT: A  320 TYR cc_start: 0.7877 (t80) cc_final: 0.7013 (t80)
REVERT: A  325 LYS cc_start: 0.8505 (tppt) cc_final: 0.8181 (tppt)
REVERT: B   33 ARG cc_start: 0.8551 (ttp80) cc_final: 0.8350 (ttp80)
REVERT: B  268 GLU cc_start: 0.8844 (pt0) cc_final: 0.8314 (pm20)
REVERT: B  282 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8307 (tpp)
REVERT: B  320 TYR cc_start: 0.7889 (t80) cc_final: 0.7051 (t80)
REVERT: B  325 LYS cc_start: 0.8495 (tppt) cc_final: 0.8183 (tppt)
  outliers start: 24
  outliers final: 4
  residues processed: 146
  average time/residue: 1.3939
  time to fit residues: 222.4724
Evaluate side-chains
  137 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 131
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
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  546 SER
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  282 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 111 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 479 HIS
B 696 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.123322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.086459 restraints weight = 16564.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 1.97
r_work: 0.3004 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.072  11646  Z= 0.273
  Angle     :  1.101  46.183  15622  Z= 0.439
  Chirality :  0.045   0.164   1632
  Planarity :  0.004   0.034   1914
  Dihedral  : 22.432 164.710   2250
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 15.30 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.24), residues: 1274
  helix:  1.93 (0.17), residues: 898
  sheet: -1.03 (0.90), residues: 44
  loop : -1.51 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 141 
 HIS   0.004   0.001   HIS A 611 
 PHE   0.013   0.001   PHE A 388 
 TYR   0.019   0.002   TYR B  26 
 ARG   0.005   0.000   ARG A  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04755 (  694)
  hydrogen bonds       : angle       3.65196 ( 2046)
  covalent geometry    : bond        0.00659 (11646)
  covalent geometry    : angle       1.10150 (15622)

*********************** 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
  160 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 1.123 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8845 (pt0) cc_final: 0.8344 (pm20)
REVERT: A  320 TYR cc_start: 0.8110 (t80) cc_final: 0.7435 (t80)
REVERT: A  325 LYS cc_start: 0.8744 (tppt) cc_final: 0.8531 (tppt)
REVERT: B   33 ARG cc_start: 0.8591 (ttp80) cc_final: 0.8377 (ttp80)
REVERT: B  268 GLU cc_start: 0.8846 (pt0) cc_final: 0.8340 (pm20)
REVERT: B  320 TYR cc_start: 0.8107 (t80) cc_final: 0.7403 (t80)
  outliers start: 29
  outliers final: 11
  residues processed: 137
  average time/residue: 1.2987
  time to fit residues: 192.3561
Evaluate side-chains
  135 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 1.328 
-------------------------------------------------------------------------------
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 A residue  546 SER
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  479 HIS
Chi-restraints excluded: chain B residue  507 MET
Chi-restraints excluded: chain B residue  698 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 122 optimal weight:    6.9990
   chunk 100 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 61 optimal weight:   20.0000
   chunk 7 optimal weight:    0.7980
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 GLN ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.126022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.089399 restraints weight = 16321.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 1.99
r_work: 0.3057 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.2755

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= 0.138
  Angle     :  1.072  46.265  15622  Z= 0.418
  Chirality :  0.041   0.149   1632
  Planarity :  0.004   0.038   1914
  Dihedral  : 21.779 165.243   2250
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 16.14 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.24), residues: 1274
  helix:  1.95 (0.17), residues: 910
  sheet: -1.07 (0.86), residues: 48
  loop : -1.32 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 141 
 HIS   0.010   0.001   HIS B 479 
 PHE   0.019   0.001   PHE B 406 
 TYR   0.017   0.001   TYR B  26 
 ARG   0.004   0.000   ARG A  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04044 (  694)
  hydrogen bonds       : angle       3.53558 ( 2046)
  covalent geometry    : bond        0.00321 (11646)
  covalent geometry    : angle       1.07219 (15622)

*********************** 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
  147 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 1.310 
Fit side-chains
REVERT: A  320 TYR cc_start: 0.8068 (t80) cc_final: 0.7277 (t80)
REVERT: A  325 LYS cc_start: 0.8527 (tppt) cc_final: 0.8148 (tppt)
REVERT: B  268 GLU cc_start: 0.8845 (pt0) cc_final: 0.8323 (pm20)
REVERT: B  282 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8332 (tpp)
REVERT: B  320 TYR cc_start: 0.8048 (t80) cc_final: 0.7572 (t80)
REVERT: B  437 MET cc_start: 0.8920 (tpt) cc_final: 0.8387 (tpt)
  outliers start: 18
  outliers final: 7
  residues processed: 135
  average time/residue: 1.1820
  time to fit residues: 173.6990
Evaluate side-chains
  138 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 130
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
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  546 SER
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  698 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 121 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 110 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 127 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 GLN ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.124535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.087821 restraints weight = 16425.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.97
r_work: 0.3024 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.2812

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= 0.206
  Angle     :  1.092  46.166  15622  Z= 0.433
  Chirality :  0.043   0.155   1632
  Planarity :  0.004   0.040   1914
  Dihedral  : 21.495 164.713   2250
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.51 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.24), residues: 1274
  helix:  1.93 (0.17), residues: 910
  sheet: -1.07 (0.85), residues: 48
  loop : -1.34 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 141 
 HIS   0.003   0.001   HIS A 611 
 PHE   0.019   0.001   PHE A 388 
 TYR   0.017   0.002   TYR B  26 
 ARG   0.004   0.000   ARG B  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04374 (  694)
  hydrogen bonds       : angle       3.58226 ( 2046)
  covalent geometry    : bond        0.00496 (11646)
  covalent geometry    : angle       1.09222 (15622)

*********************** 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
  152 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 1.146 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8847 (pt0) cc_final: 0.8344 (pm20)
REVERT: A  320 TYR cc_start: 0.8110 (t80) cc_final: 0.7326 (t80)
REVERT: A  325 LYS cc_start: 0.8667 (tppt) cc_final: 0.8446 (tppt)
REVERT: B  268 GLU cc_start: 0.8848 (pt0) cc_final: 0.8334 (pm20)
REVERT: B  320 TYR cc_start: 0.8140 (t80) cc_final: 0.7451 (t80)
REVERT: B  325 LYS cc_start: 0.8610 (tppt) cc_final: 0.8341 (tppt)
  outliers start: 19
  outliers final: 8
  residues processed: 138
  average time/residue: 1.2635
  time to fit residues: 189.0926
Evaluate side-chains
  143 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
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  546 SER
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  546 SER
Chi-restraints excluded: chain B residue  698 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 119 optimal weight:    4.9990
   chunk 102 optimal weight:    0.2980
   chunk 90 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   chunk 123 optimal weight:    9.9990
   chunk 120 optimal weight:    0.7980
   chunk 117 optimal weight:    1.9990
   chunk 44 optimal weight:   10.0000
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.126158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.089735 restraints weight = 16263.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 1.97
r_work: 0.3058 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2835

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= 0.141
  Angle     :  1.079  46.196  15622  Z= 0.422
  Chirality :  0.041   0.150   1632
  Planarity :  0.004   0.033   1914
  Dihedral  : 20.860 165.106   2250
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 16.60 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.24), residues: 1274
  helix:  2.00 (0.17), residues: 910
  sheet: -1.01 (0.86), residues: 48
  loop : -1.30 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 235 
 HIS   0.004   0.001   HIS B 143 
 PHE   0.036   0.001   PHE B 406 
 TYR   0.015   0.001   TYR A 457 
 ARG   0.006   0.000   ARG A 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03953 (  694)
  hydrogen bonds       : angle       3.51326 ( 2046)
  covalent geometry    : bond        0.00328 (11646)
  covalent geometry    : angle       1.07904 (15622)

********************** 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
  146 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 1.276 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8828 (pt0) cc_final: 0.8335 (pm20)
REVERT: A  320 TYR cc_start: 0.8096 (t80) cc_final: 0.7360 (t80)
REVERT: A  325 LYS cc_start: 0.8521 (tppt) cc_final: 0.8314 (tppt)
REVERT: A  437 MET cc_start: 0.8901 (tpt) cc_final: 0.8325 (tpt)
REVERT: B  282 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8321 (tpp)
REVERT: B  320 TYR cc_start: 0.8060 (t80) cc_final: 0.7635 (t80)
REVERT: B  703 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7625 (pm20)
  outliers start: 12
  outliers final: 6
  residues processed: 137
  average time/residue: 1.7533
  time to fit residues: 264.1974
Evaluate side-chains
  141 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 3.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  282 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  546 SER
Chi-restraints excluded: chain B residue  698 GLN
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 68 optimal weight:    0.0670
   chunk 88 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 95 optimal weight:    5.9990
   chunk 114 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 89 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 124 optimal weight:   20.0000
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.7924

-------------------------------------------------------------------------------
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
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.124502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.087816 restraints weight = 16321.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.96
r_work: 0.3033 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.2885

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= 0.209
  Angle     :  1.102  46.207  15622  Z= 0.439
  Chirality :  0.043   0.155   1632
  Planarity :  0.004   0.034   1914
  Dihedral  : 20.765 164.154   2250
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 17.16 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.24), residues: 1274
  helix:  1.96 (0.17), residues: 910
  sheet: -0.98 (0.86), residues: 48
  loop : -1.31 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 141 
 HIS   0.005   0.001   HIS B  25 
 PHE   0.017   0.001   PHE A 388 
 TYR   0.017   0.002   TYR A 457 
 ARG   0.006   0.000   ARG A 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04383 (  694)
  hydrogen bonds       : angle       3.58783 ( 2046)
  covalent geometry    : bond        0.00504 (11646)
  covalent geometry    : angle       1.10167 (15622)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10833.47 seconds
wall clock time: 192 minutes 7.15 seconds (11527.15 seconds total)