Starting phenix.real_space_refine
on Wed Jul 30 03:49:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7das_30626/07_2025/7das_30626.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7das_30626/07_2025/7das_30626.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7das_30626/07_2025/7das_30626.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7das_30626/07_2025/7das_30626.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7das_30626/07_2025/7das_30626.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7das_30626/07_2025/7das_30626.cif"
  }
  resolution = 3.64
  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=   0.002 sd=   0.037
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      66      5.49       5
     S      28      5.16       5
     C    7232      2.51       5
     N    1847      2.21       5
     O    2430      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 70 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11603
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 674, 5418
          Classifications: {'peptide': 674}
          Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 645}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 671, 5393
          Classifications: {'peptide': 671}
          Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 642}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 792
          Classifications: {'RNA': 66}
          Modifications used: {'rna3p_pur': 32, 'rna3p_pyr': 34}
          Link IDs: {'rna3p': 65}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 707
          Unresolved non-hydrogen angles: 1118
          Unresolved non-hydrogen dihedrals: 690
          Unresolved non-hydrogen chiralities: 66
          Planarities with less than four sites: {'  G%rna3p_pur:plan2': 17, '  C%rna3p_pyr:plan': 22, '  A%rna3p_pur:plan2': 15, '  U%rna3p_pyr:plan': 12, '  C%rna3p_pyr:plan2': 22, '  G%rna3p_pur:plan': 17, '  A%rna3p_pur:plan': 15}
          Unresolved non-hydrogen planarities: 717
  Time building chain proxies: 8.16, per 1000 atoms: 0.70
  Number of scatterers: 11603
  At special positions: 0
  Unit cell: (110.7, 110.7, 136.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P      66     15.00
     O    2430      8.00
     N    1847      7.00
     C    7232      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  29 " - pdb=" SG  CYS A  38 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  96 " - pdb=" SG  CYS A 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 650 " - pdb=" SG  CYS A 678 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 652 " - pdb=" SG  CYS A 697 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  29 " - pdb=" SG  CYS B  38 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  96 " - pdb=" SG  CYS B 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 650 " - pdb=" SG  CYS B 678 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B 652 " - pdb=" SG  CYS B 697 " distance=2.03

  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
      
  Atom "ATOM  10938  O4'   U C  19 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.83
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2586

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 14 sheets defined
      11.6% alpha, 8.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 92 through 99
      removed outlier: 4.230A  pdb=" N   CYS A  96 " --> pdb=" O   GLU A  92 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN A  97 " --> pdb=" O   PRO A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 196
      removed outlier: 3.578A  pdb=" N   GLY A 196 " --> pdb=" O   GLU A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 247
    Processing helix  chain 'A' and resid 269 through 275
      removed outlier: 3.746A  pdb=" N   LYS A 273 " --> pdb=" O   SER A 270 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   TRP A 274 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 406
    Processing helix  chain 'A' and resid 450 through 454
      removed outlier: 3.817A  pdb=" N   TRP A 453 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 547
    Processing helix  chain 'A' and resid 627 through 636
      removed outlier: 3.657A  pdb=" N   PHE A 631 " --> pdb=" O   GLU A 627 " (cutoff:3.500A)
      Proline residue:  A 633  - end of helix
    Processing helix  chain 'A' and resid 651 through 665
      removed outlier: 6.436A  pdb=" N   TRP A 657 " --> pdb=" O   GLU A 653 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   PHE A 658 " --> pdb=" O   SER A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 692
    Processing helix  chain 'B' and resid 92 through 99
      removed outlier: 4.230A  pdb=" N   CYS B  96 " --> pdb=" O   GLU B  92 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN B  97 " --> pdb=" O   PRO B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 196
      removed outlier: 3.578A  pdb=" N   GLY B 196 " --> pdb=" O   GLU B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 247
    Processing helix  chain 'B' and resid 269 through 275
      removed outlier: 3.747A  pdb=" N   LYS B 273 " --> pdb=" O   SER B 270 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   TRP B 274 " --> pdb=" O   GLY B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 406
    Processing helix  chain 'B' and resid 450 through 454
      removed outlier: 3.818A  pdb=" N   TRP B 453 " --> pdb=" O   GLY B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 547
    Processing helix  chain 'B' and resid 627 through 636
      removed outlier: 3.657A  pdb=" N   PHE B 631 " --> pdb=" O   GLU B 627 " (cutoff:3.500A)
      Proline residue:  B 633  - end of helix
    Processing helix  chain 'B' and resid 651 through 665
      removed outlier: 6.436A  pdb=" N   TRP B 657 " --> pdb=" O   GLU B 653 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   PHE B 658 " --> pdb=" O   SER B 654 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 688 through 692
    Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37
      removed outlier: 3.515A  pdb=" N   LEU A  57 " --> pdb=" O   ILE A  80 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LEU A 153 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   LEU A 177 " --> pdb=" O   ASP A 204 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   LEU A 203 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   LEU A 227 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187
      removed outlier: 3.539A  pdb=" N   LEU A 187 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 200
    Processing sheet with id=AA4, first strand: chain 'A' and resid 279 through 281
      removed outlier: 7.309A  pdb=" N   LEU A 304 " --> pdb=" O   SER A 329 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   LEU A 328 " --> pdb=" O   ASN A 362 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   LEU A 385 " --> pdb=" O   ASN A 414 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU A 413 " --> pdb=" O   ASP A 438 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   LEU A 437 " --> pdb=" O   TYR A 463 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   ILE A 462 " --> pdb=" O   MET A 487 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 314
    Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 447
      removed outlier: 7.048A  pdb=" N   GLN A 446 " --> pdb=" O   GLN A 471 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 535 through 537
      removed outlier: 6.943A  pdb=" N   LEU A 536 " --> pdb=" O   ASN A 569 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE A 592 " --> pdb=" O   ASN A 617 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU A 616 " --> pdb=" O   ASP A 642 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37
      removed outlier: 3.515A  pdb=" N   LEU B  57 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LEU B 153 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   LEU B 177 " --> pdb=" O   ASP B 204 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 228 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LEU B 227 " --> pdb=" O   SER B 255 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 187
      removed outlier: 3.539A  pdb=" N   LEU B 187 " --> pdb=" O   GLU B 212 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 199 through 200
    Processing sheet with id=AB2, first strand: chain 'B' and resid 279 through 281
      removed outlier: 7.309A  pdb=" N   LEU B 304 " --> pdb=" O   SER B 329 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   LEU B 328 " --> pdb=" O   ASN B 362 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   LEU B 385 " --> pdb=" O   ASN B 414 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   LEU B 413 " --> pdb=" O   ASP B 438 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   LEU B 437 " --> pdb=" O   TYR B 463 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   ILE B 462 " --> pdb=" O   MET B 487 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 314
    Processing sheet with id=AB4, first strand: chain 'B' and resid 445 through 447
      removed outlier: 7.048A  pdb=" N   GLN B 446 " --> pdb=" O   GLN B 471 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 535 through 537
      removed outlier: 6.944A  pdb=" N   LEU B 536 " --> pdb=" O   ASN B 569 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ILE B 592 " --> pdb=" O   ASN B 617 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU B 616 " --> pdb=" O   ASP B 642 " (cutoff:3.500A)

    100 hydrogen bonds defined for protein.
    240 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: 3.01

  Time building geometry restraints manager: 3.38 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3345
        1.33 -     1.46: 2221
        1.46 -     1.58: 6164
        1.58 -     1.70: 129
        1.70 -     1.82: 36
  Bond restraints: 11895
  Sorted by residual:
  bond pdb=" N   PRO B 579 "
       pdb=" CD  PRO B 579 "
    ideal  model  delta    sigma   weight residual
    1.473  1.535 -0.062 1.40e-02 5.10e+03 1.97e+01
  bond pdb=" N   PRO A 579 "
       pdb=" CD  PRO A 579 "
    ideal  model  delta    sigma   weight residual
    1.473  1.535 -0.062 1.40e-02 5.10e+03 1.96e+01
  bond pdb=" O3'   G C  10 "
       pdb=" P     A C  11 "
    ideal  model  delta    sigma   weight residual
    1.607  1.663 -0.056 1.50e-02 4.44e+03 1.41e+01
  bond pdb=" O3'   A C  34 "
       pdb=" P     C C  35 "
    ideal  model  delta    sigma   weight residual
    1.607  1.663 -0.056 1.50e-02 4.44e+03 1.40e+01
  bond pdb=" O3'   G C  13 "
       pdb=" P     G C  14 "
    ideal  model  delta    sigma   weight residual
    1.607  1.662 -0.055 1.50e-02 4.44e+03 1.32e+01
  ... (remaining 11890 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 15723
        2.29 -     4.58: 510
        4.58 -     6.87: 53
        6.87 -     9.16: 8
        9.16 -    11.45: 5
  Bond angle restraints: 16299
  Sorted by residual:
  angle pdb=" N   HIS B 683 "
        pdb=" CA  HIS B 683 "
        pdb=" C   HIS B 683 "
      ideal   model   delta    sigma   weight residual
     112.38  103.04    9.34 1.22e+00 6.72e-01 5.86e+01
  angle pdb=" N   HIS A 683 "
        pdb=" CA  HIS A 683 "
        pdb=" C   HIS A 683 "
      ideal   model   delta    sigma   weight residual
     112.38  103.06    9.32 1.22e+00 6.72e-01 5.83e+01
  angle pdb=" O3'   G C  13 "
        pdb=" C3'   G C  13 "
        pdb=" C2'   G C  13 "
      ideal   model   delta    sigma   weight residual
     113.70  125.15  -11.45 1.50e+00 4.44e-01 5.83e+01
  angle pdb=" C3'   G C  18 "
        pdb=" C2'   G C  18 "
        pdb=" O2'   G C  18 "
      ideal   model   delta    sigma   weight residual
     110.70  120.23   -9.53 1.50e+00 4.44e-01 4.03e+01
  angle pdb=" C4'   G C 238 "
        pdb=" C3'   G C 238 "
        pdb=" O3'   G C 238 "
      ideal   model   delta    sigma   weight residual
     113.00  122.27   -9.27 1.50e+00 4.44e-01 3.82e+01
  ... (remaining 16294 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.25: 7211
       33.25 -    66.49: 266
       66.49 -    99.74: 35
       99.74 -   132.99: 0
      132.99 -   166.23: 1
  Dihedral angle restraints: 7513
    sinusoidal: 3550
      harmonic: 3963
  Sorted by residual:
  dihedral pdb=" C5'   U C 259 "
           pdb=" C4'   U C 259 "
           pdb=" C3'   U C 259 "
           pdb=" O3'   U C 259 "
      ideal   model   delta sinusoidal    sigma   weight residual
      82.00  166.04  -84.04     1      8.00e+00 1.56e-02 1.34e+02
  dihedral pdb=" C4'   U C 259 "
           pdb=" C3'   U C 259 "
           pdb=" C2'   U C 259 "
           pdb=" C1'   U C 259 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.00  -40.89   76.89     1      8.00e+00 1.56e-02 1.16e+02
  dihedral pdb=" O4'   U C 259 "
           pdb=" C4'   U C 259 "
           pdb=" C3'   U C 259 "
           pdb=" C2'   U C 259 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   37.98  -72.98     1      8.00e+00 1.56e-02 1.06e+02
  ... (remaining 7510 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.177: 1947
       0.177 -    0.355: 41
       0.355 -    0.532: 3
       0.532 -    0.710: 1
       0.710 -    0.887: 2
  Chirality restraints: 1994
  Sorted by residual:
  chirality pdb=" C3'   G C  13 "
            pdb=" C4'   G C  13 "
            pdb=" O3'   G C  13 "
            pdb=" C2'   G C  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.59   -0.89 2.00e-01 2.50e+01 1.97e+01
  chirality pdb=" C3'   G C  18 "
            pdb=" C4'   G C  18 "
            pdb=" O3'   G C  18 "
            pdb=" C2'   G C  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.69   -0.78 2.00e-01 2.50e+01 1.54e+01
  chirality pdb=" C2'   G C  18 "
            pdb=" C3'   G C  18 "
            pdb=" O2'   G C  18 "
            pdb=" C1'   G C  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.08   -0.68 2.00e-01 2.50e+01 1.15e+01
  ... (remaining 1991 not shown)

  Planarity restraints: 1922
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 513 "   -0.025 2.00e-02 2.50e+03   5.21e-02 2.71e+01
        pdb=" C   ASP B 513 "    0.090 2.00e-02 2.50e+03
        pdb=" O   ASP B 513 "   -0.034 2.00e-02 2.50e+03
        pdb=" N   LEU B 514 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 513 "    0.025 2.00e-02 2.50e+03   5.19e-02 2.70e+01
        pdb=" C   ASP A 513 "   -0.090 2.00e-02 2.50e+03
        pdb=" O   ASP A 513 "    0.034 2.00e-02 2.50e+03
        pdb=" N   LEU A 514 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 678 "   -0.025 2.00e-02 2.50e+03   5.12e-02 2.62e+01
        pdb=" C   CYS B 678 "    0.089 2.00e-02 2.50e+03
        pdb=" O   CYS B 678 "   -0.033 2.00e-02 2.50e+03
        pdb=" N   ASN B 679 "   -0.030 2.00e-02 2.50e+03
  ... (remaining 1919 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 4
        2.18 -     2.86: 4267
        2.86 -     3.54: 15216
        3.54 -     4.22: 26677
        4.22 -     4.90: 45075
  Nonbonded interactions: 91239
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 518 "
            pdb=" O4'   U C  19 "
     model   vdw
     1.496 3.120
  nonbonded pdb=" OD1 ASN B 542 "
            pdb=" O2'   U C  17 "
     model   vdw
     1.898 3.040
  nonbonded pdb=" ND2 ASN B 518 "
            pdb=" C1'   U C  19 "
     model   vdw
     1.977 3.550
  nonbonded pdb=" CG  ASN B 518 "
            pdb=" O4'   U C  19 "
     model   vdw
     2.175 3.270
  nonbonded pdb=" O   PRO A 316 "
            pdb=" NE1 TRP A 354 "
     model   vdw
     2.213 3.120
  ... (remaining 91234 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 24 through 697)
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.440
  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:          0.500
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     31.630
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
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      :  0.006   0.062  11903  Z= 0.342
  Angle     :  0.919  11.450  16315  Z= 0.594
  Chirality :  0.071   0.887   1994
  Planarity :  0.005   0.052   1922
  Dihedral  : 16.890 166.233   4903
  Min Nonbonded Distance : 1.496

Molprobity Statistics.
  All-atom Clashscore : 17.13
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.93 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -3.87 (0.20), residues: 1337
  helix: -3.01 (0.41), residues: 88
  sheet: -2.94 (0.34), residues: 192
  loop : -2.69 (0.17), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 547 
 HIS   0.005   0.001   HIS A 109 
 PHE   0.018   0.001   PHE B 558 
 TYR   0.017   0.002   TYR B 469 
 ARG   0.011   0.001   ARG B 644 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23531 (  100)
  hydrogen bonds       : angle      10.52559 (  240)
  SS BOND              : bond        0.01190 (    8)
  SS BOND              : angle       1.62012 (   16)
  covalent geometry    : bond        0.00564 (11895)
  covalent geometry    : angle       0.91787 (16299)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 1.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  643 MET cc_start: 0.7938 (ttm) cc_final: 0.7446 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.3115
  time to fit residues: 46.4669
Evaluate side-chains
  39 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    2.9990
   chunk 106 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 71 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 127 optimal weight:    0.9980
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
A 110 ASN
A 134 ASN
A 170 GLN
A 260 GLN
A 395 GLN
A 446 GLN
A 467 ASN
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 HIS
A 573 ASN
A 585 ASN
A 610 GLN
A 621 ASN
A 646 ASN
A 679 ASN
B  61 HIS
B  62 ASN
B 110 ASN
B 134 ASN
B 149 ASN
B 170 GLN
B 395 GLN
B 446 GLN
B 451 GLN
B 467 ASN
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 566 HIS
B 573 ASN
B 585 ASN
B 610 GLN
B 621 ASN
B 639 ASN
B 646 ASN

Total number of N/Q/H flips: 32

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.076193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.063078 restraints weight = 40389.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.064658 restraints weight = 20887.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.065683 restraints weight = 13301.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11903  Z= 0.176
  Angle     :  0.610  10.568  16315  Z= 0.314
  Chirality :  0.042   0.146   1994
  Planarity :  0.004   0.041   1922
  Dihedral  : 14.765 165.341   2245
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 10.18 %
    Favored  : 88.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -2.76 (0.22), residues: 1337
  helix: -1.15 (0.55), residues: 94
  sheet: -2.64 (0.38), residues: 177
  loop : -1.91 (0.19), residues: 1066

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 547 
 HIS   0.006   0.001   HIS B 109 
 PHE   0.013   0.001   PHE B 460 
 TYR   0.015   0.001   TYR B 469 
 ARG   0.006   0.001   ARG B 326 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04112 (  100)
  hydrogen bonds       : angle       6.58133 (  240)
  SS BOND              : bond        0.00745 (    8)
  SS BOND              : angle       1.10795 (   16)
  covalent geometry    : bond        0.00409 (11895)
  covalent geometry    : angle       0.60908 (16299)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 39
  time to evaluate  : 1.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 TYR cc_start: 0.4488 (OUTLIER) cc_final: 0.4071 (t80)
REVERT: B  643 MET cc_start: 0.7816 (ttm) cc_final: 0.7284 (mtp)
  outliers start: 15
  outliers final: 7
  residues processed: 50
  average time/residue: 0.2393
  time to fit residues: 18.6161
Evaluate side-chains
  35 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  567 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 136 optimal weight:   20.0000
   chunk 33 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0010
   chunk 6 optimal weight:    4.9990
   overall best weight:    3.7994

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

Flipped N/Q/H residues before XYZ refinement:
** A  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 146 ASN
A 639 ASN
B  40 HIS
B 109 HIS
B 146 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.072269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.059514 restraints weight = 42014.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.061002 restraints weight = 22113.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.061975 restraints weight = 14258.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.048  11903  Z= 0.333
  Angle     :  0.738   8.585  16315  Z= 0.382
  Chirality :  0.047   0.179   1994
  Planarity :  0.005   0.044   1922
  Dihedral  : 15.259 161.559   2245
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.31 %
    Favored  : 86.69 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.21 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -2.84 (0.22), residues: 1337
  helix: -1.47 (0.49), residues: 106
  sheet: -2.86 (0.37), residues: 198
  loop : -1.86 (0.19), residues: 1033

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 274 
 HIS   0.010   0.001   HIS B 109 
 PHE   0.024   0.002   PHE A 538 
 TYR   0.019   0.002   TYR A 469 
 ARG   0.006   0.001   ARG B 326 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05307 (  100)
  hydrogen bonds       : angle       6.43524 (  240)
  SS BOND              : bond        0.00803 (    8)
  SS BOND              : angle       1.41207 (   16)
  covalent geometry    : bond        0.00755 (11895)
  covalent geometry    : angle       0.73699 (16299)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 32
  time to evaluate  : 1.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  512 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8776 (tt)
REVERT: B   24 TYR cc_start: 0.4423 (OUTLIER) cc_final: 0.3735 (t80)
REVERT: B  533 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9034 (tt)
  outliers start: 27
  outliers final: 14
  residues processed: 58
  average time/residue: 0.1891
  time to fit residues: 18.4478
Evaluate side-chains
  37 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 20
  time to evaluate  : 1.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  359 GLU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   75 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  384 TYR
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  567 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 112 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 126 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
B 682 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.073491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.060501 restraints weight = 41600.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.062101 restraints weight = 21366.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.063146 restraints weight = 13518.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.3614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11903  Z= 0.141
  Angle     :  0.544  10.355  16315  Z= 0.281
  Chirality :  0.041   0.174   1994
  Planarity :  0.004   0.041   1922
  Dihedral  : 14.870 165.535   2245
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 15.59 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -2.42 (0.23), residues: 1337
  helix: -1.04 (0.55), residues: 100
  sheet: -2.51 (0.41), residues: 174
  loop : -1.63 (0.19), residues: 1063

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 547 
 HIS   0.013   0.001   HIS B 682 
 PHE   0.009   0.001   PHE B 460 
 TYR   0.015   0.001   TYR B 469 
 ARG   0.003   0.000   ARG B 326 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03661 (  100)
  hydrogen bonds       : angle       5.89454 (  240)
  SS BOND              : bond        0.00365 (    8)
  SS BOND              : angle       0.89352 (   16)
  covalent geometry    : bond        0.00326 (11895)
  covalent geometry    : angle       0.54374 (16299)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 29
  time to evaluate  : 1.579 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.7329 (p90)
REVERT: A  512 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8664 (tt)
REVERT: B   24 TYR cc_start: 0.4428 (OUTLIER) cc_final: 0.3805 (t80)
REVERT: B  484 GLN cc_start: 0.7807 (tt0) cc_final: 0.7130 (tm-30)
  outliers start: 19
  outliers final: 11
  residues processed: 46
  average time/residue: 0.1803
  time to fit residues: 15.0010
Evaluate side-chains
  39 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 25
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 TYR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  567 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 111 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   chunk 131 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 133 optimal weight:    1.9990
   chunk 61 optimal weight:    8.9990
   chunk 83 optimal weight:   10.0000
   chunk 99 optimal weight:    4.9990
   chunk 137 optimal weight:   20.0000
   chunk 9 optimal weight:    7.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 106 ASN
B 312 GLN
** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.069246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.056517 restraints weight = 43906.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.057862 restraints weight = 24466.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.058743 restraints weight = 16375.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.4453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.062  11903  Z= 0.444
  Angle     :  0.860   9.518  16315  Z= 0.438
  Chirality :  0.050   0.174   1994
  Planarity :  0.006   0.048   1922
  Dihedral  : 15.837 149.641   2245
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.83 %
    Favored  : 83.17 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 15.27 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -3.05 (0.22), residues: 1337
  helix: -1.49 (0.49), residues: 106
  sheet: -3.32 (0.37), residues: 184
  loop : -1.99 (0.19), residues: 1047

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP B 547 
 HIS   0.006   0.001   HIS A 666 
 PHE   0.029   0.003   PHE B 460 
 TYR   0.023   0.003   TYR A 469 
 ARG   0.005   0.001   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05634 (  100)
  hydrogen bonds       : angle       6.71400 (  240)
  SS BOND              : bond        0.00705 (    8)
  SS BOND              : angle       1.35357 (   16)
  covalent geometry    : bond        0.01007 (11895)
  covalent geometry    : angle       0.85972 (16299)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 25
  time to evaluate  : 1.268 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7169 (p90)
REVERT: A  512 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8848 (tt)
REVERT: A  533 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9155 (tt)
REVERT: B   24 TYR cc_start: 0.4223 (OUTLIER) cc_final: 0.3449 (t80)
REVERT: B   75 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8593 (p90)
REVERT: B  533 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9104 (tt)
  outliers start: 44
  outliers final: 23
  residues processed: 67
  average time/residue: 0.1843
  time to fit residues: 20.6641
Evaluate side-chains
  52 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 23
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 TYR
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  359 GLU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  539 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   75 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  469 TYR
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  567 ILE
Chi-restraints excluded: chain B residue  650 CYS
Chi-restraints excluded: chain B residue  652 CYS
Chi-restraints excluded: chain B residue  697 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 126 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 125 optimal weight:    0.9980
   chunk 101 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.072851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.059998 restraints weight = 42420.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.061574 restraints weight = 21918.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.062610 restraints weight = 13918.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.4285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11903  Z= 0.109
  Angle     :  0.547   9.659  16315  Z= 0.278
  Chirality :  0.040   0.166   1994
  Planarity :  0.004   0.041   1922
  Dihedral  : 15.309 154.267   2245
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 17.02 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -2.45 (0.23), residues: 1337
  helix: -1.28 (0.51), residues: 112
  sheet: -2.94 (0.38), residues: 197
  loop : -1.48 (0.20), residues: 1028

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 547 
 HIS   0.002   0.001   HIS A 682 
 PHE   0.011   0.001   PHE B 120 
 TYR   0.015   0.001   TYR A 469 
 ARG   0.004   0.000   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03463 (  100)
  hydrogen bonds       : angle       5.86610 (  240)
  SS BOND              : bond        0.00396 (    8)
  SS BOND              : angle       0.90201 (   16)
  covalent geometry    : bond        0.00250 (11895)
  covalent geometry    : angle       0.54652 (16299)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 28
  time to evaluate  : 1.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.6348 (p90)
REVERT: B   24 TYR cc_start: 0.4364 (OUTLIER) cc_final: 0.3667 (t80)
REVERT: B  484 GLN cc_start: 0.8153 (tt0) cc_final: 0.7248 (tm-30)
  outliers start: 24
  outliers final: 13
  residues processed: 50
  average time/residue: 0.1793
  time to fit residues: 15.5726
Evaluate side-chains
  38 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 23
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 TYR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  650 CYS
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  650 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 118 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 124 optimal weight:    5.9990
   chunk 131 optimal weight:    8.9990
   chunk 121 optimal weight:    0.9990
   chunk 13 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.071775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.059058 restraints weight = 43207.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.060508 restraints weight = 23239.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.061429 restraints weight = 15192.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.4431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11903  Z= 0.190
  Angle     :  0.572   7.849  16315  Z= 0.292
  Chirality :  0.042   0.162   1994
  Planarity :  0.004   0.040   1922
  Dihedral  : 15.254 151.682   2245
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.22 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.71 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -2.46 (0.24), residues: 1337
  helix: -1.39 (0.49), residues: 118
  sheet: -2.92 (0.38), residues: 196
  loop : -1.48 (0.20), residues: 1023

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 274 
 HIS   0.006   0.001   HIS A  61 
 PHE   0.012   0.001   PHE B 460 
 TYR   0.014   0.001   TYR A 469 
 ARG   0.002   0.000   ARG B 326 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03762 (  100)
  hydrogen bonds       : angle       5.90596 (  240)
  SS BOND              : bond        0.00448 (    8)
  SS BOND              : angle       0.88958 (   16)
  covalent geometry    : bond        0.00439 (11895)
  covalent geometry    : angle       0.57122 (16299)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 26
  time to evaluate  : 1.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6061 (p90)
REVERT: A  512 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8648 (tt)
REVERT: B   24 TYR cc_start: 0.4407 (OUTLIER) cc_final: 0.3622 (t80)
REVERT: B  484 GLN cc_start: 0.8198 (tt0) cc_final: 0.7409 (tm-30)
  outliers start: 27
  outliers final: 19
  residues processed: 51
  average time/residue: 0.1601
  time to fit residues: 14.6029
Evaluate side-chains
  47 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 25
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 TYR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  650 CYS
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   75 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  567 ILE
Chi-restraints excluded: chain B residue  650 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0570
   chunk 81 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 93 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    2.6104

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

Flipped N/Q/H residues before XYZ refinement:
** A  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 170 GLN
B 564 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.071090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.058372 restraints weight = 42991.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.059784 restraints weight = 23442.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.060719 restraints weight = 15445.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.4734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  11903  Z= 0.226
  Angle     :  0.609   7.676  16315  Z= 0.313
  Chirality :  0.043   0.149   1994
  Planarity :  0.004   0.040   1922
  Dihedral  : 15.469 145.464   2245
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.85 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.87 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -2.56 (0.24), residues: 1337
  helix: -1.66 (0.46), residues: 130
  sheet: -3.01 (0.38), residues: 197
  loop : -1.51 (0.20), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 274 
 HIS   0.005   0.001   HIS A  61 
 PHE   0.013   0.001   PHE B 460 
 TYR   0.016   0.002   TYR A 469 
 ARG   0.003   0.000   ARG A 507 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04078 (  100)
  hydrogen bonds       : angle       5.98130 (  240)
  SS BOND              : bond        0.00492 (    8)
  SS BOND              : angle       0.99004 (   16)
  covalent geometry    : bond        0.00518 (11895)
  covalent geometry    : angle       0.60820 (16299)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 27
  time to evaluate  : 1.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.5670 (p90)
REVERT: A  512 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8720 (tt)
REVERT: A  533 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9141 (tt)
REVERT: B   24 TYR cc_start: 0.4525 (OUTLIER) cc_final: 0.3597 (t80)
REVERT: B  463 TYR cc_start: 0.6978 (t80) cc_final: 0.6670 (t80)
  outliers start: 30
  outliers final: 20
  residues processed: 54
  average time/residue: 0.1899
  time to fit residues: 17.9649
Evaluate side-chains
  48 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 24
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 TYR
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  650 CYS
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  567 ILE
Chi-restraints excluded: chain B residue  650 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 133 optimal weight:    0.3980
   chunk 73 optimal weight:   10.0000
   chunk 117 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 113 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A  61 HIS
A 337 GLN
A 585 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.072836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.060023 restraints weight = 42724.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.061580 restraints weight = 22109.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.062606 restraints weight = 14064.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.4784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11903  Z= 0.107
  Angle     :  0.521   8.580  16315  Z= 0.264
  Chirality :  0.040   0.174   1994
  Planarity :  0.004   0.041   1922
  Dihedral  : 15.144 149.977   2245
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 17.26 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -2.28 (0.24), residues: 1337
  helix: -1.47 (0.48), residues: 124
  sheet: -2.76 (0.37), residues: 219
  loop : -1.27 (0.21), residues: 994

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 547 
 HIS   0.003   0.000   HIS A  61 
 PHE   0.007   0.001   PHE A 687 
 TYR   0.013   0.001   TYR A 469 
 ARG   0.002   0.000   ARG B 326 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03118 (  100)
  hydrogen bonds       : angle       5.61888 (  240)
  SS BOND              : bond        0.00319 (    8)
  SS BOND              : angle       0.77328 (   16)
  covalent geometry    : bond        0.00249 (11895)
  covalent geometry    : angle       0.52060 (16299)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 26
  time to evaluate  : 1.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.5404 (p90)
REVERT: A  512 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8537 (tt)
REVERT: B   24 TYR cc_start: 0.4391 (OUTLIER) cc_final: 0.3502 (t80)
REVERT: B  484 GLN cc_start: 0.8149 (tt0) cc_final: 0.7785 (mt0)
  outliers start: 22
  outliers final: 16
  residues processed: 47
  average time/residue: 0.1657
  time to fit residues: 14.4366
Evaluate side-chains
  43 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 24
  time to evaluate  : 1.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 TYR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  650 CYS
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   75 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  539 GLN
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  567 ILE
Chi-restraints excluded: chain B residue  650 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 133 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 116 optimal weight:    2.9990
   chunk 135 optimal weight:    9.9990
   chunk 63 optimal weight:    0.6980
   chunk 101 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 564 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.071941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.059138 restraints weight = 42606.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.060662 restraints weight = 22261.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.061657 restraints weight = 14285.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.4868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11903  Z= 0.154
  Angle     :  0.546   8.693  16315  Z= 0.277
  Chirality :  0.040   0.185   1994
  Planarity :  0.004   0.041   1922
  Dihedral  : 15.145 150.673   2245
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.80 %
    Favored  : 90.20 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 17.66 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -2.28 (0.24), residues: 1337
  helix: -1.55 (0.46), residues: 130
  sheet: -2.75 (0.39), residues: 207
  loop : -1.29 (0.21), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 547 
 HIS   0.002   0.001   HIS A 540 
 PHE   0.010   0.001   PHE B 460 
 TYR   0.013   0.001   TYR A 469 
 ARG   0.002   0.000   ARG B 326 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03520 (  100)
  hydrogen bonds       : angle       5.69073 (  240)
  SS BOND              : bond        0.00372 (    8)
  SS BOND              : angle       0.80358 (   16)
  covalent geometry    : bond        0.00357 (11895)
  covalent geometry    : angle       0.54520 (16299)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 26
  time to evaluate  : 1.364 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.5584 (p90)
REVERT: A  512 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8568 (tt)
REVERT: B   24 TYR cc_start: 0.4637 (OUTLIER) cc_final: 0.3679 (t80)
  outliers start: 22
  outliers final: 16
  residues processed: 48
  average time/residue: 0.1729
  time to fit residues: 14.9873
Evaluate side-chains
  44 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 25
  time to evaluate  : 1.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 TYR
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  359 GLU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  539 GLN
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  567 ILE
Chi-restraints excluded: chain B residue  650 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 131 optimal weight:    8.9990
   chunk 44 optimal weight:    4.9990
   chunk 133 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 10 optimal weight:    8.9990
   chunk 80 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
B 541 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.071390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.058498 restraints weight = 42881.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.059989 restraints weight = 22818.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.060961 restraints weight = 14775.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.5022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11903  Z= 0.186
  Angle     :  0.567   7.972  16315  Z= 0.290
  Chirality :  0.041   0.184   1994
  Planarity :  0.004   0.041   1922
  Dihedral  : 15.264 147.879   2245
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.95 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 17.42 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -2.33 (0.24), residues: 1337
  helix: -1.50 (0.47), residues: 130
  sheet: -2.86 (0.37), residues: 217
  loop : -1.29 (0.21), residues: 990

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 547 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.012   0.001   PHE B 460 
 TYR   0.014   0.001   TYR A 469 
 ARG   0.002   0.000   ARG B 326 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03701 (  100)
  hydrogen bonds       : angle       5.80510 (  240)
  SS BOND              : bond        0.00430 (    8)
  SS BOND              : angle       0.85078 (   16)
  covalent geometry    : bond        0.00430 (11895)
  covalent geometry    : angle       0.56657 (16299)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3268.33 seconds
wall clock time: 57 minutes 59.52 seconds (3479.52 seconds total)