Starting phenix.real_space_refine
on Tue Mar  3 19:25:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dh7_27431/03_2026/8dh7_27431.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dh7_27431/03_2026/8dh7_27431.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dh7_27431/03_2026/8dh7_27431.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dh7_27431/03_2026/8dh7_27431.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dh7_27431/03_2026/8dh7_27431.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dh7_27431/03_2026/8dh7_27431.map"
  }
  resolution = 2.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.079
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: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    5240      2.51       5
     N    1454      2.21       5
     O    1546      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8274
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 526, 4137
          Classifications: {'peptide': 526}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 491}
    Chain: "A"
      Number of atoms: 4137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 526, 4137
          Classifications: {'peptide': 526}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 491}
  Time building chain proxies: 2.01, per 1000 atoms: 0.24
  Number of scatterers: 8274
  At special positions: 0
  Unit cell: (113.016, 82.269, 78.945, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1546      8.00
     N    1454      7.00
     C    5240      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 316.2 milliseconds
  

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 16 sheets defined
      39.4% alpha, 13.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'B' and resid 4 through 11
    Processing helix  chain 'B' and resid 13 through 20
      removed outlier: 3.964A  pdb=" N   VAL B  20 " --> pdb=" O   LEU B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 30
      removed outlier: 3.594A  pdb=" N   ILE B  27 " --> pdb=" O   HIS B  24 " (cutoff:3.500A)
      Proline residue:  B  28  - end of helix
    Processing helix  chain 'B' and resid 48 through 62
    Processing helix  chain 'B' and resid 78 through 87
      removed outlier: 3.831A  pdb=" N   ASN B  82 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 108
    Processing helix  chain 'B' and resid 120 through 127
    Processing helix  chain 'B' and resid 164 through 171
    Processing helix  chain 'B' and resid 246 through 264
    Processing helix  chain 'B' and resid 279 through 291
    Processing helix  chain 'B' and resid 305 through 315
      removed outlier: 4.024A  pdb=" N   LEU B 309 " --> pdb=" O   GLN B 305 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU B 311 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 337
    Processing helix  chain 'B' and resid 338 through 344
      removed outlier: 3.567A  pdb=" N   HIS B 344 " --> pdb=" O   GLU B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 355
    Processing helix  chain 'B' and resid 356 through 364
    Processing helix  chain 'B' and resid 396 through 404
      removed outlier: 3.534A  pdb=" N   ARG B 402 " --> pdb=" O   ALA B 398 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ASN B 403 " --> pdb=" O   ASP B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 469
    Processing helix  chain 'B' and resid 471 through 493
      removed outlier: 4.566A  pdb=" N   ALA B 476 " --> pdb=" O   PRO B 472 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   LEU B 477 " --> pdb=" O   ASP B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 505 through 515
    Processing helix  chain 'A' and resid 4 through 11
    Processing helix  chain 'A' and resid 13 through 20
      removed outlier: 3.929A  pdb=" N   VAL A  20 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 30
      removed outlier: 3.710A  pdb=" N   ILE A  27 " --> pdb=" O   HIS A  24 " (cutoff:3.500A)
      Proline residue:  A  28  - end of helix
    Processing helix  chain 'A' and resid 48 through 62
    Processing helix  chain 'A' and resid 78 through 87
      removed outlier: 3.921A  pdb=" N   ASN A  82 " --> pdb=" O   GLY A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 108
    Processing helix  chain 'A' and resid 120 through 127
    Processing helix  chain 'A' and resid 164 through 171
    Processing helix  chain 'A' and resid 246 through 264
    Processing helix  chain 'A' and resid 279 through 291
    Processing helix  chain 'A' and resid 306 through 315
      removed outlier: 3.772A  pdb=" N   ASP A 310 " --> pdb=" O   ASP A 306 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU A 311 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 338
      removed outlier: 3.760A  pdb=" N   ASN A 338 " --> pdb=" O   ARG A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 344
    Processing helix  chain 'A' and resid 350 through 355
    Processing helix  chain 'A' and resid 356 through 364
    Processing helix  chain 'A' and resid 396 through 404
      removed outlier: 3.686A  pdb=" N   ASN A 403 " --> pdb=" O   ASP A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 469
    Processing helix  chain 'A' and resid 471 through 493
      removed outlier: 4.558A  pdb=" N   ALA A 476 " --> pdb=" O   PRO A 472 " (cutoff:3.500A)
      removed outlier: 5.154A  pdb=" N   LEU A 477 " --> pdb=" O   ASP A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 515
    Processing sheet with id=AA1, first strand: chain 'B' and resid 112 through 113
      removed outlier: 6.420A  pdb=" N   ILE B  91 " --> pdb=" O   GLU B 112 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   PHE B  69 " --> pdb=" O   ILE B  91 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ARG B  93 " --> pdb=" O   PHE B  69 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   LEU B  71 " --> pdb=" O   ARG B  93 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU B  36 " --> pdb=" O   PHE B  72 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   TYR B  35 " --> pdb=" O   TYR B 142 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   ILE B 144 " --> pdb=" O   TYR B  35 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   GLY B  37 " --> pdb=" O   ILE B 144 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   GLU B 146 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   ASP B 141 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LYS B 174 " --> pdb=" O   ASP B 141 " (cutoff:3.500A)
      removed outlier: 10.970A  pdb=" N   ASP B 173 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 10.088A  pdb=" N   ALA B 227 " --> pdb=" O   ASP B 173 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   VAL B 175 " --> pdb=" O   ALA B 227 " (cutoff:3.500A)
      removed outlier: 8.333A  pdb=" N   VAL B 229 " --> pdb=" O   VAL B 175 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ILE B 177 " --> pdb=" O   VAL B 229 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   SER B 231 " --> pdb=" O   ILE B 177 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   VAL B 179 " --> pdb=" O   SER B 231 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 149 through 150
      removed outlier: 3.713A  pdb=" N   ALA B 149 " --> pdb=" O   VAL B 157 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 190 through 191
      removed outlier: 8.429A  pdb=" N   CYS B 347 " --> pdb=" O   ASP B 318 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   ALA B 320 " --> pdb=" O   CYS B 347 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   ARG B 349 " --> pdb=" O   ALA B 320 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   ALA B 322 " --> pdb=" O   ARG B 349 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   LEU B 297 " --> pdb=" O   ASP B 318 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   ALA B 320 " --> pdb=" O   LEU B 297 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL B 299 " --> pdb=" O   ALA B 320 " (cutoff:3.500A)
      removed outlier: 5.432A  pdb=" N   ALA B 322 " --> pdb=" O   VAL B 299 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 274 through 275
      removed outlier: 3.865A  pdb=" N   MET B 368 " --> pdb=" O   GLN B 275 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   SER B 407 " --> pdb=" O   ILE B 443 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   VAL B 445 " --> pdb=" O   SER B 407 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   MET B 409 " --> pdb=" O   VAL B 445 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 303 through 304
    Processing sheet with id=AA6, first strand: chain 'B' and resid 380 through 381
      removed outlier: 6.734A  pdb=" N   VAL B 374 " --> pdb=" O   VAL B 428 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 384 through 385
    Processing sheet with id=AA8, first strand: chain 'B' and resid 414 through 415
    Processing sheet with id=AA9, first strand: chain 'A' and resid 112 through 113
      removed outlier: 6.427A  pdb=" N   ILE A  91 " --> pdb=" O   GLU A 112 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   PHE A  69 " --> pdb=" O   ILE A  91 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ARG A  93 " --> pdb=" O   PHE A  69 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   LEU A  71 " --> pdb=" O   ARG A  93 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A  72 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   TYR A  35 " --> pdb=" O   TYR A 142 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   ILE A 144 " --> pdb=" O   TYR A  35 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   GLY A  37 " --> pdb=" O   ILE A 144 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLU A 146 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   ASP A 141 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
      removed outlier: 10.968A  pdb=" N   ASP A 173 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 10.127A  pdb=" N   ALA A 227 " --> pdb=" O   ASP A 173 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   VAL A 175 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
      removed outlier: 8.351A  pdb=" N   VAL A 229 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ILE A 177 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   SER A 231 " --> pdb=" O   ILE A 177 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   VAL A 179 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 149 through 150
      removed outlier: 3.653A  pdb=" N   ALA A 149 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 190 through 191
      removed outlier: 8.411A  pdb=" N   CYS A 347 " --> pdb=" O   ASP A 318 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ALA A 320 " --> pdb=" O   CYS A 347 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   ARG A 349 " --> pdb=" O   ALA A 320 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   ALA A 322 " --> pdb=" O   ARG A 349 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   LEU A 297 " --> pdb=" O   ASP A 318 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ALA A 320 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   VAL A 299 " --> pdb=" O   ALA A 320 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   ALA A 322 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 274 through 275
      removed outlier: 5.943A  pdb=" N   ALA A 367 " --> pdb=" O   ILE A 408 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   HIS A 410 " --> pdb=" O   ALA A 367 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   ASN A 369 " --> pdb=" O   HIS A 410 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   SER A 407 " --> pdb=" O   ILE A 443 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   VAL A 445 " --> pdb=" O   SER A 407 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   MET A 409 " --> pdb=" O   VAL A 445 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 303 through 304
    Processing sheet with id=AB5, first strand: chain 'A' and resid 380 through 381
      removed outlier: 6.617A  pdb=" N   VAL A 374 " --> pdb=" O   VAL A 428 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 384 through 385
    Processing sheet with id=AB7, first strand: chain 'A' and resid 414 through 415

    283 hydrogen bonds defined for protein.
    795 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.21

  Time building geometry restraints manager: 0.80 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: 1668
        1.33 -     1.45: 1918
        1.45 -     1.57: 4823
        1.57 -     1.69: 1
        1.69 -     1.81: 60
  Bond restraints: 8470
  Sorted by residual:
  bond pdb=" CA  ASP B 245 "
       pdb=" C   ASP B 245 "
    ideal  model  delta    sigma   weight residual
    1.523  1.455  0.069 1.80e-02 3.09e+03 1.45e+01
  bond pdb=" CA  ASP A 245 "
       pdb=" C   ASP A 245 "
    ideal  model  delta    sigma   weight residual
    1.523  1.456  0.067 1.80e-02 3.09e+03 1.39e+01
  bond pdb=" CA  GLN B 275 "
       pdb=" CB  GLN B 275 "
    ideal  model  delta    sigma   weight residual
    1.527  1.606 -0.078 2.48e-02 1.63e+03 9.99e+00
  bond pdb=" N   ASP B 245 "
       pdb=" CA  ASP B 245 "
    ideal  model  delta    sigma   weight residual
    1.457  1.415  0.042 1.40e-02 5.10e+03 9.02e+00
  bond pdb=" N   ASP A 245 "
       pdb=" CA  ASP A 245 "
    ideal  model  delta    sigma   weight residual
    1.457  1.416  0.041 1.40e-02 5.10e+03 8.45e+00
  ... (remaining 8465 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 11360
        2.30 -     4.61: 122
        4.61 -     6.91: 7
        6.91 -     9.22: 3
        9.22 -    11.52: 2
  Bond angle restraints: 11494
  Sorted by residual:
  angle pdb=" N   MET B 246 "
        pdb=" CA  MET B 246 "
        pdb=" C   MET B 246 "
      ideal   model   delta    sigma   weight residual
     113.41  101.89   11.52 1.22e+00 6.72e-01 8.92e+01
  angle pdb=" N   MET A 246 "
        pdb=" CA  MET A 246 "
        pdb=" C   MET A 246 "
      ideal   model   delta    sigma   weight residual
     113.12  102.23   10.89 1.25e+00 6.40e-01 7.60e+01
  angle pdb=" CA  GLN B 275 "
        pdb=" CB  GLN B 275 "
        pdb=" CG  GLN B 275 "
      ideal   model   delta    sigma   weight residual
     114.10  121.16   -7.06 2.00e+00 2.50e-01 1.25e+01
  angle pdb=" CA  ASP B 244 "
        pdb=" C   ASP B 244 "
        pdb=" O   ASP B 244 "
      ideal   model   delta    sigma   weight residual
     121.78  117.29    4.49 1.28e+00 6.10e-01 1.23e+01
  angle pdb=" CA  ASP A 244 "
        pdb=" C   ASP A 244 "
        pdb=" O   ASP A 244 "
      ideal   model   delta    sigma   weight residual
     121.78  117.38    4.40 1.28e+00 6.10e-01 1.18e+01
  ... (remaining 11489 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 4711
       17.05 -    34.10: 344
       34.10 -    51.15: 62
       51.15 -    68.19: 16
       68.19 -    85.24: 7
  Dihedral angle restraints: 5140
    sinusoidal: 2096
      harmonic: 3044
  Sorted by residual:
  dihedral pdb=" CA  ASP B 452 "
           pdb=" CB  ASP B 452 "
           pdb=" CG  ASP B 452 "
           pdb=" OD1 ASP B 452 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.02   59.02     1      2.00e+01 2.50e-03 1.16e+01
  dihedral pdb=" CA  ASP A 447 "
           pdb=" CB  ASP A 447 "
           pdb=" CG  ASP A 447 "
           pdb=" OD1 ASP A 447 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.79   56.79     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CA  ASP B 447 "
           pdb=" CB  ASP B 447 "
           pdb=" CG  ASP B 447 "
           pdb=" OD1 ASP B 447 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.16   56.16     1      2.00e+01 2.50e-03 1.06e+01
  ... (remaining 5137 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1008
       0.053 -    0.107: 212
       0.107 -    0.160: 44
       0.160 -    0.213: 2
       0.213 -    0.266: 2
  Chirality restraints: 1268
  Sorted by residual:
  chirality pdb=" CA  MET B 246 "
            pdb=" N   MET B 246 "
            pdb=" C   MET B 246 "
            pdb=" CB  MET B 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CA  MET A 246 "
            pdb=" N   MET A 246 "
            pdb=" C   MET A 246 "
            pdb=" CB  MET A 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  ASP A 245 "
            pdb=" N   ASP A 245 "
            pdb=" C   ASP A 245 "
            pdb=" CB  ASP A 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.49e-01
  ... (remaining 1265 not shown)

  Planarity restraints: 1514
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 244 "   -0.013 2.00e-02 2.50e+03   2.62e-02 6.88e+00
        pdb=" C   ASP A 244 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ASP A 244 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASP A 245 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 244 "    0.013 2.00e-02 2.50e+03   2.58e-02 6.65e+00
        pdb=" C   ASP B 244 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ASP B 244 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ASP B 245 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B  94 "    0.035 5.00e-02 4.00e+02   5.32e-02 4.53e+00
        pdb=" N   PRO B  95 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B  95 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B  95 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1511 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 162
        2.67 -     3.23: 7752
        3.23 -     3.79: 13074
        3.79 -     4.34: 19126
        4.34 -     4.90: 31483
  Nonbonded interactions: 71597
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 317 "
            pdb=" NH2 ARG B 345 "
     model   vdw
     2.117 3.120
  nonbonded pdb=" O   ASP A 211 "
            pdb=" NH2 ARG A 349 "
     model   vdw
     2.134 3.120
  nonbonded pdb=" NZ  LYS B 506 "
            pdb=" O   SER B 521 "
     model   vdw
     2.178 3.120
  nonbonded pdb=" O   ASP B 211 "
            pdb=" NH2 ARG B 349 "
     model   vdw
     2.179 3.120
  nonbonded pdb=" O   PHE B 168 "
            pdb=" OG  SER B 172 "
     model   vdw
     2.198 3.040
  ... (remaining 71592 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: 0.01
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:             4.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.980
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
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      :  0.003   0.078   8470  Z= 0.173
  Angle     :  0.594  11.524  11494  Z= 0.339
  Chirality :  0.047   0.266   1268
  Planarity :  0.005   0.053   1514
  Dihedral  : 12.958  85.242   3172
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.77 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  0.11 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.27), residues: 1048
  helix:  1.12 (0.28), residues: 384
  sheet:  1.15 (0.50), residues: 96
  loop :  0.01 (0.27), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 345 
 TYR   0.006   0.001   TYR B  13 
 PHE   0.018   0.001   PHE B 507 
 TRP   0.026   0.001   TRP B  84 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8470)
  covalent geometry    : angle       0.59405 (11494)
  hydrogen bonds       : bond        0.17283 (  283)
  hydrogen bonds       : angle       6.93021 (  795)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 119
  time to evaluate  : 0.258 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 121
  average time/residue: 0.6323
  time to fit residues: 80.9031
Evaluate side-chains
  84 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  246 MET
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  246 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0570
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.7702

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

Flipped N/Q/H residues before XYZ refinement:
** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 HIS
A 492 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.133073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.114190 restraints weight = 9775.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.65
r_work: 0.3217 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.0966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8470  Z= 0.149
  Angle     :  0.547   5.825  11494  Z= 0.286
  Chirality :  0.047   0.145   1268
  Planarity :  0.005   0.053   1514
  Dihedral  :  5.685  52.213   1140
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.19 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  8.08 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.26), residues: 1048
  helix:  1.36 (0.27), residues: 366
  sheet:  0.65 (0.46), residues: 114
  loop :  0.09 (0.27), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 259 
 TYR   0.008   0.001   TYR B 377 
 PHE   0.011   0.001   PHE B 507 
 TRP   0.015   0.001   TRP B  84 
 HIS   0.004   0.001   HIS B 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8470)
  covalent geometry    : angle       0.54677 (11494)
  hydrogen bonds       : bond        0.04123 (  283)
  hydrogen bonds       : angle       5.47785 (  795)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: B  246 MET cc_start: 0.8042 (ttm) cc_final: 0.7682 (ttt)
REVERT: B  283 ASN cc_start: 0.6941 (m110) cc_final: 0.6727 (m110)
REVERT: A  115 ASP cc_start: 0.8401 (p0) cc_final: 0.8176 (p0)
REVERT: A  246 MET cc_start: 0.8076 (ttm) cc_final: 0.7751 (ttt)
  outliers start: 11
  outliers final: 5
  residues processed: 96
  average time/residue: 0.5063
  time to fit residues: 52.0747
Evaluate side-chains
  84 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  244 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0030
   chunk 90 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 50 optimal weight:    0.1980
   chunk 13 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.7592

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

Flipped N/Q/H residues before XYZ refinement:
** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 HIS
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.133123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.114035 restraints weight = 9687.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.66
r_work: 0.3196 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8470  Z= 0.140
  Angle     :  0.529   5.633  11494  Z= 0.275
  Chirality :  0.046   0.140   1268
  Planarity :  0.005   0.052   1514
  Dihedral  :  5.450  56.368   1134
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.29 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  9.51 %
    Favored  : 89.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.26), residues: 1048
  helix:  1.39 (0.27), residues: 366
  sheet:  0.62 (0.48), residues: 114
  loop :  0.05 (0.27), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 259 
 TYR   0.007   0.001   TYR B 127 
 PHE   0.010   0.001   PHE A 336 
 TRP   0.012   0.001   TRP B 339 
 HIS   0.004   0.001   HIS B 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8470)
  covalent geometry    : angle       0.52889 (11494)
  hydrogen bonds       : bond        0.03654 (  283)
  hydrogen bonds       : angle       5.21867 (  795)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: B  283 ASN cc_start: 0.6941 (m110) cc_final: 0.6722 (m110)
REVERT: B  304 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7980 (mp)
REVERT: B  329 GLU cc_start: 0.7404 (pm20) cc_final: 0.6871 (tp30)
REVERT: B  523 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6755 (mt-10)
REVERT: A  172 SER cc_start: 0.9181 (OUTLIER) cc_final: 0.8960 (m)
REVERT: A  304 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8039 (mp)
  outliers start: 12
  outliers final: 6
  residues processed: 94
  average time/residue: 0.4652
  time to fit residues: 47.3081
Evaluate side-chains
  90 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain A residue    3 ILE
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  304 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0970
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 HIS
A 117 HIS
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.133205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.114029 restraints weight = 9919.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 1.68
r_work: 0.3210 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8470  Z= 0.130
  Angle     :  0.512   5.582  11494  Z= 0.266
  Chirality :  0.045   0.139   1268
  Planarity :  0.005   0.051   1514
  Dihedral  :  5.462  59.155   1134
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.19 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 10.07 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.26), residues: 1048
  helix:  1.47 (0.27), residues: 366
  sheet:  0.56 (0.48), residues: 114
  loop :  0.05 (0.27), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 259 
 TYR   0.008   0.001   TYR B 377 
 PHE   0.010   0.001   PHE A 336 
 TRP   0.012   0.001   TRP B 339 
 HIS   0.004   0.001   HIS B 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8470)
  covalent geometry    : angle       0.51196 (11494)
  hydrogen bonds       : bond        0.03328 (  283)
  hydrogen bonds       : angle       5.08348 (  795)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: B  115 ASP cc_start: 0.8499 (p0) cc_final: 0.8259 (p0)
REVERT: B  304 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.7999 (mp)
REVERT: B  327 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6934 (pp)
REVERT: B  329 GLU cc_start: 0.7478 (pm20) cc_final: 0.6999 (tp30)
REVERT: A   18 LYS cc_start: 0.8773 (mttt) cc_final: 0.8438 (mmtt)
REVERT: A  172 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8954 (m)
REVERT: A  304 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8028 (mp)
  outliers start: 21
  outliers final: 8
  residues processed: 101
  average time/residue: 0.4824
  time to fit residues: 52.4777
Evaluate side-chains
  90 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain A residue    3 ILE
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  304 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0570
   chunk 37 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0170
   chunk 23 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.8140

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

Flipped N/Q/H residues before XYZ refinement:
B 344 HIS
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.132429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.113231 restraints weight = 9766.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.68
r_work: 0.3202 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8470  Z= 0.142
  Angle     :  0.523   5.697  11494  Z= 0.271
  Chirality :  0.046   0.145   1268
  Planarity :  0.005   0.051   1514
  Dihedral  :  5.379  55.246   1134
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.10 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 11.62 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.26), residues: 1048
  helix:  1.49 (0.27), residues: 366
  sheet:  0.47 (0.49), residues: 114
  loop :  0.02 (0.27), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 259 
 TYR   0.007   0.001   TYR B 377 
 PHE   0.010   0.001   PHE A 336 
 TRP   0.013   0.001   TRP B 339 
 HIS   0.004   0.001   HIS B 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8470)
  covalent geometry    : angle       0.52342 (11494)
  hydrogen bonds       : bond        0.03361 (  283)
  hydrogen bonds       : angle       5.08859 (  795)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4943 (tpt) cc_final: 0.3638 (ptt)
REVERT: B  304 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.7923 (mp)
REVERT: B  327 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.6991 (pp)
REVERT: B  329 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7061 (tp30)
REVERT: A   18 LYS cc_start: 0.8748 (mttt) cc_final: 0.8436 (mmtt)
REVERT: A  156 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8565 (mt)
REVERT: A  172 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8972 (m)
REVERT: A  304 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8027 (mp)
REVERT: A  327 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.7021 (pp)
  outliers start: 16
  outliers final: 8
  residues processed: 96
  average time/residue: 0.4630
  time to fit residues: 48.0001
Evaluate side-chains
  100 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain A residue    3 ILE
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  327 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 68 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
B 344 HIS
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.131978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.112851 restraints weight = 9631.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.66
r_work: 0.3194 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8470  Z= 0.154
  Angle     :  0.532   5.550  11494  Z= 0.275
  Chirality :  0.046   0.139   1268
  Planarity :  0.005   0.051   1514
  Dihedral  :  5.318  49.991   1134
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.19 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.39 %
    Favored  : 85.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.26), residues: 1048
  helix:  1.48 (0.27), residues: 366
  sheet:  0.44 (0.49), residues: 114
  loop : -0.03 (0.27), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 259 
 TYR   0.007   0.001   TYR B 142 
 PHE   0.011   0.001   PHE A 336 
 TRP   0.014   0.001   TRP B 339 
 HIS   0.004   0.001   HIS B 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 8470)
  covalent geometry    : angle       0.53223 (11494)
  hydrogen bonds       : bond        0.03423 (  283)
  hydrogen bonds       : angle       5.09984 (  795)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5151 (tpt) cc_final: 0.3982 (ptt)
REVERT: B  304 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8091 (mp)
REVERT: B  327 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7027 (pp)
REVERT: B  329 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7080 (tp30)
REVERT: A   18 LYS cc_start: 0.8755 (mttt) cc_final: 0.8444 (mmtt)
REVERT: A  115 ASP cc_start: 0.8611 (p0) cc_final: 0.8341 (p0)
REVERT: A  156 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8561 (mt)
REVERT: A  172 SER cc_start: 0.9195 (OUTLIER) cc_final: 0.8960 (m)
REVERT: A  304 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8032 (mp)
  outliers start: 19
  outliers final: 8
  residues processed: 95
  average time/residue: 0.5071
  time to fit residues: 51.8295
Evaluate side-chains
  96 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  304 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   chunk 71 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 344 HIS
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.132105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.113113 restraints weight = 9856.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.67
r_work: 0.3185 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8470  Z= 0.136
  Angle     :  0.523   5.571  11494  Z= 0.269
  Chirality :  0.046   0.140   1268
  Planarity :  0.005   0.050   1514
  Dihedral  :  5.166  51.608   1134
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.10 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.61 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.26), residues: 1048
  helix:  1.57 (0.27), residues: 364
  sheet:  0.44 (0.49), residues: 114
  loop : -0.02 (0.27), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 259 
 TYR   0.006   0.001   TYR B 142 
 PHE   0.010   0.001   PHE A 336 
 TRP   0.015   0.001   TRP B 339 
 HIS   0.004   0.001   HIS B 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8470)
  covalent geometry    : angle       0.52310 (11494)
  hydrogen bonds       : bond        0.03287 (  283)
  hydrogen bonds       : angle       5.07018 (  795)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.224 
Fit side-chains
REVERT: B    1 MET cc_start: 0.5182 (tpt) cc_final: 0.4172 (ptt)
REVERT: B  143 THR cc_start: 0.8994 (t) cc_final: 0.8710 (m)
REVERT: B  304 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8476 (mm)
REVERT: B  305 GLN cc_start: 0.7117 (mt0) cc_final: 0.6206 (mt0)
REVERT: B  327 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7064 (pp)
REVERT: B  329 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7088 (tp30)
REVERT: A   18 LYS cc_start: 0.8743 (mttt) cc_final: 0.8443 (mmtt)
REVERT: A  172 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8966 (m)
REVERT: A  304 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8036 (mp)
  outliers start: 19
  outliers final: 10
  residues processed: 98
  average time/residue: 0.4621
  time to fit residues: 48.8583
Evaluate side-chains
  97 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  304 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0270
   chunk 23 optimal weight:    0.2980
   chunk 10 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0050
   chunk 31 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.3652

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

Flipped N/Q/H residues before XYZ refinement:
B 344 HIS
A  61 ASN
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.134418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.115639 restraints weight = 9698.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.65
r_work: 0.3226 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8470  Z= 0.100
  Angle     :  0.496   5.786  11494  Z= 0.255
  Chirality :  0.044   0.153   1268
  Planarity :  0.005   0.051   1514
  Dihedral  :  4.816  50.961   1134
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.10 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.05 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.27), residues: 1048
  helix:  1.61 (0.27), residues: 376
  sheet:  0.47 (0.50), residues: 114
  loop : -0.08 (0.27), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 259 
 TYR   0.006   0.001   TYR B 127 
 PHE   0.018   0.001   PHE B 312 
 TRP   0.018   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 8470)
  covalent geometry    : angle       0.49617 (11494)
  hydrogen bonds       : bond        0.02928 (  283)
  hydrogen bonds       : angle       4.96044 (  795)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.261 
Fit side-chains
REVERT: B    1 MET cc_start: 0.5031 (tpt) cc_final: 0.4270 (ptt)
REVERT: B  304 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.7954 (mp)
REVERT: B  305 GLN cc_start: 0.6978 (mt0) cc_final: 0.5945 (mt0)
REVERT: B  327 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.6962 (pp)
REVERT: B  329 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7090 (tp30)
REVERT: A   18 LYS cc_start: 0.8716 (mttt) cc_final: 0.8421 (mmtt)
REVERT: A  115 ASP cc_start: 0.8560 (p0) cc_final: 0.8256 (p0)
REVERT: A  304 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8040 (mp)
REVERT: A  330 LYS cc_start: 0.7813 (tptt) cc_final: 0.7514 (mtmt)
  outliers start: 15
  outliers final: 5
  residues processed: 100
  average time/residue: 0.4148
  time to fit residues: 45.0504
Evaluate side-chains
  91 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  304 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0670
   chunk 42 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
B 344 HIS
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.131046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.112394 restraints weight = 9944.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.63
r_work: 0.3212 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8470  Z= 0.126
  Angle     :  0.518   6.091  11494  Z= 0.267
  Chirality :  0.045   0.146   1268
  Planarity :  0.005   0.052   1514
  Dihedral  :  4.858  54.103   1134
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.10 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 15.04 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.27), residues: 1048
  helix:  1.64 (0.27), residues: 376
  sheet:  0.48 (0.50), residues: 114
  loop : -0.11 (0.27), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 259 
 TYR   0.008   0.001   TYR B 142 
 PHE   0.015   0.001   PHE B 312 
 TRP   0.021   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8470)
  covalent geometry    : angle       0.51846 (11494)
  hydrogen bonds       : bond        0.03180 (  283)
  hydrogen bonds       : angle       4.99272 (  795)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.330 
Fit side-chains
REVERT: B    1 MET cc_start: 0.4984 (tpt) cc_final: 0.4221 (ptt)
REVERT: B  246 MET cc_start: 0.8072 (ttp) cc_final: 0.7784 (mtm)
REVERT: B  304 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8101 (mp)
REVERT: B  305 GLN cc_start: 0.7047 (mt0) cc_final: 0.5999 (mt0)
REVERT: B  327 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7010 (pp)
REVERT: B  329 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7089 (tp30)
REVERT: A   18 LYS cc_start: 0.8709 (mttt) cc_final: 0.8409 (mmtt)
REVERT: A  304 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8015 (mp)
REVERT: A  330 LYS cc_start: 0.7817 (tptt) cc_final: 0.7549 (mtmt)
  outliers start: 15
  outliers final: 6
  residues processed: 94
  average time/residue: 0.4691
  time to fit residues: 47.5767
Evaluate side-chains
  94 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  304 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   chunk 85 optimal weight:    3.9990
   chunk 72 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 344 HIS
B 356 ASN
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.131885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.113058 restraints weight = 9776.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.66
r_work: 0.3186 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8470  Z= 0.155
  Angle     :  0.539   6.685  11494  Z= 0.278
  Chirality :  0.046   0.146   1268
  Planarity :  0.005   0.051   1514
  Dihedral  :  4.946  55.736   1132
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.48 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 15.27 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.27), residues: 1048
  helix:  1.54 (0.27), residues: 376
  sheet:  0.41 (0.50), residues: 114
  loop : -0.17 (0.27), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 259 
 TYR   0.008   0.001   TYR B 142 
 PHE   0.016   0.001   PHE B 312 
 TRP   0.024   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8470)
  covalent geometry    : angle       0.53935 (11494)
  hydrogen bonds       : bond        0.03445 (  283)
  hydrogen bonds       : angle       5.09536 (  795)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.335 
Fit side-chains
REVERT: B  246 MET cc_start: 0.8121 (ttp) cc_final: 0.7840 (mtm)
REVERT: B  304 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8078 (mp)
REVERT: B  305 GLN cc_start: 0.7110 (mt0) cc_final: 0.6056 (mt0)
REVERT: B  327 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7176 (pp)
REVERT: B  329 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7049 (tp30)
REVERT: A   18 LYS cc_start: 0.8713 (mttt) cc_final: 0.8407 (mmtt)
REVERT: A  156 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8543 (mt)
REVERT: A  304 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8129 (mp)
REVERT: A  330 LYS cc_start: 0.7805 (tptt) cc_final: 0.7452 (mtpt)
  outliers start: 15
  outliers final: 4
  residues processed: 95
  average time/residue: 0.4844
  time to fit residues: 49.5873
Evaluate side-chains
  93 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  304 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    0.0770
   chunk 17 optimal weight:    0.5980
   chunk 2 optimal weight:    0.3980
   chunk 5 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    0.2980
   chunk 63 optimal weight:    0.5980
   chunk 19 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
B 344 HIS
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.134420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.115885 restraints weight = 9743.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.64
r_work: 0.3229 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8470  Z= 0.105
  Angle     :  0.505   6.694  11494  Z= 0.260
  Chirality :  0.045   0.147   1268
  Planarity :  0.005   0.051   1514
  Dihedral  :  4.737  55.552   1130
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.19 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 15.60 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.27), residues: 1048
  helix:  1.59 (0.27), residues: 388
  sheet:  0.50 (0.51), residues: 114
  loop : -0.15 (0.28), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 259 
 TYR   0.005   0.001   TYR B 142 
 PHE   0.016   0.001   PHE B 312 
 TRP   0.022   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8470)
  covalent geometry    : angle       0.50541 (11494)
  hydrogen bonds       : bond        0.02978 (  283)
  hydrogen bonds       : angle       4.99218 (  795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2344.96 seconds
wall clock time: 40 minutes 43.72 seconds (2443.72 seconds total)