Starting phenix.real_space_refine
on Wed Mar  4 00:10:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b70_15894/03_2026/8b70_15894.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b70_15894/03_2026/8b70_15894.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b70_15894/03_2026/8b70_15894.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b70_15894/03_2026/8b70_15894.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b70_15894/03_2026/8b70_15894.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b70_15894/03_2026/8b70_15894.map"
  }
  resolution = 3.3
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     K       2      8.98       5
     P       4      5.49       5
     S      34      5.16       5
     C    6138      2.51       5
     N    1456      2.21       5
     O    1624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 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: 9258
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 4444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4444
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 24, 'TRANS': 547}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 4444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4444
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 24, 'TRANS': 547}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 150
          Unusual residues: {'  K': 1, '2BA': 1, 'LMT': 3}
          Classifications: {'RNA_mixed': 1, 'undetermined': 4}
          Link IDs: {None: 4}
    Chain: "A"
      Number of atoms: 220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 220
          Unusual residues: {'  K': 1, '2BA': 1, 'LMT': 5}
          Classifications: {'RNA_mixed': 1, 'undetermined': 6}
          Link IDs: {None: 6}
  Time building chain proxies: 2.38, per 1000 atoms: 0.26
  Number of scatterers: 9258
  At special positions: 0
  Unit cell: (112.158, 86.211, 103.788, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     K       2     19.00
     S      34     16.00
     P       4     15.00
     O    1624      8.00
     N    1456      7.00
     C    6138      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 516.1 milliseconds
  

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2132

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 1 sheets defined
      76.9% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'B' and resid 25 through 34
    Processing helix  chain 'B' and resid 39 through 42
      removed outlier: 3.795A  pdb=" N   ALA B  42 " --> pdb=" O   SER B  39 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 39 through 42'
    Processing helix  chain 'B' and resid 43 through 54
      removed outlier: 3.703A  pdb=" N   GLN B  47 " --> pdb=" O   TYR B  43 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   THR B  54 " --> pdb=" O   ILE B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 61
      removed outlier: 6.846A  pdb=" N   ALA B  58 " --> pdb=" O   ILE B  55 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   TRP B  61 " --> pdb=" O   ALA B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 88
      removed outlier: 3.856A  pdb=" N   TYR B  86 " --> pdb=" O   ARG B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 103
    Processing helix  chain 'B' and resid 104 through 137
    Processing helix  chain 'B' and resid 138 through 142
      removed outlier: 4.779A  pdb=" N   ASP B 142 " --> pdb=" O   ALA B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 161
    Processing helix  chain 'B' and resid 171 through 195
      removed outlier: 3.911A  pdb=" N   TYR B 175 " --> pdb=" O   ALA B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 226
    Processing helix  chain 'B' and resid 227 through 229
      No H-bonds generated for 'chain 'B' and resid 227 through 229'
    Processing helix  chain 'B' and resid 232 through 237
      removed outlier: 4.709A  pdb=" N   SER B 236 " --> pdb=" O   VAL B 232 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ASN B 237 " --> pdb=" O   GLU B 233 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 232 through 237'
    Processing helix  chain 'B' and resid 245 through 276
    Processing helix  chain 'B' and resid 284 through 295
    Processing helix  chain 'B' and resid 297 through 331
      Proline residue:  B 323  - end of helix
    Processing helix  chain 'B' and resid 336 through 340
    Processing helix  chain 'B' and resid 347 through 367
    Processing helix  chain 'B' and resid 369 through 400
      Proline residue:  B 375  - end of helix
      Proline residue:  B 384  - end of helix
    Processing helix  chain 'B' and resid 403 through 429
      removed outlier: 3.694A  pdb=" N   LYS B 407 " --> pdb=" O   GLY B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 462
      Proline residue:  B 435  - end of helix
      removed outlier: 3.584A  pdb=" N   ILE B 438 " --> pdb=" O   TRP B 434 " (cutoff:3.500A)
      Proline residue:  B 441  - end of helix
      removed outlier: 3.576A  pdb=" N   ARG B 462 " --> pdb=" O   GLY B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 498
    Processing helix  chain 'B' and resid 509 through 523
      removed outlier: 3.727A  pdb=" N   GLU B 513 " --> pdb=" O   ASP B 509 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   LYS B 514 " --> pdb=" O   ARG B 510 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   LYS B 515 " --> pdb=" O   GLU B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 557
      removed outlier: 4.026A  pdb=" N   PHE B 543 " --> pdb=" O   LEU B 539 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLU B 557 " --> pdb=" O   LYS B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 579
      removed outlier: 4.211A  pdb=" N   ILE B 577 " --> pdb=" O   TRP B 574 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   HIS B 579 " --> pdb=" O   THR B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 590
      removed outlier: 3.896A  pdb=" N   PHE B 584 " --> pdb=" O   ASN B 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 34
    Processing helix  chain 'A' and resid 39 through 42
      removed outlier: 3.794A  pdb=" N   ALA A  42 " --> pdb=" O   SER A  39 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 39 through 42'
    Processing helix  chain 'A' and resid 43 through 54
      removed outlier: 3.704A  pdb=" N   GLN A  47 " --> pdb=" O   TYR A  43 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   THR A  54 " --> pdb=" O   ILE A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 61
      removed outlier: 6.845A  pdb=" N   ALA A  58 " --> pdb=" O   ILE A  55 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   TRP A  61 " --> pdb=" O   ALA A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 88
      removed outlier: 3.856A  pdb=" N   TYR A  86 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 103
    Processing helix  chain 'A' and resid 104 through 137
    Processing helix  chain 'A' and resid 138 through 142
      removed outlier: 4.779A  pdb=" N   ASP A 142 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
    Processing helix  chain 'A' and resid 171 through 195
      removed outlier: 3.911A  pdb=" N   TYR A 175 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 226
    Processing helix  chain 'A' and resid 227 through 229
      No H-bonds generated for 'chain 'A' and resid 227 through 229'
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 4.708A  pdb=" N   SER A 236 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASN A 237 " --> pdb=" O   GLU A 233 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 232 through 237'
    Processing helix  chain 'A' and resid 245 through 276
    Processing helix  chain 'A' and resid 284 through 295
    Processing helix  chain 'A' and resid 297 through 331
      Proline residue:  A 323  - end of helix
    Processing helix  chain 'A' and resid 336 through 340
    Processing helix  chain 'A' and resid 347 through 367
    Processing helix  chain 'A' and resid 369 through 400
      Proline residue:  A 375  - end of helix
      Proline residue:  A 384  - end of helix
    Processing helix  chain 'A' and resid 403 through 429
      removed outlier: 3.694A  pdb=" N   LYS A 407 " --> pdb=" O   GLY A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 462
      Proline residue:  A 435  - end of helix
      removed outlier: 3.584A  pdb=" N   ILE A 438 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
      Proline residue:  A 441  - end of helix
      removed outlier: 3.576A  pdb=" N   ARG A 462 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 498
    Processing helix  chain 'A' and resid 509 through 523
      removed outlier: 3.727A  pdb=" N   GLU A 513 " --> pdb=" O   ASP A 509 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   LYS A 514 " --> pdb=" O   ARG A 510 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   LYS A 515 " --> pdb=" O   GLU A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 557
      removed outlier: 4.026A  pdb=" N   PHE A 543 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLU A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 579
      removed outlier: 4.211A  pdb=" N   ILE A 577 " --> pdb=" O   TRP A 574 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   HIS A 579 " --> pdb=" O   THR A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 590
      removed outlier: 3.896A  pdb=" N   PHE A 584 " --> pdb=" O   ASN A 580 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 528 through 533
      removed outlier: 6.614A  pdb=" N   ALA B 503 " --> pdb=" O   VAL B 530 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   LEU B 532 " --> pdb=" O   ALA B 503 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   HIS B 505 " --> pdb=" O   LEU B 532 " (cutoff:3.500A)
      removed outlier: 8.176A  pdb=" N   ILE B 502 " --> pdb=" O   THR B 474 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   VAL B 476 " --> pdb=" O   ILE B 502 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   VAL B 504 " --> pdb=" O   VAL B 476 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   VAL B 478 " --> pdb=" O   VAL B 504 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   VAL B 506 " --> pdb=" O   VAL B 478 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   MET B 597 " --> pdb=" O   VAL B 561 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL B 598 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL A 598 " --> pdb=" O   THR B 600 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   MET A 597 " --> pdb=" O   VAL A 561 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   ILE A 502 " --> pdb=" O   THR A 474 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL A 476 " --> pdb=" O   ILE A 502 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   VAL A 504 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   VAL A 478 " --> pdb=" O   VAL A 504 " (cutoff:3.500A)
      removed outlier: 8.116A  pdb=" N   VAL A 506 " --> pdb=" O   VAL A 478 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ALA A 503 " --> pdb=" O   VAL A 530 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   LEU A 532 " --> pdb=" O   ALA A 503 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   HIS A 505 " --> pdb=" O   LEU A 532 " (cutoff:3.500A)

    636 hydrogen bonds defined for protein.
    1872 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: 1.44

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2685
        1.34 -     1.46: 2066
        1.46 -     1.57: 4655
        1.57 -     1.69: 14
        1.69 -     1.81: 62
  Bond restraints: 9482
  Sorted by residual:
  bond pdb="C3'1 2BA B 901 "
       pdb="O3'1 2BA B 901 "
    ideal  model  delta    sigma   weight residual
    1.418  1.343  0.075 2.00e-02 2.50e+03 1.40e+01
  bond pdb="C3'1 2BA A1001 "
       pdb="O3'1 2BA A1001 "
    ideal  model  delta    sigma   weight residual
    1.418  1.344  0.074 2.00e-02 2.50e+03 1.38e+01
  bond pdb=" C5' 2BA A1001 "
       pdb=" O5' 2BA A1001 "
    ideal  model  delta    sigma   weight residual
    1.433  1.362  0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" C5' 2BA B 901 "
       pdb=" O5' 2BA B 901 "
    ideal  model  delta    sigma   weight residual
    1.433  1.362  0.071 2.00e-02 2.50e+03 1.25e+01
  bond pdb=" C3' 2BA A1001 "
       pdb=" O3' 2BA A1001 "
    ideal  model  delta    sigma   weight residual
    1.410  1.343  0.067 2.00e-02 2.50e+03 1.11e+01
  ... (remaining 9477 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 12366
        2.00 -     4.00: 310
        4.00 -     6.00: 134
        6.00 -     8.00: 65
        8.00 -    10.00: 15
  Bond angle restraints: 12890
  Sorted by residual:
  angle pdb=" C   LEU B 373 "
        pdb=" N   ILE B 374 "
        pdb=" CA  ILE B 374 "
      ideal   model   delta    sigma   weight residual
     120.24  123.22   -2.98 6.30e-01 2.52e+00 2.24e+01
  angle pdb=" C   LEU A 373 "
        pdb=" N   ILE A 374 "
        pdb=" CA  ILE A 374 "
      ideal   model   delta    sigma   weight residual
     120.24  123.20   -2.96 6.30e-01 2.52e+00 2.20e+01
  angle pdb=" N   ILE A 438 "
        pdb=" CA  ILE A 438 "
        pdb=" C   ILE A 438 "
      ideal   model   delta    sigma   weight residual
     111.81  108.52    3.29 8.60e-01 1.35e+00 1.46e+01
  angle pdb=" N   ILE B 438 "
        pdb=" CA  ILE B 438 "
        pdb=" C   ILE B 438 "
      ideal   model   delta    sigma   weight residual
     111.81  108.55    3.26 8.60e-01 1.35e+00 1.44e+01
  angle pdb=" C   PHE B 382 "
        pdb=" N   ILE B 383 "
        pdb=" CA  ILE B 383 "
      ideal   model   delta    sigma   weight residual
     120.33  117.64    2.69 8.00e-01 1.56e+00 1.13e+01
  ... (remaining 12885 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.25: 5478
       26.25 -    52.50: 351
       52.50 -    78.75: 93
       78.75 -   105.00: 16
      105.00 -   131.25: 30
  Dihedral angle restraints: 5968
    sinusoidal: 2658
      harmonic: 3310
  Sorted by residual:
  dihedral pdb=" C1B LMT B 904 "
           pdb=" C5B LMT B 904 "
           pdb=" O5B LMT B 904 "
           pdb=" C6B LMT B 904 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.31  -53.44 -131.25     1      3.00e+01 1.11e-03 1.77e+01
  dihedral pdb=" C1B LMT A1004 "
           pdb=" C5B LMT A1004 "
           pdb=" O5B LMT A1004 "
           pdb=" C6B LMT A1004 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.31  -53.48 -131.21     1      3.00e+01 1.11e-03 1.77e+01
  dihedral pdb=" C1B LMT B 904 "
           pdb=" C5B LMT B 904 "
           pdb=" O5B LMT B 904 "
           pdb=" C4B LMT B 904 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -59.84   67.26 -127.10     1      3.00e+01 1.11e-03 1.71e+01
  ... (remaining 5965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1324
       0.071 -    0.142: 197
       0.142 -    0.213: 35
       0.213 -    0.284: 24
       0.284 -    0.355: 6
  Chirality restraints: 1586
  Sorted by residual:
  chirality pdb=" C3' LMT A1004 "
            pdb=" C2' LMT A1004 "
            pdb=" C4' LMT A1004 "
            pdb=" O3' LMT A1004 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.78   -0.36 2.00e-01 2.50e+01 3.16e+00
  chirality pdb=" C3' LMT B 904 "
            pdb=" C2' LMT B 904 "
            pdb=" C4' LMT B 904 "
            pdb=" O3' LMT B 904 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.78   -0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" C4' LMT A1005 "
            pdb=" C3' LMT A1005 "
            pdb=" C5' LMT A1005 "
            pdb=" O1B LMT A1005 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.86    0.31 2.00e-01 2.50e+01 2.37e+00
  ... (remaining 1583 not shown)

  Planarity restraints: 1504
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 244 "   -0.035 5.00e-02 4.00e+02   5.19e-02 4.31e+00
        pdb=" N   PRO A 245 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 245 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 245 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 244 "    0.034 5.00e-02 4.00e+02   5.17e-02 4.28e+00
        pdb=" N   PRO B 245 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B 245 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 245 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 153 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.64e+00
        pdb=" C   LEU A 153 "    0.028 2.00e-02 2.50e+03
        pdb=" O   LEU A 153 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   VAL A 154 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1501 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.75: 1369
        2.75 -     3.34: 11121
        3.34 -     3.94: 17894
        3.94 -     4.54: 25745
        4.54 -     5.14: 37268
  Nonbonded interactions: 93397
  Sorted by model distance:
  nonbonded pdb=" O3' LMT A1002 "
            pdb=" O6' LMT A1005 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" OH  TYR A  81 "
            pdb=" OE1 GLU A 233 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OH  TYR B  81 "
            pdb=" OE1 GLU B 233 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O3' LMT A1004 "
            pdb=" O5B LMT A1004 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O3' LMT B 904 "
            pdb=" O5B LMT B 904 "
     model   vdw
     2.321 3.040
  ... (remaining 93392 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 22 through 1004)
  selection = (chain 'B' and resid 22 through 904)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.990
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6219
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      :  0.007   0.161   9484  Z= 0.407
  Angle     :  1.018  10.004  12890  Z= 0.446
  Chirality :  0.063   0.355   1586
  Planarity :  0.005   0.052   1504
  Dihedral  : 20.776 131.249   3836
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  0.00 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.27), residues: 1132
  helix:  1.91 (0.19), residues: 796
  sheet: -1.86 (0.47), residues: 90
  loop : -0.70 (0.47), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 331 
 TYR   0.024   0.001   TYR B 493 
 PHE   0.008   0.001   PHE A 382 
 TRP   0.008   0.001   TRP A 592 
 HIS   0.002   0.001   HIS B 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00706 ( 9482)
  covalent geometry    : angle       1.01823 (12890)
  hydrogen bonds       : bond        0.11881 (  636)
  hydrogen bonds       : angle       6.19447 ( 1872)
  Misc. bond           : bond        0.16012 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 0.293 
Fit side-chains
REVERT: B   32 MET cc_start: 0.6824 (mtp) cc_final: 0.6581 (mtp)
REVERT: B  252 ARG cc_start: 0.5420 (mtt180) cc_final: 0.5097 (mpt-90)
REVERT: B  437 LEU cc_start: 0.6776 (mm) cc_final: 0.6523 (mp)
REVERT: B  472 LYS cc_start: 0.7690 (mtmt) cc_final: 0.7391 (mttm)
REVERT: B  514 LYS cc_start: 0.7550 (mmmt) cc_final: 0.7203 (mmtp)
REVERT: B  518 LYS cc_start: 0.6371 (ttpt) cc_final: 0.6056 (tptm)
REVERT: A   32 MET cc_start: 0.6736 (mtp) cc_final: 0.6453 (mtp)
REVERT: A  243 LYS cc_start: 0.6273 (mmtp) cc_final: 0.5983 (mmmm)
REVERT: A  338 MET cc_start: 0.8337 (ptm) cc_final: 0.8004 (ptm)
REVERT: A  440 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5909 (mmm)
REVERT: A  472 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7372 (mttm)
  outliers start: 8
  outliers final: 1
  residues processed: 135
  average time/residue: 0.1102
  time to fit residues: 20.2824
Evaluate side-chains
  92 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  440 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0020
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    1.7996

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

Flipped N/Q/H residues before XYZ refinement:
B 196 GLN
B 411 ASN
B 580 ASN
A 196 GLN
A 389 GLN
A 580 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.120616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.103058 restraints weight = 10397.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 0.97
r_work: 0.2886 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9484  Z= 0.192
  Angle     :  0.764  11.639  12890  Z= 0.340
  Chirality :  0.048   0.254   1586
  Planarity :  0.005   0.049   1504
  Dihedral  : 14.861  83.571   1829
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  7.93 %
    Favored  : 90.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.26), residues: 1132
  helix:  2.22 (0.18), residues: 792
  sheet: -1.62 (0.50), residues: 90
  loop : -0.42 (0.45), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 510 
 TYR   0.023   0.002   TYR A  81 
 PHE   0.011   0.002   PHE B 516 
 TRP   0.012   0.002   TRP B 574 
 HIS   0.003   0.001   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 9482)
  covalent geometry    : angle       0.76374 (12890)
  hydrogen bonds       : bond        0.04631 (  636)
  hydrogen bonds       : angle       4.40574 ( 1872)
  Misc. bond           : bond        0.00061 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.328 
Fit side-chains
REVERT: B  141 HIS cc_start: 0.7153 (m-70) cc_final: 0.6762 (m-70)
REVERT: B  437 LEU cc_start: 0.7953 (mm) cc_final: 0.7697 (mp)
REVERT: B  514 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8127 (mmtp)
REVERT: B  518 LYS cc_start: 0.7653 (ttpt) cc_final: 0.7235 (tptm)
REVERT: B  536 TYR cc_start: 0.8023 (m-80) cc_final: 0.7691 (m-80)
REVERT: B  553 LYS cc_start: 0.7854 (ttmt) cc_final: 0.6759 (tttt)
REVERT: A  437 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8188 (mm)
  outliers start: 16
  outliers final: 7
  residues processed: 110
  average time/residue: 0.1044
  time to fit residues: 16.0800
Evaluate side-chains
  92 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  370 THR
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  484 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 95 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 4 optimal weight:    0.2980
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
B 196 GLN
B 580 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.122885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.099272 restraints weight = 10336.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 1.37
r_work: 0.2847 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2698 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9484  Z= 0.137
  Angle     :  0.599   8.937  12890  Z= 0.278
  Chirality :  0.043   0.318   1586
  Planarity :  0.004   0.041   1504
  Dihedral  : 11.254  59.808   1824
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.17 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.30 (0.26), residues: 1132
  helix:  2.46 (0.18), residues: 788
  sheet: -1.44 (0.49), residues: 90
  loop : -0.34 (0.46), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 510 
 TYR   0.016   0.001   TYR B  81 
 PHE   0.012   0.001   PHE B 322 
 TRP   0.013   0.001   TRP B 574 
 HIS   0.003   0.001   HIS B 579 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9482)
  covalent geometry    : angle       0.59859 (12890)
  hydrogen bonds       : bond        0.04206 (  636)
  hydrogen bonds       : angle       4.15664 ( 1872)
  Misc. bond           : bond        0.00089 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.370 
Fit side-chains
REVERT: B   32 MET cc_start: 0.7956 (mtp) cc_final: 0.7696 (mtp)
REVERT: B  215 LEU cc_start: 0.7701 (tp) cc_final: 0.7411 (tp)
REVERT: B  437 LEU cc_start: 0.8137 (mm) cc_final: 0.7828 (mp)
REVERT: B  514 LYS cc_start: 0.8403 (mmmt) cc_final: 0.7910 (mmtp)
REVERT: B  518 LYS cc_start: 0.7373 (ttpt) cc_final: 0.6918 (tptm)
REVERT: B  536 TYR cc_start: 0.7967 (m-80) cc_final: 0.7589 (m-80)
REVERT: A  392 MET cc_start: 0.8438 (tpt) cc_final: 0.8177 (mmm)
REVERT: A  437 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8058 (mm)
  outliers start: 14
  outliers final: 7
  residues processed: 100
  average time/residue: 0.0976
  time to fit residues: 14.0311
Evaluate side-chains
  94 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  437 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 43 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 24 optimal weight:    0.1980
   chunk 16 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
B 389 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.123773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.100185 restraints weight = 10335.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 1.36
r_work: 0.2860 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9484  Z= 0.122
  Angle     :  0.564   8.137  12890  Z= 0.264
  Chirality :  0.041   0.208   1586
  Planarity :  0.004   0.044   1504
  Dihedral  : 10.543  57.725   1824
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.11 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.37 (0.26), residues: 1132
  helix:  2.44 (0.18), residues: 796
  sheet: -1.23 (0.49), residues: 90
  loop : -0.23 (0.47), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 510 
 TYR   0.015   0.001   TYR A  81 
 PHE   0.009   0.001   PHE B 322 
 TRP   0.015   0.001   TRP B 574 
 HIS   0.002   0.000   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9482)
  covalent geometry    : angle       0.56443 (12890)
  hydrogen bonds       : bond        0.03890 (  636)
  hydrogen bonds       : angle       4.00986 ( 1872)
  Misc. bond           : bond        0.00089 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.363 
Fit side-chains
REVERT: B  514 LYS cc_start: 0.8421 (mmmt) cc_final: 0.8141 (mmmt)
REVERT: B  518 LYS cc_start: 0.7349 (ttpt) cc_final: 0.6878 (tptm)
REVERT: B  536 TYR cc_start: 0.8011 (m-80) cc_final: 0.7583 (m-80)
REVERT: A   32 MET cc_start: 0.7910 (mtp) cc_final: 0.7626 (mtp)
REVERT: A  392 MET cc_start: 0.8383 (tpt) cc_final: 0.8107 (mmm)
REVERT: A  437 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8153 (mm)
REVERT: A  459 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7306 (mt-10)
REVERT: A  514 LYS cc_start: 0.8370 (mmmt) cc_final: 0.8109 (mmmt)
  outliers start: 14
  outliers final: 11
  residues processed: 99
  average time/residue: 0.0953
  time to fit residues: 13.5952
Evaluate side-chains
  98 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  484 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 100 optimal weight:    0.0980
   chunk 1 optimal weight:    7.9990
   chunk 54 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 102 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
B 389 GLN
B 460 GLN
A 324 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.124335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.100733 restraints weight = 10246.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.36
r_work: 0.2871 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2724 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9484  Z= 0.117
  Angle     :  0.555   7.717  12890  Z= 0.258
  Chirality :  0.041   0.203   1586
  Planarity :  0.004   0.047   1504
  Dihedral  : 10.419  59.813   1824
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.84 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.26), residues: 1132
  helix:  2.50 (0.18), residues: 792
  sheet: -1.05 (0.50), residues: 90
  loop : -0.37 (0.46), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 510 
 TYR   0.014   0.001   TYR A  81 
 PHE   0.008   0.001   PHE B 366 
 TRP   0.015   0.001   TRP B 574 
 HIS   0.002   0.000   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9482)
  covalent geometry    : angle       0.55494 (12890)
  hydrogen bonds       : bond        0.03790 (  636)
  hydrogen bonds       : angle       3.94081 ( 1872)
  Misc. bond           : bond        0.00092 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.275 
Fit side-chains
REVERT: B  215 LEU cc_start: 0.7769 (tp) cc_final: 0.7475 (tp)
REVERT: B  355 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8055 (tp)
REVERT: B  514 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8147 (mmmt)
REVERT: B  518 LYS cc_start: 0.7310 (ttpt) cc_final: 0.6853 (tptm)
REVERT: B  536 TYR cc_start: 0.8036 (m-80) cc_final: 0.7613 (m-80)
REVERT: A   32 MET cc_start: 0.7961 (mtp) cc_final: 0.7710 (mtp)
REVERT: A  392 MET cc_start: 0.8412 (tpt) cc_final: 0.8132 (mmm)
REVERT: A  437 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8153 (mm)
REVERT: A  514 LYS cc_start: 0.8382 (mmmt) cc_final: 0.8107 (mmmt)
  outliers start: 20
  outliers final: 12
  residues processed: 101
  average time/residue: 0.0891
  time to fit residues: 13.0804
Evaluate side-chains
  98 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  484 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 112 optimal weight:    2.9990
   chunk 101 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 196 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.123081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.100703 restraints weight = 10344.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.27
r_work: 0.2875 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9484  Z= 0.125
  Angle     :  0.561   7.006  12890  Z= 0.263
  Chirality :  0.041   0.200   1586
  Planarity :  0.004   0.045   1504
  Dihedral  : 10.319  59.132   1824
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.05 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.40 (0.26), residues: 1132
  helix:  2.50 (0.18), residues: 792
  sheet: -0.78 (0.51), residues: 92
  loop : -0.50 (0.45), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 510 
 TYR   0.014   0.001   TYR A  81 
 PHE   0.007   0.001   PHE B 319 
 TRP   0.014   0.001   TRP B 574 
 HIS   0.001   0.000   HIS A 575 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9482)
  covalent geometry    : angle       0.56085 (12890)
  hydrogen bonds       : bond        0.03881 (  636)
  hydrogen bonds       : angle       3.95397 ( 1872)
  Misc. bond           : bond        0.00126 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.396 
Fit side-chains
REVERT: B   32 MET cc_start: 0.7840 (mtp) cc_final: 0.7577 (mtp)
REVERT: B  355 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7986 (tp)
REVERT: B  518 LYS cc_start: 0.7260 (ttpt) cc_final: 0.6801 (tptm)
REVERT: A  437 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8136 (mm)
REVERT: A  514 LYS cc_start: 0.8290 (mmmt) cc_final: 0.8003 (mmmt)
  outliers start: 20
  outliers final: 14
  residues processed: 98
  average time/residue: 0.0801
  time to fit residues: 11.6158
Evaluate side-chains
  99 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  550 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 57 optimal weight:   10.0000
   chunk 101 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 112 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 460 GLN
A 196 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.121260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.099027 restraints weight = 10340.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 1.26
r_work: 0.2852 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9484  Z= 0.147
  Angle     :  0.587   7.226  12890  Z= 0.274
  Chirality :  0.042   0.222   1586
  Planarity :  0.004   0.045   1504
  Dihedral  : 10.429  59.964   1824
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.26 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.26), residues: 1132
  helix:  2.30 (0.18), residues: 804
  sheet: -0.74 (0.51), residues: 92
  loop : -0.47 (0.46), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 510 
 TYR   0.015   0.001   TYR B  81 
 PHE   0.008   0.001   PHE B 382 
 TRP   0.012   0.001   TRP B 574 
 HIS   0.002   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9482)
  covalent geometry    : angle       0.58660 (12890)
  hydrogen bonds       : bond        0.04075 (  636)
  hydrogen bonds       : angle       4.01255 ( 1872)
  Misc. bond           : bond        0.00145 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.205 
Fit side-chains
REVERT: B  512 GLN cc_start: 0.7727 (mp10) cc_final: 0.7126 (mt0)
REVERT: B  518 LYS cc_start: 0.7234 (ttpt) cc_final: 0.6773 (tptm)
REVERT: B  553 LYS cc_start: 0.7611 (ttmt) cc_final: 0.6394 (ttpp)
REVERT: A   32 MET cc_start: 0.7905 (mtp) cc_final: 0.7603 (mtp)
REVERT: A  355 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7894 (tp)
REVERT: A  437 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8151 (mm)
REVERT: A  514 LYS cc_start: 0.8272 (mmmt) cc_final: 0.7989 (mmmt)
  outliers start: 25
  outliers final: 18
  residues processed: 106
  average time/residue: 0.0898
  time to fit residues: 13.7079
Evaluate side-chains
  107 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  243 LYS
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  550 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0470
   chunk 82 optimal weight:    0.0970
   chunk 83 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
A 196 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.124485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.102220 restraints weight = 10206.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 1.26
r_work: 0.2896 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2750 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9484  Z= 0.114
  Angle     :  0.555   7.069  12890  Z= 0.258
  Chirality :  0.040   0.205   1586
  Planarity :  0.004   0.048   1504
  Dihedral  : 10.166  59.515   1824
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.30 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.42 (0.26), residues: 1132
  helix:  2.44 (0.18), residues: 804
  sheet: -0.63 (0.52), residues: 92
  loop : -0.41 (0.47), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 510 
 TYR   0.013   0.001   TYR A  81 
 PHE   0.008   0.001   PHE B 366 
 TRP   0.014   0.001   TRP B 574 
 HIS   0.002   0.000   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9482)
  covalent geometry    : angle       0.55478 (12890)
  hydrogen bonds       : bond        0.03753 (  636)
  hydrogen bonds       : angle       3.90148 ( 1872)
  Misc. bond           : bond        0.00129 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.353 
Fit side-chains
REVERT: B  215 LEU cc_start: 0.7601 (tp) cc_final: 0.7221 (tt)
REVERT: B  355 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7906 (tp)
REVERT: B  512 GLN cc_start: 0.7731 (mp10) cc_final: 0.7148 (mt0)
REVERT: B  518 LYS cc_start: 0.7228 (ttpt) cc_final: 0.6759 (tptm)
REVERT: A   32 MET cc_start: 0.7914 (mtp) cc_final: 0.7598 (mtp)
REVERT: A  355 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7822 (tp)
REVERT: A  392 MET cc_start: 0.8307 (tpt) cc_final: 0.8056 (mmm)
REVERT: A  437 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8156 (mm)
  outliers start: 18
  outliers final: 15
  residues processed: 100
  average time/residue: 0.0945
  time to fit residues: 13.7792
Evaluate side-chains
  105 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  243 LYS
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  550 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 102 optimal weight:    0.8980
   chunk 51 optimal weight:    8.9990
   chunk 80 optimal weight:    0.9990
   chunk 104 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.123598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.101489 restraints weight = 10240.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 1.25
r_work: 0.2888 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9484  Z= 0.121
  Angle     :  0.558   7.011  12890  Z= 0.260
  Chirality :  0.041   0.216   1586
  Planarity :  0.004   0.048   1504
  Dihedral  : 10.074  59.695   1824
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.99 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.26), residues: 1132
  helix:  2.42 (0.18), residues: 808
  sheet: -0.57 (0.53), residues: 92
  loop : -0.32 (0.47), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 510 
 TYR   0.014   0.001   TYR A  81 
 PHE   0.008   0.001   PHE B 605 
 TRP   0.013   0.001   TRP B 574 
 HIS   0.002   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9482)
  covalent geometry    : angle       0.55841 (12890)
  hydrogen bonds       : bond        0.03808 (  636)
  hydrogen bonds       : angle       3.90359 ( 1872)
  Misc. bond           : bond        0.00130 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.368 
Fit side-chains
REVERT: B  355 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7927 (tp)
REVERT: B  512 GLN cc_start: 0.7742 (mp10) cc_final: 0.7172 (mt0)
REVERT: B  518 LYS cc_start: 0.7238 (ttpt) cc_final: 0.6757 (tptm)
REVERT: B  553 LYS cc_start: 0.7614 (ttmt) cc_final: 0.6400 (ttpp)
REVERT: A   32 MET cc_start: 0.7886 (mtp) cc_final: 0.7590 (mtp)
REVERT: A  355 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7844 (tp)
REVERT: A  392 MET cc_start: 0.8318 (tpt) cc_final: 0.8064 (mmm)
REVERT: A  437 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8195 (mm)
  outliers start: 21
  outliers final: 15
  residues processed: 102
  average time/residue: 0.0967
  time to fit residues: 14.2233
Evaluate side-chains
  103 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  550 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 43 optimal weight:    0.1980
   chunk 74 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 101 optimal weight:    3.9990
   chunk 109 optimal weight:    4.9990
   chunk 93 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 57 optimal weight:   10.0000
   overall best weight:    0.9584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.123182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.100905 restraints weight = 10233.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 1.26
r_work: 0.2880 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9484  Z= 0.127
  Angle     :  0.568   7.511  12890  Z= 0.263
  Chirality :  0.041   0.225   1586
  Planarity :  0.004   0.048   1504
  Dihedral  : 10.149  59.584   1824
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.88 %
    Favored  : 84.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.43 (0.26), residues: 1132
  helix:  2.41 (0.18), residues: 808
  sheet: -0.55 (0.53), residues: 92
  loop : -0.33 (0.47), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 510 
 TYR   0.014   0.001   TYR A  81 
 PHE   0.011   0.001   PHE B 366 
 TRP   0.020   0.001   TRP B 574 
 HIS   0.003   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9482)
  covalent geometry    : angle       0.56761 (12890)
  hydrogen bonds       : bond        0.03858 (  636)
  hydrogen bonds       : angle       3.91581 ( 1872)
  Misc. bond           : bond        0.00141 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.339 
Fit side-chains
REVERT: B  215 LEU cc_start: 0.7644 (tp) cc_final: 0.7268 (tt)
REVERT: B  355 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7909 (tp)
REVERT: B  518 LYS cc_start: 0.7250 (ttpt) cc_final: 0.6766 (tptm)
REVERT: B  553 LYS cc_start: 0.7665 (ttmt) cc_final: 0.6451 (ttpp)
REVERT: A   32 MET cc_start: 0.7894 (mtp) cc_final: 0.7595 (mtp)
REVERT: A  355 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7869 (tp)
REVERT: A  392 MET cc_start: 0.8344 (tpt) cc_final: 0.8078 (mmm)
REVERT: A  437 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8197 (mm)
  outliers start: 20
  outliers final: 17
  residues processed: 100
  average time/residue: 0.0853
  time to fit residues: 12.5551
Evaluate side-chains
  103 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  316 ASN
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  550 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 12 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 69 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 97 optimal weight:    0.3980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.125099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.102867 restraints weight = 10208.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 1.26
r_work: 0.2906 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9484  Z= 0.113
  Angle     :  0.550   7.367  12890  Z= 0.255
  Chirality :  0.040   0.208   1586
  Planarity :  0.004   0.049   1504
  Dihedral  :  9.943  58.044   1824
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.41 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.55 (0.26), residues: 1132
  helix:  2.49 (0.18), residues: 808
  sheet: -0.45 (0.53), residues: 92
  loop : -0.28 (0.47), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 510 
 TYR   0.013   0.001   TYR A  81 
 PHE   0.007   0.001   PHE B 605 
 TRP   0.020   0.001   TRP B 574 
 HIS   0.003   0.000   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 9482)
  covalent geometry    : angle       0.54971 (12890)
  hydrogen bonds       : bond        0.03675 (  636)
  hydrogen bonds       : angle       3.84982 ( 1872)
  Misc. bond           : bond        0.00120 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2123.36 seconds
wall clock time: 37 minutes 16.43 seconds (2236.43 seconds total)