Starting phenix.real_space_refine
on Mon May 12 23:06:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b70_15894/05_2025/8b70_15894.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b70_15894/05_2025/8b70_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b70_15894/05_2025/8b70_15894.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b70_15894/05_2025/8b70_15894.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b70_15894/05_2025/8b70_15894.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b70_15894/05_2025/8b70_15894.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9258
  Number of models: 1
  Model: ""
    Number of chains: 3
    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: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'  K': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 220
          Unusual residues: {'  K': 1, 'LMT': 5}
          Classifications: {'RNA': 1, 'undetermined': 6}
          Link IDs: {None: 6}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.81, per 1000 atoms: 0.95
  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: 2.60
  Conformation dependent library (CDL) restraints added in 996.6 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: 0.86
  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: 2.54

  Time building geometry restraints manager: 2.94 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 606 or resid 1001 through 1004))
  selection = (chain 'B' and (resid 22 through 606 or resid 901 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:             0.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     25.880
  Find NCS groups from input model:        0.370
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.370
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (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
 TRP   0.008   0.001   TRP A 592 
 HIS   0.002   0.001   HIS B 505 
 PHE   0.008   0.001   PHE A 382 
 TYR   0.024   0.001   TYR B 493 
 ARG   0.002   0.000   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11881 (  636)
  hydrogen bonds       : angle       6.19447 ( 1872)
  covalent geometry    : bond        0.00706 ( 9482)
  covalent geometry    : angle       1.01823 (12890)
  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  : 1.002 
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: 0.5098 (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: 0.2399
  time to fit residues: 43.7135
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  : 0.984 
-------------------------------------------------------------------------------
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 96 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 103 optimal weight:    6.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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
A 196 GLN
A 389 GLN
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.125545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.108319 restraints weight = 10260.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 0.95
r_work: 0.2965 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2836 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1411

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= 0.146
  Angle     :  0.703  11.319  12890  Z= 0.311
  Chirality :  0.045   0.219   1586
  Planarity :  0.005   0.048   1504
  Dihedral  : 15.070  86.451   1829
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  6.37 %
    Favored  : 92.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.26), residues: 1132
  helix:  2.51 (0.18), residues: 788
  sheet: -1.50 (0.51), residues: 90
  loop : -0.35 (0.46), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 574 
 HIS   0.004   0.001   HIS A 372 
 PHE   0.008   0.001   PHE B 516 
 TYR   0.019   0.001   TYR A  81 
 ARG   0.003   0.000   ARG B 510 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04300 (  636)
  hydrogen bonds       : angle       4.28774 ( 1872)
  covalent geometry    : bond        0.00318 ( 9482)
  covalent geometry    : angle       0.70292 (12890)
  Misc. bond           : bond        0.00181 (    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
  120 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.972 
Fit side-chains
REVERT: B  252 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7517 (mpt-90)
REVERT: B  357 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6856 (t80)
REVERT: B  437 LEU cc_start: 0.7742 (mm) cc_final: 0.7483 (mp)
REVERT: B  514 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8120 (mmtp)
REVERT: B  518 LYS cc_start: 0.7642 (ttpt) cc_final: 0.7267 (tptm)
REVERT: B  536 TYR cc_start: 0.7839 (m-80) cc_final: 0.7560 (m-10)
  outliers start: 14
  outliers final: 8
  residues processed: 114
  average time/residue: 0.2004
  time to fit residues: 32.5556
Evaluate side-chains
  96 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  357 PHE
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  389 GLN
Chi-restraints excluded: chain A residue  436 VAL
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:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 70 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0050
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
B 141 HIS
B 144 HIS
B 196 GLN
A 389 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.126381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.104220 restraints weight = 10216.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.25
r_work: 0.2928 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1852

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= 0.126
  Angle     :  0.588   8.644  12890  Z= 0.272
  Chirality :  0.042   0.310   1586
  Planarity :  0.004   0.038   1504
  Dihedral  : 10.941  58.177   1824
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.29 %
    Favored  : 89.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.27), residues: 1132
  helix:  2.62 (0.18), residues: 792
  sheet: -1.30 (0.49), residues: 90
  loop : -0.30 (0.47), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 574 
 HIS   0.003   0.001   HIS B 141 
 PHE   0.010   0.001   PHE B 605 
 TYR   0.016   0.001   TYR B  81 
 ARG   0.004   0.000   ARG B 510 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04048 (  636)
  hydrogen bonds       : angle       4.05512 ( 1872)
  covalent geometry    : bond        0.00268 ( 9482)
  covalent geometry    : angle       0.58797 (12890)
  Misc. bond           : bond        0.00077 (    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
  106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 1.030 
Fit side-chains
REVERT: B  252 ARG cc_start: 0.7197 (mtt90) cc_final: 0.6878 (mpt-90)
REVERT: B  437 LEU cc_start: 0.7841 (mm) cc_final: 0.7499 (mp)
REVERT: B  514 LYS cc_start: 0.8360 (mmmt) cc_final: 0.7904 (mmtp)
REVERT: B  518 LYS cc_start: 0.7349 (ttpt) cc_final: 0.6901 (tptm)
REVERT: B  536 TYR cc_start: 0.7752 (m-80) cc_final: 0.7442 (m-10)
REVERT: A  392 MET cc_start: 0.8301 (tpt) cc_final: 0.8038 (mmm)
REVERT: A  437 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7819 (mm)
  outliers start: 10
  outliers final: 5
  residues processed: 102
  average time/residue: 0.2050
  time to fit residues: 29.9033
Evaluate side-chains
  91 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  436 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 45 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 110 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 109 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   chunk 93 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B 196 GLN
A 558 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.122592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.099848 restraints weight = 10321.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 1.31
r_work: 0.2861 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2714 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9484  Z= 0.140
  Angle     :  0.587   9.066  12890  Z= 0.275
  Chirality :  0.042   0.200   1586
  Planarity :  0.004   0.041   1504
  Dihedral  : 10.537  58.320   1824
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.15
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.26), residues: 1132
  helix:  2.51 (0.18), residues: 792
  sheet: -1.15 (0.50), residues: 90
  loop : -0.32 (0.46), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 574 
 HIS   0.003   0.001   HIS B 144 
 PHE   0.016   0.001   PHE A 605 
 TYR   0.017   0.001   TYR B  81 
 ARG   0.005   0.000   ARG B 510 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04084 (  636)
  hydrogen bonds       : angle       4.06053 ( 1872)
  covalent geometry    : bond        0.00323 ( 9482)
  covalent geometry    : angle       0.58701 (12890)
  Misc. bond           : bond        0.00114 (    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
  106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.929 
Fit side-chains
REVERT: B   32 MET cc_start: 0.7958 (mtp) cc_final: 0.7647 (mtp)
REVERT: B  141 HIS cc_start: 0.7143 (m90) cc_final: 0.6773 (m-70)
REVERT: B  252 ARG cc_start: 0.7166 (mtt90) cc_final: 0.6845 (mpt-90)
REVERT: B  437 LEU cc_start: 0.8085 (mm) cc_final: 0.7754 (mp)
REVERT: B  460 GLN cc_start: 0.8184 (tt0) cc_final: 0.7944 (tt0)
REVERT: B  514 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8141 (mmmt)
REVERT: B  518 LYS cc_start: 0.7335 (ttpt) cc_final: 0.6869 (tptm)
REVERT: B  536 TYR cc_start: 0.7924 (m-80) cc_final: 0.7563 (m-80)
REVERT: A   32 MET cc_start: 0.7896 (mtp) cc_final: 0.7618 (mtp)
REVERT: A  392 MET cc_start: 0.8354 (tpt) cc_final: 0.8143 (tpt)
REVERT: A  437 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7830 (mm)
REVERT: A  459 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7206 (mt-10)
REVERT: A  514 LYS cc_start: 0.8355 (mmmt) cc_final: 0.8068 (mmmt)
  outliers start: 14
  outliers final: 7
  residues processed: 101
  average time/residue: 0.2048
  time to fit residues: 29.3419
Evaluate side-chains
  91 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  232 VAL
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  243 LYS
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 49 optimal weight:    7.9990
   chunk 96 optimal weight:    3.9990
   chunk 71 optimal weight:    7.9990
   chunk 36 optimal weight:    0.4980
   chunk 98 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 103 optimal weight:    6.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3291 r_free = 0.3291 target = 0.122934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.100605 restraints weight = 10265.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 1.26
r_work: 0.2874 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2728 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9484  Z= 0.130
  Angle     :  0.571   8.615  12890  Z= 0.266
  Chirality :  0.041   0.205   1586
  Planarity :  0.004   0.042   1504
  Dihedral  : 10.410  59.794   1824
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.63 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.26), residues: 1132
  helix:  2.49 (0.18), residues: 792
  sheet: -1.06 (0.50), residues: 90
  loop : -0.36 (0.46), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 574 
 HIS   0.001   0.001   HIS A 575 
 PHE   0.007   0.001   PHE B 605 
 TYR   0.015   0.001   TYR A  81 
 ARG   0.004   0.000   ARG B 510 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03942 (  636)
  hydrogen bonds       : angle       3.98657 ( 1872)
  covalent geometry    : bond        0.00296 ( 9482)
  covalent geometry    : angle       0.57121 (12890)
  Misc. bond           : bond        0.00121 (    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
  102 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 1.006 
Fit side-chains
REVERT: B  215 LEU cc_start: 0.7665 (tp) cc_final: 0.7382 (tp)
REVERT: B  252 ARG cc_start: 0.7040 (mtt90) cc_final: 0.6739 (mpt-90)
REVERT: B  460 GLN cc_start: 0.8101 (tt0) cc_final: 0.7830 (tt0)
REVERT: B  514 LYS cc_start: 0.8357 (mmmt) cc_final: 0.7852 (mmtm)
REVERT: B  518 LYS cc_start: 0.7253 (ttpt) cc_final: 0.6800 (tptm)
REVERT: B  536 TYR cc_start: 0.7968 (m-80) cc_final: 0.7590 (m-80)
REVERT: A   32 MET cc_start: 0.7861 (mtp) cc_final: 0.7620 (mtp)
REVERT: A  392 MET cc_start: 0.8332 (tpt) cc_final: 0.8025 (mmm)
REVERT: A  420 MET cc_start: 0.7588 (tmm) cc_final: 0.7370 (tmm)
REVERT: A  437 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7829 (mm)
REVERT: A  459 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7141 (mt-10)
REVERT: A  514 LYS cc_start: 0.8344 (mmmt) cc_final: 0.8075 (mmmt)
  outliers start: 15
  outliers final: 11
  residues processed: 96
  average time/residue: 0.2106
  time to fit residues: 28.9303
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  : 0.905 
-------------------------------------------------------------------------------
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 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  317 THR
Chi-restraints excluded: chain A residue  370 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 9 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 101 optimal weight:    4.9990
   chunk 108 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 57 optimal weight:   10.0000
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
B 141 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.120630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.097211 restraints weight = 10370.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 1.36
r_work: 0.2818 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2670 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9484  Z= 0.151
  Angle     :  0.593   7.293  12890  Z= 0.278
  Chirality :  0.042   0.203   1586
  Planarity :  0.004   0.042   1504
  Dihedral  : 10.555  59.249   1824
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.42 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.26), residues: 1132
  helix:  2.34 (0.18), residues: 792
  sheet: -0.86 (0.51), residues: 92
  loop : -0.53 (0.45), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 574 
 HIS   0.002   0.001   HIS B 144 
 PHE   0.008   0.001   PHE A 382 
 TYR   0.016   0.001   TYR B  81 
 ARG   0.008   0.000   ARG B 510 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04162 (  636)
  hydrogen bonds       : angle       4.07569 ( 1872)
  covalent geometry    : bond        0.00358 ( 9482)
  covalent geometry    : angle       0.59305 (12890)
  Misc. bond           : bond        0.00156 (    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
  111 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.916 
Fit side-chains
REVERT: B   32 MET cc_start: 0.7945 (mtp) cc_final: 0.7664 (mtp)
REVERT: B  518 LYS cc_start: 0.7353 (ttpt) cc_final: 0.6897 (tptm)
REVERT: A   32 MET cc_start: 0.7952 (mtp) cc_final: 0.7695 (mtp)
REVERT: A  437 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7893 (mm)
REVERT: A  459 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7374 (mt-10)
  outliers start: 20
  outliers final: 15
  residues processed: 104
  average time/residue: 0.2109
  time to fit residues: 31.0910
Evaluate side-chains
  104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
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 B residue  486 VAL
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  243 LYS
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  370 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 104 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
B 141 HIS
B 389 GLN
A 196 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.122440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.100179 restraints weight = 10301.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 1.26
r_work: 0.2868 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2721 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2996

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   7.285  12890  Z= 0.265
  Chirality :  0.041   0.206   1586
  Planarity :  0.004   0.046   1504
  Dihedral  : 10.346  58.241   1824
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.84 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.26), residues: 1132
  helix:  2.31 (0.18), residues: 804
  sheet: -0.70 (0.52), residues: 92
  loop : -0.45 (0.46), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 574 
 HIS   0.003   0.001   HIS B 144 
 PHE   0.008   0.001   PHE B 366 
 TYR   0.015   0.001   TYR A  81 
 ARG   0.007   0.000   ARG B 510 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03917 (  636)
  hydrogen bonds       : angle       3.98441 ( 1872)
  covalent geometry    : bond        0.00289 ( 9482)
  covalent geometry    : angle       0.56812 (12890)
  Misc. bond           : bond        0.00150 (    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
  107 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 1.009 
Fit side-chains
REVERT: B   32 MET cc_start: 0.7858 (mtp) cc_final: 0.7586 (mtp)
REVERT: B  215 LEU cc_start: 0.7638 (tp) cc_final: 0.7261 (tt)
REVERT: B  518 LYS cc_start: 0.7272 (ttpt) cc_final: 0.6811 (tptm)
REVERT: A   32 MET cc_start: 0.7892 (mtp) cc_final: 0.7624 (mtp)
REVERT: A  392 MET cc_start: 0.8322 (tpt) cc_final: 0.8050 (mmm)
REVERT: A  437 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7827 (mm)
REVERT: A  459 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7209 (mt-10)
REVERT: A  514 LYS cc_start: 0.8304 (mmmt) cc_final: 0.8020 (mmmt)
  outliers start: 19
  outliers final: 14
  residues processed: 100
  average time/residue: 0.2044
  time to fit residues: 29.4587
Evaluate side-chains
  104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
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  370 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  243 LYS
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  370 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 24 optimal weight:    0.2980
   chunk 58 optimal weight:    8.9990
   chunk 32 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 104 optimal weight:    7.9990
   chunk 92 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 141 HIS
B 389 GLN
A 196 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.123553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.101182 restraints weight = 10364.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 1.27
r_work: 0.2885 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.3096

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     :  0.559   7.153  12890  Z= 0.260
  Chirality :  0.041   0.220   1586
  Planarity :  0.004   0.047   1504
  Dihedral  : 10.175  59.521   1824
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.94 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.26), residues: 1132
  helix:  2.37 (0.18), residues: 808
  sheet: -0.59 (0.53), residues: 92
  loop : -0.32 (0.47), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 574 
 HIS   0.003   0.001   HIS B 144 
 PHE   0.012   0.001   PHE B 605 
 TYR   0.014   0.001   TYR A  81 
 ARG   0.007   0.000   ARG B 510 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03809 (  636)
  hydrogen bonds       : angle       3.93314 ( 1872)
  covalent geometry    : bond        0.00271 ( 9482)
  covalent geometry    : angle       0.55897 (12890)
  Misc. bond           : bond        0.00141 (    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
  107 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.899 
Fit side-chains
REVERT: B  215 LEU cc_start: 0.7623 (tp) cc_final: 0.7393 (tp)
REVERT: B  355 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7891 (tp)
REVERT: B  486 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8200 (m)
REVERT: B  518 LYS cc_start: 0.7228 (ttpt) cc_final: 0.6760 (tptm)
REVERT: A   32 MET cc_start: 0.7908 (mtp) cc_final: 0.7608 (mtp)
REVERT: A  392 MET cc_start: 0.8332 (tpt) cc_final: 0.8069 (mmm)
REVERT: A  437 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7871 (mm)
  outliers start: 19
  outliers final: 14
  residues processed: 100
  average time/residue: 0.1975
  time to fit residues: 28.3519
Evaluate side-chains
  104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
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  355 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain B residue  389 GLN
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  486 VAL
Chi-restraints excluded: chain B residue  562 MET
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 20 optimal weight:    0.2980
   chunk 87 optimal weight:    0.1980
   chunk 79 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   chunk 22 optimal weight:    7.9990
   chunk 29 optimal weight:    0.0370
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
B 141 HIS
B 389 GLN
A 196 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.125361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.103315 restraints weight = 10229.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 1.24
r_work: 0.2916 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2773 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9484  Z= 0.110
  Angle     :  0.546   7.056  12890  Z= 0.254
  Chirality :  0.040   0.193   1586
  Planarity :  0.004   0.048   1504
  Dihedral  : 10.008  58.509   1824
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.15 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.26), residues: 1132
  helix:  2.45 (0.18), residues: 808
  sheet: -0.45 (0.53), residues: 92
  loop : -0.29 (0.47), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 574 
 HIS   0.003   0.001   HIS B 144 
 PHE   0.006   0.001   PHE B 366 
 TYR   0.013   0.001   TYR B  81 
 ARG   0.006   0.000   ARG B 510 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03646 (  636)
  hydrogen bonds       : angle       3.86861 ( 1872)
  covalent geometry    : bond        0.00234 ( 9482)
  covalent geometry    : angle       0.54581 (12890)
  Misc. bond           : bond        0.00120 (    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
  107 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 1.201 
Fit side-chains
REVERT: B  215 LEU cc_start: 0.7631 (tp) cc_final: 0.7384 (tp)
REVERT: B  355 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7871 (tp)
REVERT: B  486 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8187 (m)
REVERT: B  518 LYS cc_start: 0.7259 (ttpt) cc_final: 0.6783 (tptm)
REVERT: A   32 MET cc_start: 0.7879 (mtp) cc_final: 0.7621 (mtp)
REVERT: A  392 MET cc_start: 0.8332 (tpt) cc_final: 0.8090 (mmm)
REVERT: A  437 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7840 (mm)
  outliers start: 18
  outliers final: 13
  residues processed: 100
  average time/residue: 0.2135
  time to fit residues: 30.4962
Evaluate side-chains
  100 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
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  355 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain B residue  389 GLN
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  486 VAL
Chi-restraints excluded: chain B residue  562 MET
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  213 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 52 optimal weight:    0.4980
   chunk 103 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 74 optimal weight:    8.9990
   chunk 99 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    1.2988

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

Flipped N/Q/H residues before XYZ refinement:
B 141 HIS
B 196 GLN
B 389 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.122153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.099830 restraints weight = 10434.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 1.27
r_work: 0.2865 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.3192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9484  Z= 0.145
  Angle     :  0.583   7.271  12890  Z= 0.272
  Chirality :  0.042   0.254   1586
  Planarity :  0.004   0.047   1504
  Dihedral  : 10.141  56.661   1824
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.47 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.26), residues: 1132
  helix:  2.35 (0.18), residues: 808
  sheet: -0.53 (0.53), residues: 92
  loop : -0.38 (0.46), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 574 
 HIS   0.003   0.001   HIS B 141 
 PHE   0.011   0.001   PHE B 605 
 TYR   0.015   0.001   TYR A  81 
 ARG   0.007   0.000   ARG B 510 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03954 (  636)
  hydrogen bonds       : angle       3.95552 ( 1872)
  covalent geometry    : bond        0.00342 ( 9482)
  covalent geometry    : angle       0.58292 (12890)
  Misc. bond           : bond        0.00140 (    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
  103 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 1.002 
Fit side-chains
REVERT: B  215 LEU cc_start: 0.7679 (tp) cc_final: 0.7470 (tp)
REVERT: B  355 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7914 (tp)
REVERT: B  518 LYS cc_start: 0.7243 (ttpt) cc_final: 0.6761 (tptm)
REVERT: A   32 MET cc_start: 0.7897 (mtp) cc_final: 0.7626 (mtp)
REVERT: A  392 MET cc_start: 0.8321 (tpt) cc_final: 0.8050 (mmm)
REVERT: A  437 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7872 (mm)
  outliers start: 17
  outliers final: 14
  residues processed: 97
  average time/residue: 0.2048
  time to fit residues: 28.5732
Evaluate side-chains
  100 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
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  389 GLN
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  562 MET
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  213 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 111 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0980
   chunk 85 optimal weight:    0.6980
   chunk 112 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 141 HIS
B 389 GLN
A 196 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.123814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.101506 restraints weight = 10215.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 1.26
r_work: 0.2889 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3223

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= 0.119
  Angle     :  0.561   7.270  12890  Z= 0.262
  Chirality :  0.041   0.227   1586
  Planarity :  0.004   0.050   1504
  Dihedral  : 10.042  58.456   1824
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.57 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.26), residues: 1132
  helix:  2.41 (0.18), residues: 808
  sheet: -0.49 (0.53), residues: 92
  loop : -0.32 (0.46), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 574 
 HIS   0.003   0.001   HIS B 141 
 PHE   0.008   0.001   PHE B 605 
 TYR   0.015   0.001   TYR B  81 
 ARG   0.006   0.000   ARG B 510 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03785 (  636)
  hydrogen bonds       : angle       3.90615 ( 1872)
  covalent geometry    : bond        0.00264 ( 9482)
  covalent geometry    : angle       0.56133 (12890)
  Misc. bond           : bond        0.00131 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3926.87 seconds
wall clock time: 69 minutes 15.09 seconds (4155.09 seconds total)