Starting phenix.real_space_refine
on Tue Jan 14 08:18:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8s86_19798/01_2025/8s86_19798.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8s86_19798/01_2025/8s86_19798.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8s86_19798/01_2025/8s86_19798.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8s86_19798/01_2025/8s86_19798.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8s86_19798/01_2025/8s86_19798.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8s86_19798/01_2025/8s86_19798.cif"
  }
  resolution = 2.8
  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=  -0.003 sd=   0.093
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    3919      2.51       5
     N    1080      2.21       5
     O    1148      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6177
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3085
          Classifications: {'peptide': 392}
          Link IDs: {'PTRANS': 22, 'TRANS': 369}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 3092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 3092
          Classifications: {'peptide': 393}
          Link IDs: {'PTRANS': 23, 'TRANS': 369}
          Chain breaks: 7
  Time building chain proxies: 4.45, per 1000 atoms: 0.72
  Number of scatterers: 6177
  At special positions: 0
  Unit cell: (71.06, 122.265, 72.105, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    1148      8.00
     N    1080      7.00
     C    3919      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.51
  Conformation dependent library (CDL) restraints added in 939.1 milliseconds
  

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1478

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 9 sheets defined
      40.8% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 104 through 116
    Processing helix  chain 'A' and resid 130 through 135
    Processing helix  chain 'A' and resid 138 through 140
      No H-bonds generated for 'chain 'A' and resid 138 through 140'
    Processing helix  chain 'A' and resid 141 through 158
      removed outlier: 3.703A  pdb=" N   ALA A 155 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
      Proline residue:  A 156  - end of helix
    Processing helix  chain 'A' and resid 176 through 184
    Processing helix  chain 'A' and resid 191 through 196
    Processing helix  chain 'A' and resid 221 through 226
    Processing helix  chain 'A' and resid 237 through 255
      removed outlier: 3.736A  pdb=" N   ASP A 243 " --> pdb=" O   CYS A 239 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   LYS A 246 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   TYR A 251 " --> pdb=" O   ILE A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 270
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 296 through 300
    Processing helix  chain 'A' and resid 307 through 318
    Processing helix  chain 'A' and resid 343 through 357
      removed outlier: 3.575A  pdb=" N   GLY A 348 " --> pdb=" O   ALA A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 383
      removed outlier: 4.235A  pdb=" N   ALA A 376 " --> pdb=" O   PRO A 372 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   PHE A 377 " --> pdb=" O   SER A 373 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU A 381 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 438
      No H-bonds generated for 'chain 'A' and resid 436 through 438'
    Processing helix  chain 'A' and resid 454 through 470
      removed outlier: 3.655A  pdb=" N   SER A 458 " --> pdb=" O   GLY A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 484
    Processing helix  chain 'B' and resid 104 through 116
    Processing helix  chain 'B' and resid 130 through 135
    Processing helix  chain 'B' and resid 138 through 140
      No H-bonds generated for 'chain 'B' and resid 138 through 140'
    Processing helix  chain 'B' and resid 141 through 158
      removed outlier: 3.670A  pdb=" N   ALA B 155 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
      Proline residue:  B 156  - end of helix
    Processing helix  chain 'B' and resid 176 through 184
    Processing helix  chain 'B' and resid 191 through 197
    Processing helix  chain 'B' and resid 220 through 226
    Processing helix  chain 'B' and resid 237 through 255
      removed outlier: 3.798A  pdb=" N   ASP B 243 " --> pdb=" O   CYS B 239 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   LYS B 246 " --> pdb=" O   ARG B 242 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ILE B 247 " --> pdb=" O   ASP B 243 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA B 250 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TYR B 251 " --> pdb=" O   ILE B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 270
    Processing helix  chain 'B' and resid 282 through 286
    Processing helix  chain 'B' and resid 296 through 300
    Processing helix  chain 'B' and resid 307 through 318
    Processing helix  chain 'B' and resid 343 through 356
    Processing helix  chain 'B' and resid 373 through 383
      removed outlier: 3.931A  pdb=" N   PHE B 377 " --> pdb=" O   SER B 373 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU B 381 " --> pdb=" O   PHE B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 438
      No H-bonds generated for 'chain 'B' and resid 436 through 438'
    Processing helix  chain 'B' and resid 454 through 470
      removed outlier: 3.670A  pdb=" N   SER B 458 " --> pdb=" O   GLY B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 484
      removed outlier: 3.734A  pdb=" N   GLY B 484 " --> pdb=" O   ASP B 481 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 88
      removed outlier: 3.511A  pdb=" N   PHE A 212 " --> pdb=" O   MET A 234 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   LEU A 120 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   ALA A 164 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ILE A 122 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 8.574A  pdb=" N   SER A 166 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
      removed outlier: 8.702A  pdb=" N   SER A 124 " --> pdb=" O   SER A 166 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   VAL A 161 " --> pdb=" O   GLN A 186 " (cutoff:3.500A)
      removed outlier: 8.361A  pdb=" N   ARG A 188 " --> pdb=" O   VAL A 161 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   ILE A 163 " --> pdb=" O   ARG A 188 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   VAL A 190 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   VAL A 165 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128
    Processing sheet with id=AA3, first strand: chain 'A' and resid 279 through 281
      removed outlier: 4.685A  pdb=" N   THR A 305 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 279 through 281
      removed outlier: 4.626A  pdb=" N   LYS A 418 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ILE A 322 " --> pdb=" O   ARG A 361 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   LEU A 363 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   VAL A 324 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   SER A 365 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   VAL A 326 " --> pdb=" O   SER A 365 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   VAL A 360 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   LYS A 396 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   LEU A 362 " --> pdb=" O   LYS A 396 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   PHE A 398 " --> pdb=" O   LEU A 362 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ILE A 364 " --> pdb=" O   PHE A 398 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 330
    Processing sheet with id=AA6, first strand: chain 'B' and resid 82 through 88
      removed outlier: 3.628A  pdb=" N   PHE B 212 " --> pdb=" O   MET B 234 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LYS B 203 " --> pdb=" O   GLY B 215 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ARG B 162 " --> pdb=" O   LEU B 120 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA B 164 " --> pdb=" O   ILE B 122 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   SER B 166 " --> pdb=" O   SER B 124 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ILE B 163 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   VAL B 190 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   VAL B 165 " --> pdb=" O   VAL B 190 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 279 through 281
      removed outlier: 4.618A  pdb=" N   THR B 305 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 279 through 281
      removed outlier: 4.589A  pdb=" N   LYS B 418 " --> pdb=" O   GLY B 429 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ILE B 322 " --> pdb=" O   ARG B 361 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   LEU B 363 " --> pdb=" O   ILE B 322 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   VAL B 324 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   SER B 365 " --> pdb=" O   VAL B 324 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   VAL B 326 " --> pdb=" O   SER B 365 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   VAL B 360 " --> pdb=" O   GLN B 394 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   LYS B 396 " --> pdb=" O   VAL B 360 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU B 362 " --> pdb=" O   LYS B 396 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   PHE B 398 " --> pdb=" O   LEU B 362 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ILE B 364 " --> pdb=" O   PHE B 398 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 329 through 330

    270 hydrogen bonds defined for protein.
    717 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: 2.38

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1527
        1.33 -     1.45: 1294
        1.45 -     1.57: 3459
        1.57 -     1.69: 1
        1.69 -     1.81: 46
  Bond restraints: 6327
  Sorted by residual:
  bond pdb=" N   ASN B 218 "
       pdb=" CA  ASN B 218 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.00e-02 1.00e+04 1.14e+01
  bond pdb=" CZ  ARG B 350 "
       pdb=" NH2 ARG B 350 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.46e+00
  bond pdb=" N   VAL B 227 "
       pdb=" CA  VAL B 227 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.18e-02 7.18e+03 9.27e+00
  bond pdb=" CZ  ARG A 350 "
       pdb=" NH2 ARG A 350 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.60e+00
  bond pdb=" N   ASP B 220 "
       pdb=" CA  ASP B 220 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.037 1.27e-02 6.20e+03 8.34e+00
  ... (remaining 6322 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 7533
        1.66 -     3.32: 862
        3.32 -     4.99: 171
        4.99 -     6.65: 47
        6.65 -     8.31: 5
  Bond angle restraints: 8618
  Sorted by residual:
  angle pdb=" C   PRO B 296 "
        pdb=" N   PRO B 297 "
        pdb=" CA  PRO B 297 "
      ideal   model   delta    sigma   weight residual
     120.38  126.73   -6.35 1.03e+00 9.43e-01 3.80e+01
  angle pdb=" CA  ASP B 307 "
        pdb=" CB  ASP B 307 "
        pdb=" CG  ASP B 307 "
      ideal   model   delta    sigma   weight residual
     112.60  118.17   -5.57 1.00e+00 1.00e+00 3.10e+01
  angle pdb=" CA  ASP A 316 "
        pdb=" CB  ASP A 316 "
        pdb=" CG  ASP A 316 "
      ideal   model   delta    sigma   weight residual
     112.60  118.11   -5.51 1.00e+00 1.00e+00 3.03e+01
  angle pdb=" CB  HIS B 416 "
        pdb=" CG  HIS B 416 "
        pdb=" CD2 HIS B 416 "
      ideal   model   delta    sigma   weight residual
     131.20  124.45    6.75 1.30e+00 5.92e-01 2.69e+01
  angle pdb=" CA  TYR B 323 "
        pdb=" C   TYR B 323 "
        pdb=" N   VAL B 324 "
      ideal   model   delta    sigma   weight residual
     116.37  122.05   -5.68 1.19e+00 7.06e-01 2.28e+01
  ... (remaining 8613 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.93: 3395
       16.93 -    33.86: 275
       33.86 -    50.78: 64
       50.78 -    67.71: 7
       67.71 -    84.64: 4
  Dihedral angle restraints: 3745
    sinusoidal: 1465
      harmonic: 2280
  Sorted by residual:
  dihedral pdb=" CA  HIS B 337 "
           pdb=" C   HIS B 337 "
           pdb=" N   PRO B 338 "
           pdb=" CA  PRO B 338 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.02  -27.98     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  SER B  99 "
           pdb=" C   SER B  99 "
           pdb=" N   THR B 100 "
           pdb=" CA  THR B 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.47   27.53     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  ALA A 486 "
           pdb=" C   ALA A 486 "
           pdb=" N   CYS A 487 "
           pdb=" CA  CYS A 487 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.36  -25.64     0      5.00e+00 4.00e-02 2.63e+01
  ... (remaining 3742 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 782
       0.084 -    0.167: 166
       0.167 -    0.251: 12
       0.251 -    0.335: 2
       0.335 -    0.418: 2
  Chirality restraints: 964
  Sorted by residual:
  chirality pdb=" CA  ALA B 295 "
            pdb=" N   ALA B 295 "
            pdb=" C   ALA B 295 "
            pdb=" CB  ALA B 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.07    0.42 2.00e-01 2.50e+01 4.37e+00
  chirality pdb=" CA  ASP A 316 "
            pdb=" N   ASP A 316 "
            pdb=" C   ASP A 316 "
            pdb=" CB  ASP A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.47e+00
  chirality pdb=" CA  TRP A 433 "
            pdb=" N   TRP A 433 "
            pdb=" C   TRP A 433 "
            pdb=" CB  TRP A 433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.54e+00
  ... (remaining 961 not shown)

  Planarity restraints: 1107
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 433 "   -0.092 2.00e-02 2.50e+03   6.66e-02 1.11e+02
        pdb=" CG  TRP A 433 "    0.007 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 433 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 433 "    0.087 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 433 "    0.035 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 433 "    0.050 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 433 "    0.107 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 433 "   -0.026 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 433 "   -0.026 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 433 "   -0.101 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 342 "    0.102 2.00e-02 2.50e+03   5.77e-02 8.32e+01
        pdb=" CG  TRP B 342 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 342 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 342 "   -0.068 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 342 "   -0.036 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 342 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 342 "   -0.079 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 342 "    0.057 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 342 "   -0.013 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 342 "    0.079 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 433 "   -0.038 2.00e-02 2.50e+03   5.43e-02 7.38e+01
        pdb=" CG  TRP B 433 "    0.002 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 433 "   -0.074 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 433 "    0.073 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 433 "    0.020 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 433 "    0.058 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 433 "    0.072 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 433 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 433 "   -0.048 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 433 "   -0.078 2.00e-02 2.50e+03
  ... (remaining 1104 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1582
        2.81 -     3.34: 6174
        3.34 -     3.86: 10904
        3.86 -     4.38: 13688
        4.38 -     4.90: 21974
  Nonbonded interactions: 54322
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  87 "
            pdb=" NH2 ARG A 466 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" NH1 ARG B 466 "
            pdb=" OD1 ASP B 467 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" NE1 TRP B 265 "
            pdb=" O   PRO B 298 "
     model   vdw
     2.338 3.120
  nonbonded pdb=" N   ASP B 191 "
            pdb=" OD1 ASP B 191 "
     model   vdw
     2.372 3.120
  nonbonded pdb=" NH1 ARG A 466 "
            pdb=" OD1 ASP A 467 "
     model   vdw
     2.373 3.120
  ... (remaining 54317 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 79 through 386 or resid 388 through 389 or resid 391 throu \ 
gh 490))
  selection = (chain 'B' and (resid 79 through 256 or resid 265 through 334 or resid 338 throu \ 
gh 490))
}

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:             1.750
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     18.840
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6012
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      :  0.008   0.055   6327  Z= 0.497
  Angle     :  1.182   8.309   8618  Z= 0.770
  Chirality :  0.068   0.418    964
  Planarity :  0.013   0.142   1107
  Dihedral  : 13.436  84.640   2267
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  8.37 %
    Favored  : 89.39 %
  Cbeta Deviations :  0.27 %
  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: -2.43 (0.26), residues: 759
  helix: -2.00 (0.23), residues: 266
  sheet: -0.09 (0.35), residues: 203
  loop : -2.22 (0.32), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.107   0.013   TRP A 433 
 HIS   0.018   0.002   HIS A 416 
 PHE   0.042   0.005   PHE B 377 
 TYR   0.103   0.010   TYR B 329 
 ARG   0.028   0.003   ARG A 424 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 LYS cc_start: 0.6510 (tttp) cc_final: 0.6169 (pttp)
REVERT: A  234 MET cc_start: 0.7164 (ttm) cc_final: 0.6910 (tpp)
REVERT: A  276 GLU cc_start: 0.5666 (mt-10) cc_final: 0.5404 (mt-10)
REVERT: B   94 ASP cc_start: 0.4739 (p0) cc_final: 0.4536 (p0)
REVERT: B  107 GLN cc_start: 0.7357 (mt0) cc_final: 0.7094 (mt0)
REVERT: B  276 GLU cc_start: 0.5716 (mm-30) cc_final: 0.5192 (pt0)
REVERT: B  340 ARG cc_start: 0.6052 (mmm-85) cc_final: 0.5406 (tpp80)
  outliers start: 15
  outliers final: 1
  residues processed: 147
  average time/residue: 1.0691
  time to fit residues: 165.8238
Evaluate side-chains
  93 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  463 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.2980
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0970
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
A 201 HIS
A 284 ASN
A 485 ASN
B 117 HIS
B 197 HIS
B 201 HIS
B 218 ASN
** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 416 HIS
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.189051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.170089 restraints weight = 6320.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.4506 rms_B_bonded: 1.77
r_work: 0.4422 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.4299 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.4299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6283
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6327  Z= 0.255
  Angle     :  0.701   9.155   8618  Z= 0.363
  Chirality :  0.047   0.174    964
  Planarity :  0.005   0.045   1107
  Dihedral  :  5.379  18.949    850
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.55 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.29), residues: 759
  helix: -0.44 (0.29), residues: 271
  sheet:  0.27 (0.36), residues: 201
  loop : -1.30 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 205 
 HIS   0.007   0.001   HIS A 416 
 PHE   0.019   0.003   PHE B 204 
 TYR   0.023   0.002   TYR B 291 
 ARG   0.003   0.000   ARG B 356 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.4943 (p0) cc_final: 0.4743 (p0)
REVERT: A  100 THR cc_start: 0.3441 (OUTLIER) cc_final: 0.3202 (p)
REVERT: A  167 LYS cc_start: 0.6329 (tttp) cc_final: 0.5979 (pttp)
REVERT: A  276 GLU cc_start: 0.6119 (mt-10) cc_final: 0.5898 (mt-10)
REVERT: A  294 SER cc_start: 0.4661 (p) cc_final: 0.4429 (m)
REVERT: B   94 ASP cc_start: 0.4740 (p0) cc_final: 0.4468 (p0)
REVERT: B  327 MET cc_start: 0.5968 (ttt) cc_final: 0.5668 (tpp)
REVERT: B  346 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6317 (m-30)
  outliers start: 21
  outliers final: 3
  residues processed: 118
  average time/residue: 1.0990
  time to fit residues: 137.0849
Evaluate side-chains
  90 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 416 HIS
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 485 ASN
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.182874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.163762 restraints weight = 6458.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.4426 rms_B_bonded: 1.79
r_work: 0.4335 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.4208 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6392
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6327  Z= 0.313
  Angle     :  0.709   9.036   8618  Z= 0.367
  Chirality :  0.047   0.154    964
  Planarity :  0.005   0.045   1107
  Dihedral  :  5.242  21.952    848
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 14.50 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.29), residues: 759
  helix: -0.30 (0.30), residues: 271
  sheet:  0.22 (0.36), residues: 196
  loop : -1.37 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP B 205 
 HIS   0.011   0.002   HIS A 416 
 PHE   0.027   0.003   PHE B 212 
 TYR   0.025   0.003   TYR B 273 
 ARG   0.009   0.001   ARG B 340 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 92
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.4944 (p0) cc_final: 0.4722 (p0)
REVERT: A  100 THR cc_start: 0.3548 (OUTLIER) cc_final: 0.3318 (p)
REVERT: A  180 LEU cc_start: 0.5573 (OUTLIER) cc_final: 0.5152 (mp)
REVERT: A  242 ARG cc_start: 0.6294 (ttm110) cc_final: 0.5905 (ttm110)
REVERT: A  277 THR cc_start: 0.7060 (p) cc_final: 0.6835 (p)
REVERT: B   94 ASP cc_start: 0.4973 (p0) cc_final: 0.4650 (p0)
REVERT: B  104 SER cc_start: 0.5713 (m) cc_final: 0.5261 (p)
REVERT: B  272 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.5126 (mpp-170)
REVERT: B  340 ARG cc_start: 0.6411 (mmm160) cc_final: 0.5772 (tpt170)
REVERT: B  346 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6271 (m-30)
  outliers start: 38
  outliers final: 13
  residues processed: 122
  average time/residue: 0.9038
  time to fit residues: 117.5504
Evaluate side-chains
  93 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  272 ARG
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    0.0370
   chunk 44 optimal weight:    0.0970
   chunk 71 optimal weight:    0.4980
   chunk 50 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0010
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.2862

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 485 ASN
B 117 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.191062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.171732 restraints weight = 6406.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.4511 rms_B_bonded: 1.81
r_work: 0.4425 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.4300 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6279
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6327  Z= 0.188
  Angle     :  0.602   7.004   8618  Z= 0.314
  Chirality :  0.044   0.154    964
  Planarity :  0.005   0.045   1107
  Dihedral  :  4.661  17.077    848
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.34 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.30), residues: 759
  helix:  0.13 (0.31), residues: 271
  sheet:  0.33 (0.37), residues: 200
  loop : -0.94 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 205 
 HIS   0.006   0.001   HIS A 416 
 PHE   0.019   0.002   PHE B 398 
 TYR   0.034   0.002   TYR A 291 
 ARG   0.003   0.000   ARG B 340 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 THR cc_start: 0.3564 (OUTLIER) cc_final: 0.3279 (p)
REVERT: A  208 ASP cc_start: 0.7377 (m-30) cc_final: 0.7008 (m-30)
REVERT: A  276 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.5609 (pp20)
REVERT: A  346 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6394 (m-30)
REVERT: B   94 ASP cc_start: 0.4900 (p0) cc_final: 0.4579 (p0)
REVERT: B  104 SER cc_start: 0.5707 (m) cc_final: 0.5358 (p)
REVERT: B  160 ASN cc_start: 0.7097 (t0) cc_final: 0.6428 (m110)
REVERT: B  180 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5204 (mp)
REVERT: B  327 MET cc_start: 0.5841 (ttt) cc_final: 0.5638 (tpp)
REVERT: B  340 ARG cc_start: 0.6552 (mmm160) cc_final: 0.5819 (tpt170)
REVERT: B  346 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6585 (m-30)
REVERT: B  420 MET cc_start: 0.6335 (ttp) cc_final: 0.6111 (ttm)
  outliers start: 23
  outliers final: 6
  residues processed: 105
  average time/residue: 0.8254
  time to fit residues: 93.1878
Evaluate side-chains
  88 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 9 optimal weight:    0.4980
   chunk 67 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 54 optimal weight:    0.3980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.188034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.167883 restraints weight = 6354.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.4480 rms_B_bonded: 1.87
r_work: 0.4390 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.4265 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.4265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6392
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6327  Z= 0.238
  Angle     :  0.639   8.970   8618  Z= 0.330
  Chirality :  0.046   0.192    964
  Planarity :  0.005   0.043   1107
  Dihedral  :  4.740  18.217    848
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 17.79 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.30), residues: 759
  helix:  0.15 (0.31), residues: 272
  sheet:  0.30 (0.36), residues: 200
  loop : -0.79 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 205 
 HIS   0.006   0.001   HIS B 117 
 PHE   0.023   0.003   PHE A 398 
 TYR   0.027   0.002   TYR A 291 
 ARG   0.005   0.000   ARG A 242 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 82
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 THR cc_start: 0.3647 (OUTLIER) cc_final: 0.3365 (p)
REVERT: A  246 LYS cc_start: 0.4959 (ttpt) cc_final: 0.4542 (ttpt)
REVERT: A  276 GLU cc_start: 0.6670 (pt0) cc_final: 0.5944 (pp20)
REVERT: A  346 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6398 (m-30)
REVERT: B   94 ASP cc_start: 0.4932 (p0) cc_final: 0.4617 (p0)
REVERT: B  104 SER cc_start: 0.5860 (m) cc_final: 0.5618 (p)
REVERT: B  180 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.5195 (mp)
REVERT: B  272 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.6366 (pmm-80)
REVERT: B  305 THR cc_start: 0.6974 (OUTLIER) cc_final: 0.6749 (m)
REVERT: B  340 ARG cc_start: 0.6286 (mmm160) cc_final: 0.6077 (mmm160)
REVERT: B  346 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6301 (m-30)
REVERT: B  420 MET cc_start: 0.6445 (ttp) cc_final: 0.6223 (ttm)
  outliers start: 31
  outliers final: 9
  residues processed: 107
  average time/residue: 0.9605
  time to fit residues: 109.5446
Evaluate side-chains
  91 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  272 ARG
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0980
   chunk 5 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0040
   chunk 58 optimal weight:    0.2980
   overall best weight:    0.3392

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

Flipped N/Q/H residues before XYZ refinement:
A 275 GLN
** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.191962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.172203 restraints weight = 6257.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.4514 rms_B_bonded: 1.82
r_work: 0.4427 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.4305 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.4305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6337
moved from start:          0.3970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6327  Z= 0.198
  Angle     :  0.609   7.864   8618  Z= 0.313
  Chirality :  0.044   0.153    964
  Planarity :  0.005   0.040   1107
  Dihedral  :  4.581  17.233    848
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 14.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 19.58 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.30), residues: 759
  helix:  0.29 (0.31), residues: 272
  sheet:  0.35 (0.37), residues: 197
  loop : -0.70 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 205 
 HIS   0.005   0.001   HIS A 416 
 PHE   0.023   0.002   PHE B 398 
 TYR   0.028   0.002   TYR A 291 
 ARG   0.007   0.000   ARG A 242 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 79
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A  100 THR cc_start: 0.3395 (OUTLIER) cc_final: 0.3123 (p)
REVERT: A  180 LEU cc_start: 0.5848 (OUTLIER) cc_final: 0.5342 (mp)
REVERT: A  208 ASP cc_start: 0.7338 (m-30) cc_final: 0.7043 (m-30)
REVERT: A  346 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6401 (m-30)
REVERT: B   94 ASP cc_start: 0.4893 (p0) cc_final: 0.4583 (p0)
REVERT: B  180 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.5253 (mp)
REVERT: B  346 ASP cc_start: 0.6924 (OUTLIER) cc_final: 0.6289 (m-30)
REVERT: B  371 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5682 (mp0)
  outliers start: 27
  outliers final: 9
  residues processed: 101
  average time/residue: 0.8704
  time to fit residues: 94.2202
Evaluate side-chains
  86 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  371 GLU
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 58 optimal weight:    0.1980
   chunk 46 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 275 GLN
** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.187728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.167958 restraints weight = 6398.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.4470 rms_B_bonded: 1.80
r_work: 0.4379 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.4256 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.4256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6429
moved from start:          0.4008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6327  Z= 0.275
  Angle     :  0.671   7.963   8618  Z= 0.346
  Chirality :  0.047   0.170    964
  Planarity :  0.005   0.044   1107
  Dihedral  :  4.777  16.916    848
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 20.18 %
    Favored  : 75.49 %
  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: -0.22 (0.30), residues: 759
  helix:  0.32 (0.31), residues: 266
  sheet:  0.22 (0.36), residues: 200
  loop : -0.71 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 205 
 HIS   0.006   0.001   HIS A 416 
 PHE   0.025   0.003   PHE A 398 
 TYR   0.028   0.003   TYR B 291 
 ARG   0.013   0.001   ARG B 340 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 THR cc_start: 0.6578 (p) cc_final: 0.6220 (t)
REVERT: A  180 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5389 (mp)
REVERT: A  208 ASP cc_start: 0.7353 (m-30) cc_final: 0.7039 (m-30)
REVERT: A  246 LYS cc_start: 0.5171 (ttpt) cc_final: 0.4624 (ttpt)
REVERT: A  276 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6125 (pp20)
REVERT: B   94 ASP cc_start: 0.4915 (p0) cc_final: 0.4604 (p0)
REVERT: B  180 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5337 (mp)
REVERT: B  340 ARG cc_start: 0.6388 (mmm160) cc_final: 0.6114 (mmm160)
REVERT: B  346 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6233 (m-30)
  outliers start: 29
  outliers final: 13
  residues processed: 98
  average time/residue: 0.9567
  time to fit residues: 99.7493
Evaluate side-chains
  90 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  294 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 76 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 27 optimal weight:    0.3980
   chunk 41 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 67 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 275 GLN
** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.189394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.169679 restraints weight = 6295.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.4485 rms_B_bonded: 1.79
r_work: 0.4395 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.4272 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.4272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6404
moved from start:          0.4131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6327  Z= 0.249
  Angle     :  0.665  12.979   8618  Z= 0.340
  Chirality :  0.047   0.212    964
  Planarity :  0.005   0.054   1107
  Dihedral  :  4.745  16.407    848
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 15.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 21.38 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.30), residues: 759
  helix:  0.24 (0.31), residues: 269
  sheet:  0.25 (0.37), residues: 200
  loop : -0.83 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 205 
 HIS   0.005   0.001   HIS A 416 
 PHE   0.023   0.003   PHE A 398 
 TYR   0.040   0.003   TYR B 273 
 ARG   0.014   0.001   ARG B 242 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 THR cc_start: 0.6584 (p) cc_final: 0.6256 (t)
REVERT: A  180 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5399 (mp)
REVERT: A  208 ASP cc_start: 0.7368 (m-30) cc_final: 0.7055 (m-30)
REVERT: A  246 LYS cc_start: 0.5123 (ttpt) cc_final: 0.4610 (ttpt)
REVERT: B   94 ASP cc_start: 0.4944 (p0) cc_final: 0.4641 (p0)
REVERT: B  180 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5349 (mp)
REVERT: B  340 ARG cc_start: 0.6395 (mmm160) cc_final: 0.6123 (mmm160)
REVERT: B  346 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6275 (m-30)
  outliers start: 22
  outliers final: 10
  residues processed: 97
  average time/residue: 0.9501
  time to fit residues: 98.2369
Evaluate side-chains
  86 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  294 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 20 optimal weight:    0.3980
   chunk 31 optimal weight:    0.0980
   chunk 56 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0870
   chunk 18 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 HIS
B 218 ASN
** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.191966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.172222 restraints weight = 6365.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.4518 rms_B_bonded: 1.82
r_work: 0.4431 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.4306 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6291
moved from start:          0.4221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6327  Z= 0.214
  Angle     :  0.646  11.761   8618  Z= 0.329
  Chirality :  0.046   0.192    964
  Planarity :  0.005   0.043   1107
  Dihedral  :  4.562  15.931    848
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 22.27 %
    Favored  : 75.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.31), residues: 759
  helix:  0.31 (0.32), residues: 269
  sheet:  0.46 (0.37), residues: 198
  loop : -0.77 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 468 
 HIS   0.005   0.001   HIS A 416 
 PHE   0.017   0.002   PHE A 212 
 TYR   0.027   0.002   TYR B 291 
 ARG   0.009   0.001   ARG B 340 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.641 
Fit side-chains
REVERT: A  160 ASN cc_start: 0.6889 (t0) cc_final: 0.5925 (m-40)
REVERT: A  180 LEU cc_start: 0.5776 (OUTLIER) cc_final: 0.5284 (mp)
REVERT: A  208 ASP cc_start: 0.7380 (m-30) cc_final: 0.7052 (m-30)
REVERT: A  246 LYS cc_start: 0.4959 (ttpt) cc_final: 0.4552 (tmmt)
REVERT: A  374 MET cc_start: 0.6177 (ptm) cc_final: 0.5801 (ptp)
REVERT: B   94 ASP cc_start: 0.4951 (p0) cc_final: 0.4633 (p0)
REVERT: B  180 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5187 (mp)
REVERT: B  239 CYS cc_start: 0.7217 (m) cc_final: 0.6418 (p)
REVERT: B  340 ARG cc_start: 0.6292 (mmm160) cc_final: 0.6014 (mmm160)
REVERT: B  346 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.6221 (m-30)
  outliers start: 18
  outliers final: 11
  residues processed: 88
  average time/residue: 0.8805
  time to fit residues: 83.0504
Evaluate side-chains
  84 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  294 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 51 optimal weight:    0.1980
   chunk 44 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 72 optimal weight:    0.5980
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.189079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.169176 restraints weight = 6443.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.4492 rms_B_bonded: 1.82
r_work: 0.4402 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.4278 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6413
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6327  Z= 0.264
  Angle     :  0.685  12.402   8618  Z= 0.349
  Chirality :  0.048   0.192    964
  Planarity :  0.005   0.041   1107
  Dihedral  :  4.685  16.160    848
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 22.87 %
    Favored  : 75.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.30), residues: 759
  helix:  0.32 (0.32), residues: 266
  sheet:  0.28 (0.36), residues: 204
  loop : -0.81 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 468 
 HIS   0.004   0.001   HIS A 416 
 PHE   0.020   0.003   PHE A 212 
 TYR   0.027   0.002   TYR B 291 
 ARG   0.008   0.001   ARG B 340 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.681 
Fit side-chains
REVERT: A  160 ASN cc_start: 0.6950 (t0) cc_final: 0.6045 (m-40)
REVERT: A  180 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5432 (mp)
REVERT: A  208 ASP cc_start: 0.7377 (m-30) cc_final: 0.7071 (m-30)
REVERT: A  246 LYS cc_start: 0.5167 (ttpt) cc_final: 0.4649 (ttpt)
REVERT: A  272 ARG cc_start: 0.6332 (mpp80) cc_final: 0.5913 (tpt90)
REVERT: A  374 MET cc_start: 0.6282 (ptm) cc_final: 0.5909 (ptp)
REVERT: B   94 ASP cc_start: 0.5002 (p0) cc_final: 0.4653 (p0)
REVERT: B  180 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5355 (mp)
REVERT: B  340 ARG cc_start: 0.6374 (mmm160) cc_final: 0.6110 (mmm160)
REVERT: B  346 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6242 (m-30)
  outliers start: 14
  outliers final: 11
  residues processed: 89
  average time/residue: 0.8801
  time to fit residues: 84.0649
Evaluate side-chains
  85 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  294 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 63 optimal weight:    0.1980
   chunk 23 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0970
   chunk 6 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 8 optimal weight:    0.3980
   chunk 77 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.192374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.172444 restraints weight = 6415.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.4517 rms_B_bonded: 1.83
r_work: 0.4429 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.4303 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.4303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6368
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6327  Z= 0.225
  Angle     :  0.654  11.726   8618  Z= 0.334
  Chirality :  0.046   0.185    964
  Planarity :  0.005   0.041   1107
  Dihedral  :  4.558  15.921    848
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 23.17 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.31), residues: 759
  helix:  0.49 (0.32), residues: 260
  sheet:  0.27 (0.37), residues: 204
  loop : -0.74 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 468 
 HIS   0.004   0.001   HIS A 416 
 PHE   0.017   0.002   PHE B 212 
 TYR   0.027   0.002   TYR B 291 
 ARG   0.008   0.000   ARG B 340 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5616.51 seconds
wall clock time: 100 minutes 0.29 seconds (6000.29 seconds total)