Starting phenix.real_space_refine
on Thu May 22 14:45:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qz8_18772/05_2025/8qz8_18772.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qz8_18772/05_2025/8qz8_18772.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qz8_18772/05_2025/8qz8_18772.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qz8_18772/05_2025/8qz8_18772.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qz8_18772/05_2025/8qz8_18772.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qz8_18772/05_2025/8qz8_18772.cif"
  }
  resolution = 3.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.072
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: 8
    Type Number    sf(0)   Gaussians
     Zn      3      6.06       5
     P      45      5.49       5
     Mg      1      5.21       5
     S      63      5.16       5
     C    7113      2.51       5
     N    2035      2.21       5
     O    2292      1.98       5
     H   11077      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 22629
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 6652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 417, 6652
          Classifications: {'peptide': 417}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 394}
    Chain: "B"
      Number of atoms: 7910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 7910
          Classifications: {'peptide': 512}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 491}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 6696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 6696
          Classifications: {'peptide': 427}
          Link IDs: {'PTRANS': 22, 'TRANS': 404}
    Chain: "V"
      Number of atoms: 1046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 1046
          Classifications: {'RNA': 33}
          Modifications used: {'3*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 8, 'rna3p_pur': 5, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 17, 'rna3p': 15}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 289
          Classifications: {'RNA': 9}
          Modifications used: {'3*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 4}
          Link IDs: {'rna3p': 8}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'G2P': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2585  SG  CYS A 161      47.930  47.016  19.706  1.00 76.37           S
  ATOM   4473  SG  CYS A 282      45.639  45.224  17.052  1.00 87.29           S
  ATOM  18195  SG  CYS C 233      21.177  52.353 108.814  1.00129.37           S
  ATOM  18219  SG  CYS C 235      21.445  54.226 105.382  1.00120.87           S
  ATOM  16861  SG  CYS C 146       9.859  61.301  88.729  1.00133.35           S
  ATOM  17049  SG  CYS C 159       9.623  64.497  90.979  1.00131.26           S
  ATOM  17105  SG  CYS C 163      12.623  62.252  91.247  1.00119.92           S
  ATOM  17115  SG  CYS C 164      12.238  64.813  88.738  1.00123.42           S

  Time building chain proxies: 11.04, per 1000 atoms: 0.49
  Number of scatterers: 22629
  At special positions: 0
  Unit cell: (92.19, 101.848, 125.554, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Zn      3     29.99
     S      63     16.00
     P      45     15.00
     Mg      1     11.99
     O    2292      8.00
     N    2035      7.00
     C    7113      6.00
     H   11077      1.00
    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: 5.89
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" NE2 HIS A 296 "
        pdb="ZN    ZN A 501 " - pdb=" ND1 HIS A 284 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 161 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 282 "
      pdb="  ZN C 501 "
        pdb="ZN    ZN C 501 " - pdb=" NE2 HIS C 191 "
        pdb="ZN    ZN C 501 " - pdb=" ND1 HIS C 184 "
        pdb="ZN    ZN C 501 " - pdb=" SG  CYS C 235 "
        pdb="ZN    ZN C 501 " - pdb=" SG  CYS C 233 "
      pdb="  ZN C 502 "
        pdb="ZN    ZN C 502 " - pdb=" SG  CYS C 159 "
        pdb="ZN    ZN C 502 " - pdb=" SG  CYS C 163 "
        pdb="ZN    ZN C 502 " - pdb=" SG  CYS C 164 "
        pdb="ZN    ZN C 502 " - pdb=" SG  CYS C 146 "
      Number of angles added : 8


  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2546

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 15 sheets defined
      41.7% alpha, 14.0% beta
      10 base pairs and 16 stacking pairs defined.
    Time for finding SS restraints: 10.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 4
      No H-bonds generated for 'chain 'A' and resid 2 through 4'
    Processing helix  chain 'A' and resid 5 through 13
    Processing helix  chain 'A' and resid 83 through 94
    Processing helix  chain 'A' and resid 112 through 123
    Processing helix  chain 'A' and resid 141 through 157
      removed outlier: 3.538A  pdb=" N   ILE A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 169
    Processing helix  chain 'A' and resid 174 through 189
    Processing helix  chain 'A' and resid 223 through 234
    Processing helix  chain 'A' and resid 301 through 311
      removed outlier: 3.665A  pdb=" N   GLN A 311 " --> pdb=" O   ASN A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 323
      removed outlier: 3.936A  pdb=" N   THR A 316 " --> pdb=" O   ASP A 312 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   ASP A 323 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 356
    Processing helix  chain 'A' and resid 359 through 374
      removed outlier: 3.901A  pdb=" N   ALA A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 415
    Processing helix  chain 'B' and resid 1 through 5
      removed outlier: 3.733A  pdb=" N   GLN B   5 " --> pdb=" O   TRP B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 39
    Processing helix  chain 'B' and resid 65 through 70
      removed outlier: 3.567A  pdb=" N   TYR B  70 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 103
    Processing helix  chain 'B' and resid 107 through 117
    Processing helix  chain 'B' and resid 129 through 138
      removed outlier: 3.660A  pdb=" N   ARG B 138 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 183
      removed outlier: 4.020A  pdb=" N   VAL B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   VAL B 171 " --> pdb=" O   LEU B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 203
    Processing helix  chain 'B' and resid 204 through 206
      No H-bonds generated for 'chain 'B' and resid 204 through 206'
    Processing helix  chain 'B' and resid 216 through 221
    Processing helix  chain 'B' and resid 222 through 233
    Processing helix  chain 'B' and resid 236 through 248
    Processing helix  chain 'B' and resid 266 through 268
      No H-bonds generated for 'chain 'B' and resid 266 through 268'
    Processing helix  chain 'B' and resid 269 through 279
      removed outlier: 3.687A  pdb=" N   LEU B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 311
    Processing helix  chain 'B' and resid 356 through 372
      removed outlier: 3.607A  pdb=" N   SER B 372 " --> pdb=" O   GLY B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 396
    Processing helix  chain 'B' and resid 409 through 413
      removed outlier: 3.894A  pdb=" N   GLY B 413 " --> pdb=" O   THR B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 425
    Processing helix  chain 'B' and resid 429 through 433
    Processing helix  chain 'B' and resid 442 through 454
    Processing helix  chain 'B' and resid 480 through 497
    Processing helix  chain 'B' and resid 506 through 514
    Processing helix  chain 'C' and resid 3 through 8
      removed outlier: 3.534A  pdb=" N   PHE C   8 " --> pdb=" O   PHE C   4 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 23
    Processing helix  chain 'C' and resid 33 through 40
    Processing helix  chain 'C' and resid 42 through 54
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'C' and resid 87 through 97
    Processing helix  chain 'C' and resid 100 through 108
    Processing helix  chain 'C' and resid 144 through 152
      removed outlier: 3.655A  pdb=" N   SER C 148 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 219
    Processing helix  chain 'C' and resid 234 through 241
    Processing helix  chain 'C' and resid 281 through 289
    Processing helix  chain 'C' and resid 303 through 317
      removed outlier: 4.415A  pdb=" N   ARG C 317 " --> pdb=" O   ALA C 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 319 through 334
    Processing helix  chain 'C' and resid 350 through 355
    Processing helix  chain 'C' and resid 370 through 375
    Processing helix  chain 'C' and resid 421 through 426
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18
    Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27
      removed outlier: 6.663A  pdb=" N   TRP A  52 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   CYS A  71 " --> pdb=" O   TRP A  52 " (cutoff:3.500A)
      removed outlier: 7.213A  pdb=" N   ALA A  54 " --> pdb=" O   CYS A  71 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   LEU A  73 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   GLU A  56 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137
      removed outlier: 3.632A  pdb=" N   PHE B 291 " --> pdb=" O   GLY B 212 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137
    Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194
      removed outlier: 6.614A  pdb=" N   TRP A 198 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   TYR A 202 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 192 through 194
      removed outlier: 6.614A  pdb=" N   TRP A 198 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   TYR A 202 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   LEU A 277 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   HIS A 271 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 80
    Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 160
      removed outlier: 7.072A  pdb=" N   PHE B 140 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 329
    Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 479
    Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 81
    Processing sheet with id=AB4, first strand: chain 'C' and resid 221 through 224
      removed outlier: 6.943A  pdb=" N   GLY C 262 " --> pdb=" O   PHE C 258 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 360 through 363
    Processing sheet with id=AB6, first strand: chain 'C' and resid 383 through 388
      removed outlier: 3.614A  pdb=" N   THR C 385 " --> pdb=" O   LEU C 417 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   MET C 415 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)

    478 hydrogen bonds defined for protein.
    1320 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      23 hydrogen bonds
      46 hydrogen bond angles
      0 basepair planarities
      10 basepair parallelities
      16 stacking parallelities
  Total time for adding SS restraints: 8.22

  Time building geometry restraints manager: 7.03 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 11045
        1.04 -     1.24: 1512
        1.24 -     1.44: 3735
        1.44 -     1.65: 6568
        1.65 -     1.85: 90
  Bond restraints: 22950
  Sorted by residual:
  bond pdb=" CB  CYS C 146 "
       pdb=" SG  CYS C 146 "
    ideal  model  delta    sigma   weight residual
    1.808  1.776  0.032 3.30e-02 9.18e+02 9.37e-01
  bond pdb=" C3'   A V  29 "
       pdb=" O3'   A V  29 "
    ideal  model  delta    sigma   weight residual
    1.427  1.440 -0.013 1.50e-02 4.44e+03 7.70e-01
  bond pdb=" CA  ASN A  50 "
       pdb=" CB  ASN A  50 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.013 1.51e-02 4.39e+03 7.57e-01
  bond pdb=" N   SER B 288 "
       pdb=" CA  SER B 288 "
    ideal  model  delta    sigma   weight residual
    1.471  1.456  0.015 1.74e-02 3.30e+03 7.30e-01
  bond pdb=" CB  CYS C 146 "
       pdb=" HB2 CYS C 146 "
    ideal  model  delta    sigma   weight residual
    0.970  0.953  0.017 2.00e-02 2.50e+03 7.16e-01
  ... (remaining 22945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.96: 38440
        0.96 -     1.91: 2699
        1.91 -     2.87: 207
        2.87 -     3.83: 82
        3.83 -     4.79: 7
  Bond angle restraints: 41435
  Sorted by residual:
  angle pdb=" C   SER B 288 "
        pdb=" CA  SER B 288 "
        pdb=" CB  SER B 288 "
      ideal   model   delta    sigma   weight residual
     116.34  111.55    4.79 1.40e+00 5.10e-01 1.17e+01
  angle pdb=" N   ASP C 187 "
        pdb=" CA  ASP C 187 "
        pdb=" C   ASP C 187 "
      ideal   model   delta    sigma   weight residual
     113.18  109.41    3.77 1.33e+00 5.65e-01 8.04e+00
  angle pdb=" N   ASP A 380 "
        pdb=" CA  ASP A 380 "
        pdb=" CB  ASP A 380 "
      ideal   model   delta    sigma   weight residual
     113.65  109.84    3.81 1.47e+00 4.63e-01 6.72e+00
  angle pdb=" C3'   U V  17 "
        pdb=" O3'   U V  17 "
        pdb=" P     C V  18 "
      ideal   model   delta    sigma   weight residual
     120.20  123.61   -3.41 1.50e+00 4.44e-01 5.17e+00
  angle pdb=" N   CYS C 146 "
        pdb=" CA  CYS C 146 "
        pdb=" C   CYS C 146 "
      ideal   model   delta    sigma   weight residual
     113.18  110.43    2.75 1.21e+00 6.83e-01 5.15e+00
  ... (remaining 41430 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.87: 10198
       28.87 -    57.74: 565
       57.74 -    86.61: 88
       86.61 -   115.48: 6
      115.48 -   144.35: 3
  Dihedral angle restraints: 10860
    sinusoidal: 6271
      harmonic: 4589
  Sorted by residual:
  dihedral pdb=" C4'   U V  17 "
           pdb=" C3'   U V  17 "
           pdb=" O3'   U V  17 "
           pdb=" P     C V  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   11.04 -121.04     1      3.50e+01 8.16e-04 1.19e+01
  dihedral pdb=" CA  ASP B 406 "
           pdb=" CB  ASP B 406 "
           pdb=" CG  ASP B 406 "
           pdb=" OD1 ASP B 406 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.98   58.98     1      2.00e+01 2.50e-03 1.16e+01
  dihedral pdb=" C4'   A V  29 "
           pdb=" C3'   A V  29 "
           pdb=" O3'   A V  29 "
           pdb=" P     G V  30 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00    2.88 -112.88     1      3.50e+01 8.16e-04 1.09e+01
  ... (remaining 10857 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1162
       0.027 -    0.053: 498
       0.053 -    0.080: 89
       0.080 -    0.107: 59
       0.107 -    0.134: 37
  Chirality restraints: 1845
  Sorted by residual:
  chirality pdb=" CA  VAL C 112 "
            pdb=" N   VAL C 112 "
            pdb=" C   VAL C 112 "
            pdb=" CB  VAL C 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CA  VAL A 252 "
            pdb=" N   VAL A 252 "
            pdb=" C   VAL A 252 "
            pdb=" CB  VAL A 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.19e-01
  chirality pdb=" CA  ILE A 199 "
            pdb=" N   ILE A 199 "
            pdb=" C   ILE A 199 "
            pdb=" CB  ILE A 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.18e-01
  ... (remaining 1842 not shown)

  Planarity restraints: 3252
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 161 "   -0.029 5.00e-02 4.00e+02   4.47e-02 3.20e+00
        pdb=" N   PRO B 162 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 162 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 162 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 141 "   -0.109 9.50e-02 1.11e+02   3.66e-02 1.66e+00
        pdb=" NE  ARG A 141 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 141 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 141 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 141 "    0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG A 141 "    0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG A 141 "    0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG A 141 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A 141 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A  60 "   -0.020 5.00e-02 4.00e+02   3.10e-02 1.54e+00
        pdb=" N   PRO A  61 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A  61 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A  61 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 3249 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 1558
        2.20 -     2.80: 45940
        2.80 -     3.40: 62293
        3.40 -     4.00: 84193
        4.00 -     4.60: 129077
  Nonbonded interactions: 323061
  Sorted by model distance:
  nonbonded pdb=" H   ASN C 299 "
            pdb=" OE2 GLU C 364 "
     model   vdw
     1.599 2.450
  nonbonded pdb="HH12 ARG A 372 "
            pdb=" O   GLY B   7 "
     model   vdw
     1.601 2.450
  nonbonded pdb=" O   LEU A 215 "
            pdb=" HH  TYR A 403 "
     model   vdw
     1.605 2.450
  nonbonded pdb=" OP2   U V  37 "
            pdb="HO2'   U V  38 "
     model   vdw
     1.612 2.450
  nonbonded pdb="HH22 ARG C  11 "
            pdb=" OE2 GLU C  18 "
     model   vdw
     1.643 2.450
  ... (remaining 323056 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             2.010
  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:             0.410
  Extract box with map and model:          0.950
  Check model and map are aligned:         0.180
  Set scattering table:                    0.230
  Process input model:                     64.100
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   70.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11885  Z= 0.114
  Angle     :  0.497  18.434  16259  Z= 0.243
  Chirality :  0.036   0.134   1845
  Planarity :  0.003   0.048   1937
  Dihedral  : 18.088 144.349   4710
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.34 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  : 15.71 %
    Favored  : 84.21 %
  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:  1.13 (0.24), residues: 1348
  helix:  2.10 (0.24), residues: 526
  sheet: -0.65 (0.42), residues: 147
  loop :  0.07 (0.25), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 239 
 HIS   0.002   0.001   HIS A 367 
 PHE   0.009   0.001   PHE C  44 
 TYR   0.008   0.001   TYR A 403 
 ARG   0.007   0.000   ARG A 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11681 (  487)
  hydrogen bonds       : angle       5.51974 ( 1366)
  metal coordination   : bond        0.01458 (   12)
  metal coordination   : angle       8.82890 (    8)
  covalent geometry    : bond        0.00257 (11873)
  covalent geometry    : angle       0.45719 (16251)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 1.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 ARG cc_start: 0.8417 (mtp-110) cc_final: 0.8171 (ttp80)
  outliers start: 1
  outliers final: 1
  residues processed: 112
  average time/residue: 0.8941
  time to fit residues: 127.7663
Evaluate side-chains
  111 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 1.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  103 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 115 optimal weight:    6.9990
   chunk 103 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0980
   chunk 55 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 124 optimal weight:    2.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A  50 ASN
** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 369 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.132214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.104966 restraints weight = 41567.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.87
r_work: 0.2988 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.0544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11885  Z= 0.127
  Angle     :  0.487  10.671  16259  Z= 0.242
  Chirality :  0.036   0.141   1845
  Planarity :  0.004   0.041   1937
  Dihedral  : 14.472 145.301   2139
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 2.08
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.93 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 14.94 %
    Favored  : 84.12 %
  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:  1.06 (0.24), residues: 1348
  helix:  2.12 (0.24), residues: 524
  sheet: -0.78 (0.42), residues: 144
  loop : -0.03 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 239 
 HIS   0.003   0.001   HIS A 367 
 PHE   0.008   0.001   PHE C  44 
 TYR   0.009   0.001   TYR A 403 
 ARG   0.004   0.000   ARG C 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03665 (  487)
  hydrogen bonds       : angle       4.45284 ( 1366)
  metal coordination   : bond        0.00894 (   12)
  metal coordination   : angle       6.24966 (    8)
  covalent geometry    : bond        0.00292 (11873)
  covalent geometry    : angle       0.46648 (16251)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 1.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   59 LEU cc_start: 0.8763 (mt) cc_final: 0.8472 (mt)
  outliers start: 11
  outliers final: 6
  residues processed: 122
  average time/residue: 0.8326
  time to fit residues: 129.6839
Evaluate side-chains
  115 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 1.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  402 THR
Chi-restraints excluded: chain C residue  146 CYS
Chi-restraints excluded: chain C residue  185 MET
Chi-restraints excluded: chain C residue  264 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 133 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  50 ASN
B 218 ASN
** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  28 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.130153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.102618 restraints weight = 41713.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 1.88
r_work: 0.2951 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.0848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  11885  Z= 0.201
  Angle     :  0.523  14.136  16259  Z= 0.258
  Chirality :  0.038   0.167   1845
  Planarity :  0.004   0.065   1937
  Dihedral  : 14.092 144.426   2139
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.01 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 14.51 %
    Favored  : 84.46 %
  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:  0.81 (0.24), residues: 1348
  helix:  1.93 (0.24), residues: 529
  sheet: -1.00 (0.41), residues: 151
  loop : -0.17 (0.24), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 239 
 HIS   0.003   0.001   HIS A 367 
 PHE   0.010   0.001   PHE C  44 
 TYR   0.010   0.001   TYR A 403 
 ARG   0.006   0.000   ARG A 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03878 (  487)
  hydrogen bonds       : angle       4.37029 ( 1366)
  metal coordination   : bond        0.01372 (   12)
  metal coordination   : angle       7.66426 (    8)
  covalent geometry    : bond        0.00470 (11873)
  covalent geometry    : angle       0.49492 (16251)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 1.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 ASP cc_start: 0.8295 (t0) cc_final: 0.7826 (t0)
REVERT: B    1 MET cc_start: 0.8214 (mtt) cc_final: 0.7794 (mtt)
REVERT: B   63 ARG cc_start: 0.7814 (mtt-85) cc_final: 0.7602 (mmt90)
REVERT: B   68 ASP cc_start: 0.8517 (m-30) cc_final: 0.8286 (m-30)
REVERT: B  159 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8424 (mt)
REVERT: C   59 LEU cc_start: 0.8777 (mt) cc_final: 0.8474 (mt)
REVERT: C  389 ARG cc_start: 0.8395 (mmt180) cc_final: 0.8081 (mmt180)
  outliers start: 12
  outliers final: 6
  residues processed: 120
  average time/residue: 0.8521
  time to fit residues: 131.2725
Evaluate side-chains
  118 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 111
  time to evaluate  : 1.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain C residue  146 CYS
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  185 MET
Chi-restraints excluded: chain C residue  264 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 122 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 114 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 111 optimal weight:    6.9990
   chunk 92 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
B 378 HIS
** B 506 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 = 0.3522 r_free = 0.3522 target = 0.130095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.102766 restraints weight = 41874.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 1.87
r_work: 0.2923 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11885  Z= 0.166
  Angle     :  0.501  13.515  16259  Z= 0.246
  Chirality :  0.037   0.145   1845
  Planarity :  0.004   0.071   1937
  Dihedral  : 14.063 144.082   2139
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.01 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.85 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.76 (0.23), residues: 1348
  helix:  1.90 (0.24), residues: 531
  sheet: -0.93 (0.41), residues: 147
  loop : -0.24 (0.24), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 239 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.012   0.001   PHE C 161 
 TYR   0.009   0.001   TYR A 403 
 ARG   0.009   0.000   ARG A 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03503 (  487)
  hydrogen bonds       : angle       4.23150 ( 1366)
  metal coordination   : bond        0.01249 (   12)
  metal coordination   : angle       7.38757 (    8)
  covalent geometry    : bond        0.00388 (11873)
  covalent geometry    : angle       0.47345 (16251)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 1.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 ASP cc_start: 0.8301 (t0) cc_final: 0.7757 (t70)
REVERT: B   63 ARG cc_start: 0.7805 (mtt-85) cc_final: 0.7594 (mmt90)
REVERT: B  159 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8394 (mt)
REVERT: C   59 LEU cc_start: 0.8753 (mt) cc_final: 0.8438 (mt)
REVERT: C  358 GLU cc_start: 0.7689 (mm-30) cc_final: 0.6936 (mm-30)
REVERT: C  389 ARG cc_start: 0.8342 (mmt180) cc_final: 0.7998 (mmt180)
  outliers start: 15
  outliers final: 11
  residues processed: 129
  average time/residue: 0.8140
  time to fit residues: 135.7632
Evaluate side-chains
  123 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 1.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  146 CYS
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  185 MET
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  342 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 115 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 117 optimal weight:    4.9990
   chunk 116 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** B 506 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 = 0.3540 r_free = 0.3540 target = 0.130105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.101307 restraints weight = 41857.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.03
r_work: 0.3031 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11885  Z= 0.152
  Angle     :  0.488  12.410  16259  Z= 0.241
  Chirality :  0.037   0.148   1845
  Planarity :  0.004   0.075   1937
  Dihedral  : 14.018 143.040   2139
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.86 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 14.76 %
    Favored  : 84.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.76 (0.24), residues: 1348
  helix:  1.91 (0.24), residues: 531
  sheet: -0.99 (0.41), residues: 147
  loop : -0.24 (0.24), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 239 
 HIS   0.003   0.001   HIS A 367 
 PHE   0.011   0.001   PHE C 161 
 TYR   0.009   0.001   TYR A 403 
 ARG   0.010   0.000   ARG A 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03432 (  487)
  hydrogen bonds       : angle       4.16431 ( 1366)
  metal coordination   : bond        0.01143 (   12)
  metal coordination   : angle       6.78391 (    8)
  covalent geometry    : bond        0.00357 (11873)
  covalent geometry    : angle       0.46430 (16251)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 1.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 ASP cc_start: 0.8351 (t0) cc_final: 0.7855 (t70)
REVERT: B  148 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8280 (mt-10)
REVERT: B  159 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8525 (mt)
REVERT: C   59 LEU cc_start: 0.8927 (mt) cc_final: 0.8607 (mt)
REVERT: C  343 ASP cc_start: 0.8437 (t0) cc_final: 0.8161 (t0)
REVERT: C  358 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7077 (mm-30)
REVERT: C  389 ARG cc_start: 0.8357 (mmt180) cc_final: 0.8008 (mmt180)
  outliers start: 14
  outliers final: 9
  residues processed: 129
  average time/residue: 0.8357
  time to fit residues: 137.9060
Evaluate side-chains
  121 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 1.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  146 CYS
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  185 MET
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  342 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 111 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 124 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 121 optimal weight:    2.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 506 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 = 0.3525 r_free = 0.3525 target = 0.128962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.100194 restraints weight = 41741.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 2.01
r_work: 0.3011 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11885  Z= 0.202
  Angle     :  0.522  14.297  16259  Z= 0.257
  Chirality :  0.038   0.146   1845
  Planarity :  0.004   0.076   1937
  Dihedral  : 14.074 141.903   2139
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.82 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.19 %
    Favored  : 83.26 %
  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:  0.59 (0.23), residues: 1348
  helix:  1.75 (0.23), residues: 531
  sheet: -1.13 (0.40), residues: 147
  loop : -0.31 (0.24), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 239 
 HIS   0.004   0.001   HIS B 208 
 PHE   0.012   0.001   PHE C 161 
 TYR   0.010   0.001   TYR A 403 
 ARG   0.011   0.000   ARG A 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03742 (  487)
  hydrogen bonds       : angle       4.26628 ( 1366)
  metal coordination   : bond        0.01404 (   12)
  metal coordination   : angle       7.71341 (    8)
  covalent geometry    : bond        0.00472 (11873)
  covalent geometry    : angle       0.49327 (16251)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 1.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 ASP cc_start: 0.8341 (t0) cc_final: 0.7823 (t70)
REVERT: B  148 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8315 (mt-10)
REVERT: B  159 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8573 (mt)
REVERT: C   59 LEU cc_start: 0.8937 (mt) cc_final: 0.8654 (mt)
REVERT: C  343 ASP cc_start: 0.8441 (t0) cc_final: 0.8140 (t0)
REVERT: C  358 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7146 (mm-30)
REVERT: C  389 ARG cc_start: 0.8373 (mmt180) cc_final: 0.8000 (mmt180)
  outliers start: 18
  outliers final: 14
  residues processed: 123
  average time/residue: 0.8509
  time to fit residues: 133.6783
Evaluate side-chains
  126 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 1.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  146 CYS
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  185 MET
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  342 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9980
   chunk 106 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 74 optimal weight:    0.5980
   chunk 136 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 123 optimal weight:    0.2980
   chunk 2 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  50 ASN
** B 506 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 = 0.3616 r_free = 0.3616 target = 0.134196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.106062 restraints weight = 42911.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 1.97
r_work: 0.3124 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11885  Z= 0.113
  Angle     :  0.472  11.826  16259  Z= 0.233
  Chirality :  0.036   0.142   1845
  Planarity :  0.004   0.078   1937
  Dihedral  : 13.956 141.563   2139
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.01 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 15.54 %
    Favored  : 83.00 %
  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:  0.79 (0.24), residues: 1348
  helix:  1.96 (0.24), residues: 531
  sheet: -1.09 (0.41), residues: 147
  loop : -0.22 (0.25), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 239 
 HIS   0.003   0.001   HIS A 367 
 PHE   0.010   0.001   PHE C 161 
 TYR   0.008   0.001   TYR A 403 
 ARG   0.013   0.000   ARG A 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03195 (  487)
  hydrogen bonds       : angle       4.07176 ( 1366)
  metal coordination   : bond        0.00886 (   12)
  metal coordination   : angle       6.44446 (    8)
  covalent geometry    : bond        0.00260 (11873)
  covalent geometry    : angle       0.45039 (16251)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 1.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 ASP cc_start: 0.8253 (t0) cc_final: 0.7894 (t70)
REVERT: B  159 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8663 (mt)
REVERT: C   59 LEU cc_start: 0.9017 (mt) cc_final: 0.8739 (mt)
REVERT: C  343 ASP cc_start: 0.8504 (t0) cc_final: 0.8232 (t0)
REVERT: C  346 LYS cc_start: 0.8164 (mttt) cc_final: 0.7889 (mttt)
REVERT: C  389 ARG cc_start: 0.8392 (mmt180) cc_final: 0.8046 (mmt180)
  outliers start: 17
  outliers final: 14
  residues processed: 124
  average time/residue: 0.8301
  time to fit residues: 131.7439
Evaluate side-chains
  124 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 1.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  146 CYS
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  185 MET
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  342 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 111 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 114 optimal weight:    0.8980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A  50 ASN
** B 506 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 = 0.3609 r_free = 0.3609 target = 0.133731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.105484 restraints weight = 42867.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.97
r_work: 0.3117 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11885  Z= 0.145
  Angle     :  0.484  11.612  16259  Z= 0.240
  Chirality :  0.037   0.143   1845
  Planarity :  0.004   0.071   1937
  Dihedral  : 13.958 140.871   2139
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 15.88 %
    Favored  : 82.75 %
  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:  0.76 (0.24), residues: 1348
  helix:  1.95 (0.24), residues: 531
  sheet: -1.17 (0.41), residues: 149
  loop : -0.23 (0.25), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 239 
 HIS   0.003   0.001   HIS A 367 
 PHE   0.010   0.001   PHE C 161 
 TYR   0.009   0.001   TYR A 403 
 ARG   0.010   0.000   ARG A 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03337 (  487)
  hydrogen bonds       : angle       4.09009 ( 1366)
  metal coordination   : bond        0.01037 (   12)
  metal coordination   : angle       6.42322 (    8)
  covalent geometry    : bond        0.00340 (11873)
  covalent geometry    : angle       0.46314 (16251)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 1.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 ASP cc_start: 0.8277 (t0) cc_final: 0.7897 (t70)
REVERT: B  148 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8327 (mt-10)
REVERT: B  159 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8655 (mt)
REVERT: C  187 ASP cc_start: 0.6134 (t0) cc_final: 0.5875 (t0)
REVERT: C  343 ASP cc_start: 0.8514 (t0) cc_final: 0.8271 (t0)
REVERT: C  346 LYS cc_start: 0.8158 (mttt) cc_final: 0.7896 (mttt)
REVERT: C  358 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7278 (mm-30)
REVERT: C  389 ARG cc_start: 0.8382 (mmt180) cc_final: 0.8028 (mmt180)
  outliers start: 16
  outliers final: 13
  residues processed: 122
  average time/residue: 0.8410
  time to fit residues: 130.9221
Evaluate side-chains
  123 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 1.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  146 CYS
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  185 MET
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  342 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 113 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 111 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 81 optimal weight:    0.3980
   chunk 102 optimal weight:    4.9990
   chunk 125 optimal weight:    0.0980
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A  50 ASN
** B 506 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 = 0.3619 r_free = 0.3619 target = 0.134470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.106289 restraints weight = 42808.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.97
r_work: 0.3127 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11885  Z= 0.125
  Angle     :  0.471  10.874  16259  Z= 0.233
  Chirality :  0.036   0.142   1845
  Planarity :  0.004   0.096   1937
  Dihedral  : 13.917 139.937   2139
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 15.71 %
    Favored  : 82.92 %
  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:  0.82 (0.24), residues: 1348
  helix:  2.03 (0.24), residues: 531
  sheet: -1.19 (0.41), residues: 149
  loop : -0.19 (0.25), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 239 
 HIS   0.003   0.001   HIS A 367 
 PHE   0.010   0.001   PHE C 161 
 TYR   0.009   0.001   TYR A 403 
 ARG   0.014   0.000   ARG A 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03177 (  487)
  hydrogen bonds       : angle       4.02809 ( 1366)
  metal coordination   : bond        0.00912 (   12)
  metal coordination   : angle       6.01658 (    8)
  covalent geometry    : bond        0.00294 (11873)
  covalent geometry    : angle       0.45198 (16251)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 1.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 ASP cc_start: 0.8259 (t0) cc_final: 0.7889 (t70)
REVERT: B  159 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8650 (mt)
REVERT: C  111 ARG cc_start: 0.7291 (ptp90) cc_final: 0.6890 (ptt-90)
REVERT: C  343 ASP cc_start: 0.8518 (t0) cc_final: 0.8264 (t0)
REVERT: C  346 LYS cc_start: 0.8166 (mttt) cc_final: 0.7897 (mttt)
REVERT: C  389 ARG cc_start: 0.8402 (mmt180) cc_final: 0.8051 (mmt180)
  outliers start: 16
  outliers final: 15
  residues processed: 120
  average time/residue: 0.8299
  time to fit residues: 128.5607
Evaluate side-chains
  123 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 1.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  146 CYS
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  185 MET
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  342 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0970
   chunk 34 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 30 optimal weight:    0.3980
   chunk 131 optimal weight:    3.9990
   chunk 91 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
** B 506 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 = 0.3617 r_free = 0.3617 target = 0.134198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.105986 restraints weight = 42856.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.97
r_work: 0.3128 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.214  11885  Z= 0.200
  Angle     :  0.781  59.194  16259  Z= 0.444
  Chirality :  0.038   0.468   1845
  Planarity :  0.004   0.092   1937
  Dihedral  : 13.917 139.924   2139
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 15.62 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.08 %
  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:  0.83 (0.24), residues: 1348
  helix:  2.03 (0.24), residues: 531
  sheet: -1.18 (0.40), residues: 149
  loop : -0.19 (0.25), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 239 
 HIS   0.003   0.001   HIS A 367 
 PHE   0.009   0.001   PHE C  44 
 TYR   0.008   0.001   TYR A 403 
 ARG   0.012   0.000   ARG A 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03149 (  487)
  hydrogen bonds       : angle       4.02779 ( 1366)
  metal coordination   : bond        0.04471 (   12)
  metal coordination   : angle      11.04318 (    8)
  covalent geometry    : bond        0.00419 (11873)
  covalent geometry    : angle       0.74137 (16251)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 1.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 ASP cc_start: 0.8254 (t0) cc_final: 0.7887 (t70)
REVERT: B  148 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8302 (mt-10)
REVERT: B  159 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8646 (mt)
REVERT: C  111 ARG cc_start: 0.7290 (ptp90) cc_final: 0.6897 (ptt-90)
REVERT: C  343 ASP cc_start: 0.8520 (t0) cc_final: 0.8263 (t0)
REVERT: C  346 LYS cc_start: 0.8162 (mttt) cc_final: 0.7892 (mttt)
REVERT: C  389 ARG cc_start: 0.8401 (mmt180) cc_final: 0.8049 (mmt180)
  outliers start: 16
  outliers final: 14
  residues processed: 119
  average time/residue: 0.8857
  time to fit residues: 136.0990
Evaluate side-chains
  123 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 1.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  146 CYS
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  185 MET
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  342 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 104 optimal weight:    2.9990
   chunk 91 optimal weight:    0.4980
   chunk 32 optimal weight:    0.0870
   chunk 56 optimal weight:    0.6980
   chunk 94 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 115 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0570
   chunk 34 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.4676

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

Flipped N/Q/H residues before XYZ refinement:
** A  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 506 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 = 0.3621 r_free = 0.3621 target = 0.134470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.106238 restraints weight = 42792.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.96
r_work: 0.3128 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.214  11885  Z= 0.200
  Angle     :  0.781  59.194  16259  Z= 0.444
  Chirality :  0.038   0.468   1845
  Planarity :  0.004   0.092   1937
  Dihedral  : 13.917 139.924   2139
  Min Nonbonded Distance : 1.193

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 15.71 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.08 %
  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:  0.83 (0.24), residues: 1348
  helix:  2.03 (0.24), residues: 531
  sheet: -1.18 (0.40), residues: 149
  loop : -0.19 (0.25), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 239 
 HIS   0.003   0.001   HIS A 367 
 PHE   0.009   0.001   PHE C  44 
 TYR   0.008   0.001   TYR A 403 
 ARG   0.012   0.000   ARG A 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03149 (  487)
  hydrogen bonds       : angle       4.02779 ( 1366)
  metal coordination   : bond        0.04471 (   12)
  metal coordination   : angle      11.04318 (    8)
  covalent geometry    : bond        0.00419 (11873)
  covalent geometry    : angle       0.74137 (16251)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11096.36 seconds
wall clock time: 190 minutes 44.77 seconds (11444.77 seconds total)