Starting phenix.real_space_refine
on Mon May 19 06:37:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ptj_17872/05_2025/8ptj_17872.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ptj_17872/05_2025/8ptj_17872.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ptj_17872/05_2025/8ptj_17872.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ptj_17872/05_2025/8ptj_17872.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ptj_17872/05_2025/8ptj_17872.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ptj_17872/05_2025/8ptj_17872.cif"
  }
  resolution = 2.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      18      5.49       5
     S      54      5.16       5
     C    5616      2.51       5
     N    1587      2.21       5
     O    1757      1.98       5
     H    8841      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 17874
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 6651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 417, 6651
          Classifications: {'peptide': 417}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 394}
    Chain: "B"
      Number of atoms: 7862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 511, 7862
          Classifications: {'peptide': 511}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 490}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 2792
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 8, 'TRANS': 165}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 285
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 6, 192
          Classifications: {'RNA': 6}
          Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pyr': 1}
          Link IDs: {'rna2p': 4, 'rna3p': 1}
      Conformer: "B"
        Number of residues, atoms: 6, 192
          Classifications: {'RNA': 6}
          Modifications used: {'3*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 2, 'rna3p': 3}
          bond proxies already assigned to first conformer: 106
    Chain: "V"
      Number of atoms: 281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 281
          Classifications: {'RNA': 9}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 1, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 5, 'rna3p': 3}
    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: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2584  SG  CYS A 161      45.530  46.138  18.978  1.00 67.01           S
  ATOM   4472  SG  CYS A 282      43.431  44.368  16.160  1.00 66.74           S

  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" P  A  A D  12 " occ=0.60
      ... (64 atoms not shown)
      pdb=" H2 B  A D  12 " occ=0.40
    residue:
      pdb=" P  A  U D  13 " occ=0.60
      ... (58 atoms not shown)
      pdb=" H6 B  U D  13 " occ=0.40
    residue:
      pdb=" P  A  U D  14 " occ=0.60
      ... (58 atoms not shown)
      pdb=" H6 B  U D  14 " occ=0.40
  Time building chain proxies: 8.37, per 1000 atoms: 0.47
  Number of scatterers: 17874
  At special positions: 0
  Unit cell: (88.2, 87.36, 123.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      54     16.00
     P      18     15.00
     O    1757      8.00
     N    1587      7.00
     C    5616      6.00
     H    8841      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: 4.98
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" ND1 HIS A 284 "
        pdb="ZN    ZN A 501 " - pdb=" NE2 HIS A 296 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 161 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 282 "
      Number of angles added : 2


  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2078

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 13 sheets defined
      45.0% alpha, 12.3% beta
      2 base pairs and 4 stacking pairs defined.
    Time for finding SS restraints: 7.76
  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
      removed outlier: 3.931A  pdb=" N   CYS A  13 " --> pdb=" O   THR A   9 " (cutoff:3.500A)
    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
    Processing helix  chain 'A' and resid 162 through 169
      removed outlier: 3.719A  pdb=" N   GLY A 168 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 189
    Processing helix  chain 'A' and resid 223 through 235
    Processing helix  chain 'A' and resid 301 through 310
    Processing helix  chain 'A' and resid 312 through 323
      removed outlier: 4.395A  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 373
      removed outlier: 3.866A  pdb=" N   ALA A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 386
      removed outlier: 3.669A  pdb=" N   TYR A 386 " --> pdb=" O   ARG A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 392
      removed outlier: 3.617A  pdb=" N   ILE A 392 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 415
    Processing helix  chain 'B' and resid 1 through 5
      removed outlier: 3.713A  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 66 through 70
      removed outlier: 3.769A  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 118
    Processing helix  chain 'B' and resid 129 through 138
      removed outlier: 3.651A  pdb=" N   ARG B 138 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 183
    Processing helix  chain 'B' and resid 184 through 187
    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 269 through 281
      removed outlier: 3.824A  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: 3.562A  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: 3.589A  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 436
      removed outlier: 3.999A  pdb=" N   GLN B 434 " --> pdb=" O   PHE B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 455
    Processing helix  chain 'B' and resid 479 through 497
    Processing helix  chain 'B' and resid 506 through 514
    Processing helix  chain 'C' and resid 3 through 8
    Processing helix  chain 'C' and resid 16 through 24
    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 sheet with id=AA1, first strand: chain 'A' and resid 25 through 27
      removed outlier: 6.387A  pdb=" N   TRP A  52 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   CYS A  71 " --> pdb=" O   TRP A  52 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ALA A  54 " --> pdb=" O   CYS A  71 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   LEU A  73 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   GLU A  56 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 137
    Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194
      removed outlier: 7.592A  pdb=" N   TRP A 198 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   MET A 255 " --> pdb=" O   TRP A 198 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   GLN A 200 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194
      removed outlier: 7.592A  pdb=" N   TRP A 198 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   MET A 255 " --> pdb=" O   TRP A 198 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   GLN A 200 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   LEU A 277 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 80
    Processing sheet with id=AA6, first strand: chain 'B' and resid 155 through 159
      removed outlier: 7.083A  pdb=" N   PHE B 140 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 208 through 209
    Processing sheet with id=AA8, first strand: chain 'B' and resid 212 through 213
    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 478
    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 83
    Processing sheet with id=AB4, first strand: chain 'C' and resid 385 through 388
      removed outlier: 6.501A  pdb=" N   MET C 415 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA C 414 " --> pdb=" O   CYS C 409 " (cutoff:3.500A)

    398 hydrogen bonds defined for protein.
    1083 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      4 hydrogen bonds
      8 hydrogen bond angles
      0 basepair planarities
      2 basepair parallelities
      6 stacking parallelities
  Total time for adding SS restraints: 5.99

  Time building geometry restraints manager: 5.88 seconds

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

  Histogram of bond lengths:
        0.84 -     1.05: 8811
        1.05 -     1.25: 1477
        1.25 -     1.46: 3622
        1.46 -     1.67: 4094
        1.67 -     1.88: 77
  Bond restraints: 18081
  Sorted by residual:
  bond pdb=" O3'B  U D  14 "
       pdb=" P     U D  15 "
    ideal  model  delta    sigma   weight residual
    1.607  1.879 -0.272 1.50e-02 4.44e+03 3.28e+02
  bond pdb=" N   GLN C  88 "
       pdb=" CA  GLN C  88 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.17e-02 7.31e+03 7.74e+00
  bond pdb=" N   ILE C  92 "
       pdb=" CA  ILE C  92 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.19e-02 7.06e+03 7.42e+00
  bond pdb=" N   THR C  87 "
       pdb=" H   THR C  87 "
    ideal  model  delta    sigma   weight residual
    0.860  0.914 -0.054 2.00e-02 2.50e+03 7.39e+00
  bond pdb=" N   THR C  87 "
       pdb=" CA  THR C  87 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 1.31e-02 5.83e+03 7.32e+00
  ... (remaining 18076 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 32182
        1.54 -     3.08: 409
        3.08 -     4.62: 53
        4.62 -     6.17: 6
        6.17 -     7.71: 1
  Bond angle restraints: 32651
  Sorted by residual:
  angle pdb=" O3'B  U D  14 "
        pdb=" P     U D  15 "
        pdb=" O5'   U D  15 "
      ideal   model   delta    sigma   weight residual
     104.00   96.29    7.71 1.50e+00 4.44e-01 2.64e+01
  angle pdb=" C3'B  U D  14 "
        pdb=" O3'B  U D  14 "
        pdb=" P     U D  15 "
      ideal   model   delta    sigma   weight residual
     120.20  126.06   -5.86 1.50e+00 4.44e-01 1.52e+01
  angle pdb=" CA  THR C  87 "
        pdb=" C   THR C  87 "
        pdb=" O   THR C  87 "
      ideal   model   delta    sigma   weight residual
     121.81  117.61    4.20 1.18e+00 7.18e-01 1.27e+01
  angle pdb=" C   GLU C  90 "
        pdb=" N   ALA C  91 "
        pdb=" CA  ALA C  91 "
      ideal   model   delta    sigma   weight residual
     120.54  125.25   -4.71 1.35e+00 5.49e-01 1.22e+01
  angle pdb=" C   GLN C  88 "
        pdb=" N   GLU C  89 "
        pdb=" CA  GLU C  89 "
      ideal   model   delta    sigma   weight residual
     120.54  125.19   -4.65 1.35e+00 5.49e-01 1.18e+01
  ... (remaining 32646 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 7491
       17.80 -    35.60: 678
       35.60 -    53.39: 267
       53.39 -    71.19: 72
       71.19 -    88.99: 20
  Dihedral angle restraints: 8528
    sinusoidal: 4821
      harmonic: 3707
  Sorted by residual:
  dihedral pdb=" CA  SER A  19 "
           pdb=" C   SER A  19 "
           pdb=" N   GLU A  20 "
           pdb=" CA  GLU A  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.81   17.19     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  ASP B 213 "
           pdb=" CB  ASP B 213 "
           pdb=" CG  ASP B 213 "
           pdb=" OD1 ASP B 213 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.21   56.21     1      2.00e+01 2.50e-03 1.07e+01
  dihedral pdb=" CB  GLU B  29 "
           pdb=" CG  GLU B  29 "
           pdb=" CD  GLU B  29 "
           pdb=" OE1 GLU B  29 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.51  -88.51     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 8525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1008
       0.032 -    0.063: 298
       0.063 -    0.095: 68
       0.095 -    0.126: 50
       0.126 -    0.158: 3
  Chirality restraints: 1427
  Sorted by residual:
  chirality pdb=" CA  ILE C  92 "
            pdb=" N   ILE C  92 "
            pdb=" C   ILE C  92 "
            pdb=" CB  ILE C  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.25e-01
  chirality pdb=" CA  LEU C  86 "
            pdb=" N   LEU C  86 "
            pdb=" C   LEU C  86 "
            pdb=" CB  LEU C  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.01e-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 4.04e-01
  ... (remaining 1424 not shown)

  Planarity restraints: 2600
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  34 "   -0.203 9.50e-02 1.11e+02   6.80e-02 5.70e+00
        pdb=" NE  ARG A  34 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  34 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  34 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  34 "    0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG A  34 "    0.006 2.00e-02 2.50e+03
        pdb="HH12 ARG A  34 "   -0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG A  34 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A  34 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 217 "   -0.023 5.00e-02 4.00e+02   3.46e-02 1.91e+00
        pdb=" N   PRO A 218 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 218 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 218 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A V   4 "    0.019 2.00e-02 2.50e+03   7.50e-03 1.83e+00
        pdb=" N9    A V   4 "   -0.017 2.00e-02 2.50e+03
        pdb=" C8    A V   4 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A V   4 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    A V   4 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A V   4 "    0.003 2.00e-02 2.50e+03
        pdb=" N6    A V   4 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    A V   4 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    A V   4 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A V   4 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A V   4 "   -0.005 2.00e-02 2.50e+03
        pdb=" H8    A V   4 "   -0.001 2.00e-02 2.50e+03
        pdb=" H2    A V   4 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2597 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 538
        2.14 -     2.76: 33099
        2.76 -     3.37: 50583
        3.37 -     3.99: 66482
        3.99 -     4.60: 103404
  Nonbonded interactions: 254106
  Sorted by model distance:
  nonbonded pdb="HG21 THR A 236 "
            pdb=" OP1B  U D  13 "
     model   vdw
     1.529 2.620
  nonbonded pdb=" OE1 GLU B 119 "
            pdb=" H   GLU B 119 "
     model   vdw
     1.532 2.450
  nonbonded pdb=" O   SER A 128 "
            pdb="HD22 ASN B  44 "
     model   vdw
     1.592 2.450
  nonbonded pdb=" OE1 GLU B 381 "
            pdb=" H   PHE B 420 "
     model   vdw
     1.620 2.450
  nonbonded pdb=" O   PHE A  55 "
            pdb="HH11 ARG A  62 "
     model   vdw
     1.642 2.450
  ... (remaining 254101 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=0.40 max=1.00 mean=0.99
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:             1.150
  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:             0.300
  Extract box with map and model:          0.650
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     50.220
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  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:10.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   63.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8892
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      :  0.004   0.272   9244  Z= 0.232
  Angle     :  0.485   7.708  12561  Z= 0.273
  Chirality :  0.036   0.158   1427
  Planarity :  0.004   0.089   1550
  Dihedral  : 17.879  88.990   3586
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 20.38 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.27), residues: 1090
  helix:  2.18 (0.26), residues: 446
  sheet: -0.21 (0.53), residues: 99
  loop : -0.16 (0.27), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 
 PHE   0.018   0.001   PHE B 407 
 TYR   0.008   0.001   TYR A 403 
 ARG   0.014   0.000   ARG A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13896 (  398)
  hydrogen bonds       : angle       4.94562 ( 1091)
  metal coordination   : bond        0.00051 (    4)
  metal coordination   : angle       0.84953 (    2)
  covalent geometry    : bond        0.00378 ( 9240)
  covalent geometry    : angle       0.48452 (12559)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 1.515 
Fit side-chains
   revert: symmetry clash
REVERT: C   18 GLU cc_start: 0.8886 (tt0) cc_final: 0.8686 (tt0)
REVERT: C   89 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7729 (tm-30)
REVERT: C   93 ASP cc_start: 0.8323 (m-30) cc_final: 0.7928 (m-30)
REVERT: C  113 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.8029 (t)
  outliers start: 27
  outliers final: 23
  residues processed: 124
  average time/residue: 2.5240
  time to fit residues: 335.5008
Evaluate side-chains
  118 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 1.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  381 GLU
Chi-restraints excluded: chain B residue  402 THR
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  123 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 98 optimal weight:    0.7980
   overall best weight:    1.2986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.098020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.074918 restraints weight = 51236.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.2748 rms_B_bonded: 2.19
r_work: 0.2636 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2521 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2521
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2511
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2511 r_free = 0.2511    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2510 r_free = 0.2510    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2510
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8910
moved from start:          0.0660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9244  Z= 0.169
  Angle     :  0.490   5.236  12561  Z= 0.255
  Chirality :  0.037   0.132   1427
  Planarity :  0.004   0.040   1550
  Dihedral  : 10.660  73.557   1508
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 1.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 19.54 %
    Favored  : 77.53 %
  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:  1.08 (0.26), residues: 1090
  helix:  2.10 (0.25), residues: 451
  sheet: -0.30 (0.52), residues: 107
  loop : -0.24 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 
 PHE   0.020   0.001   PHE B 407 
 TYR   0.011   0.001   TYR A 403 
 ARG   0.006   0.000   ARG A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04669 (  398)
  hydrogen bonds       : angle       4.16078 ( 1091)
  metal coordination   : bond        0.00588 (    4)
  metal coordination   : angle       0.81929 (    2)
  covalent geometry    : bond        0.00384 ( 9240)
  covalent geometry    : angle       0.48945 (12559)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 1.433 
Fit side-chains
REVERT: A   34 ARG cc_start: 0.7528 (ttp-110) cc_final: 0.7192 (ttp-110)
REVERT: A  323 ASP cc_start: 0.8546 (t0) cc_final: 0.8220 (t0)
REVERT: A  326 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7973 (tm-30)
REVERT: B  497 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8351 (tp)
REVERT: C   93 ASP cc_start: 0.8561 (m-30) cc_final: 0.8298 (m-30)
REVERT: C  113 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8130 (t)
  outliers start: 28
  outliers final: 14
  residues processed: 120
  average time/residue: 2.7000
  time to fit residues: 346.8596
Evaluate side-chains
  113 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 1.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain B residue   57 GLN
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  213 ASP
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  388 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
C 124 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.096268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.073208 restraints weight = 49594.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.2726 rms_B_bonded: 2.14
r_work: 0.2616 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2500 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2500
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2489
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2489 r_free = 0.2489    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2489 r_free = 0.2489    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2489
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8930
moved from start:          0.0943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9244  Z= 0.217
  Angle     :  0.513   4.315  12561  Z= 0.269
  Chirality :  0.039   0.132   1427
  Planarity :  0.004   0.038   1550
  Dihedral  : 10.451  73.597   1488
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 1.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 19.64 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.89 (0.26), residues: 1090
  helix:  1.96 (0.25), residues: 450
  sheet: -0.45 (0.51), residues: 107
  loop : -0.35 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 346 
 HIS   0.005   0.001   HIS B 174 
 PHE   0.023   0.001   PHE B 407 
 TYR   0.011   0.001   TYR A 403 
 ARG   0.003   0.000   ARG A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04959 (  398)
  hydrogen bonds       : angle       4.11771 ( 1091)
  metal coordination   : bond        0.01116 (    4)
  metal coordination   : angle       0.55472 (    2)
  covalent geometry    : bond        0.00505 ( 9240)
  covalent geometry    : angle       0.51271 (12559)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 1.437 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7540 (mtm180)
REVERT: A  323 ASP cc_start: 0.8669 (t0) cc_final: 0.8261 (t0)
REVERT: A  326 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8017 (tm-30)
REVERT: C  113 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8109 (t)
  outliers start: 28
  outliers final: 16
  residues processed: 123
  average time/residue: 2.7727
  time to fit residues: 364.1978
Evaluate side-chains
  116 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 1.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ARG
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain B residue   57 GLN
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain C residue   83 ARG
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  388 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   overall best weight:    1.5986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.096258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.073083 restraints weight = 52162.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.2727 rms_B_bonded: 2.21
r_work: 0.2617 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2502 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2502
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2492
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2492 r_free = 0.2492    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2492 r_free = 0.2492    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2492
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8929
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9244  Z= 0.192
  Angle     :  0.498   4.257  12561  Z= 0.261
  Chirality :  0.038   0.130   1427
  Planarity :  0.004   0.038   1550
  Dihedral  : 10.234  73.593   1484
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 19.02 %
    Favored  : 77.22 %
  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:  0.87 (0.26), residues: 1090
  helix:  1.97 (0.25), residues: 450
  sheet: -0.43 (0.46), residues: 125
  loop : -0.38 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 346 
 HIS   0.005   0.001   HIS A 367 
 PHE   0.022   0.001   PHE B 407 
 TYR   0.011   0.001   TYR A 403 
 ARG   0.004   0.000   ARG A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04606 (  398)
  hydrogen bonds       : angle       4.05550 ( 1091)
  metal coordination   : bond        0.00808 (    4)
  metal coordination   : angle       0.67847 (    2)
  covalent geometry    : bond        0.00443 ( 9240)
  covalent geometry    : angle       0.49780 (12559)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 97
  time to evaluate  : 1.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ASP cc_start: 0.8629 (t0) cc_final: 0.8202 (t0)
REVERT: A  326 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8001 (tm-30)
REVERT: C  113 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8078 (t)
  outliers start: 36
  outliers final: 20
  residues processed: 122
  average time/residue: 2.8784
  time to fit residues: 373.2999
Evaluate side-chains
  118 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 1.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ARG
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain B residue   57 GLN
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  339 ASP
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain C residue   83 ARG
Chi-restraints excluded: chain C residue   89 GLU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  396 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0970
   chunk 94 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 86 optimal weight:    0.2980
   chunk 76 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
C 124 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.098537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.075707 restraints weight = 45794.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.2776 rms_B_bonded: 2.15
r_work: 0.2667 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2551 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2551
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2500
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2500 r_free = 0.2500    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2500 r_free = 0.2500    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2500
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8896
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   9244  Z= 0.100
  Angle     :  0.451   4.085  12561  Z= 0.235
  Chirality :  0.036   0.131   1427
  Planarity :  0.003   0.037   1550
  Dihedral  : 10.052  73.536   1484
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 19.75 %
    Favored  : 77.85 %
  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:  1.05 (0.26), residues: 1090
  helix:  2.17 (0.25), residues: 451
  sheet: -0.40 (0.46), residues: 125
  loop : -0.31 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.018   0.001   PHE B 407 
 TYR   0.009   0.001   TYR A 403 
 ARG   0.004   0.000   ARG A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03781 (  398)
  hydrogen bonds       : angle       3.86024 ( 1091)
  metal coordination   : bond        0.00076 (    4)
  metal coordination   : angle       0.81841 (    2)
  covalent geometry    : bond        0.00226 ( 9240)
  covalent geometry    : angle       0.45119 (12559)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 1.350 
Fit side-chains
   revert: symmetry clash
REVERT: A  323 ASP cc_start: 0.8354 (t0) cc_final: 0.7995 (t0)
REVERT: A  326 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7979 (tm-30)
REVERT: C  113 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.8070 (t)
  outliers start: 23
  outliers final: 14
  residues processed: 123
  average time/residue: 2.6738
  time to fit residues: 350.6434
Evaluate side-chains
  116 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 1.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain B residue   57 GLN
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  339 ASP
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain C residue   83 ARG
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  396 GLU
Chi-restraints excluded: chain C residue  419 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0980
   chunk 105 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 361 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.097474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.074464 restraints weight = 45032.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.2754 rms_B_bonded: 2.16
r_work: 0.2644 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2528 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2528
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2506
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2506 r_free = 0.2506    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2506 r_free = 0.2506    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2506
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8910
moved from start:          0.1233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9244  Z= 0.148
  Angle     :  0.469   4.290  12561  Z= 0.245
  Chirality :  0.037   0.129   1427
  Planarity :  0.004   0.038   1550
  Dihedral  :  9.992  73.604   1481
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.44 %
    Favored  : 77.53 %
  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:  1.02 (0.26), residues: 1090
  helix:  2.15 (0.25), residues: 450
  sheet: -0.42 (0.46), residues: 125
  loop : -0.34 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 
 PHE   0.020   0.001   PHE B 407 
 TYR   0.010   0.001   TYR A 403 
 ARG   0.005   0.000   ARG A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04123 (  398)
  hydrogen bonds       : angle       3.89413 ( 1091)
  metal coordination   : bond        0.00394 (    4)
  metal coordination   : angle       0.67164 (    2)
  covalent geometry    : bond        0.00343 ( 9240)
  covalent geometry    : angle       0.46904 (12559)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 1.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ASP cc_start: 0.8532 (t0) cc_final: 0.8154 (t0)
REVERT: A  326 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8012 (tm-30)
REVERT: C  113 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8078 (t)
  outliers start: 29
  outliers final: 17
  residues processed: 119
  average time/residue: 2.6532
  time to fit residues: 337.8120
Evaluate side-chains
  118 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain A residue  391 GLU
Chi-restraints excluded: chain B residue   57 GLN
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain C residue   83 ARG
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  396 GLU
Chi-restraints excluded: chain C residue  419 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
B 361 GLN
C 124 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.096066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.072428 restraints weight = 55474.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 2.37
r_work: 0.2589 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2471 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2447
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2447 r_free = 0.2447    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2447 r_free = 0.2447    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2447
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8943
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   9244  Z= 0.210
  Angle     :  0.504   4.392  12561  Z= 0.264
  Chirality :  0.038   0.130   1427
  Planarity :  0.004   0.040   1550
  Dihedral  : 10.093  73.600   1481
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 2.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.32 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 19.85 %
    Favored  : 77.32 %
  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:  0.90 (0.26), residues: 1090
  helix:  2.02 (0.25), residues: 450
  sheet: -0.47 (0.46), residues: 125
  loop : -0.38 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.005   0.001   HIS B 174 
 PHE   0.022   0.001   PHE B 407 
 TYR   0.010   0.001   TYR A 403 
 ARG   0.005   0.000   ARG A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04612 (  398)
  hydrogen bonds       : angle       4.01268 ( 1091)
  metal coordination   : bond        0.00939 (    4)
  metal coordination   : angle       0.54717 (    2)
  covalent geometry    : bond        0.00490 ( 9240)
  covalent geometry    : angle       0.50436 (12559)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 1.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ASP cc_start: 0.8642 (t0) cc_final: 0.8212 (t0)
REVERT: A  326 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8068 (tm-30)
REVERT: C  113 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.8109 (t)
  outliers start: 27
  outliers final: 18
  residues processed: 114
  average time/residue: 2.6812
  time to fit residues: 327.0255
Evaluate side-chains
  117 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain A residue  391 GLU
Chi-restraints excluded: chain B residue   57 GLN
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   83 ARG
Chi-restraints excluded: chain C residue   89 GLU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  419 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0020
   chunk 4 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.1994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.096969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.073963 restraints weight = 51402.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.2733 rms_B_bonded: 2.18
r_work: 0.2623 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2508 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2508
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2494
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2494 r_free = 0.2494    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2494 r_free = 0.2494    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2494
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8920
moved from start:          0.1322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9244  Z= 0.153
  Angle     :  0.476   4.608  12561  Z= 0.249
  Chirality :  0.037   0.130   1427
  Planarity :  0.004   0.039   1550
  Dihedral  : 10.073  73.592   1481
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.96 %
    Favored  : 77.01 %
  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:  0.96 (0.26), residues: 1090
  helix:  2.09 (0.25), residues: 450
  sheet: -0.47 (0.46), residues: 125
  loop : -0.35 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.021   0.001   PHE B 407 
 TYR   0.010   0.001   TYR A 403 
 ARG   0.006   0.000   ARG A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04213 (  398)
  hydrogen bonds       : angle       3.94471 ( 1091)
  metal coordination   : bond        0.00461 (    4)
  metal coordination   : angle       0.60714 (    2)
  covalent geometry    : bond        0.00353 ( 9240)
  covalent geometry    : angle       0.47646 (12559)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 1.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ASP cc_start: 0.8564 (t0) cc_final: 0.8169 (t0)
REVERT: A  326 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8020 (tm-30)
REVERT: C  113 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8100 (t)
  outliers start: 29
  outliers final: 21
  residues processed: 119
  average time/residue: 2.5140
  time to fit residues: 320.9151
Evaluate side-chains
  121 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 1.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain A residue  391 GLU
Chi-restraints excluded: chain B residue   57 GLN
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain C residue   83 ARG
Chi-restraints excluded: chain C residue   89 GLU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  396 GLU
Chi-restraints excluded: chain C residue  419 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    0.2980
   chunk 92 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
C 124 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.098370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.075150 restraints weight = 52089.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.2764 rms_B_bonded: 2.29
r_work: 0.2651 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2534 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2534
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2470
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2470 r_free = 0.2470    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2470 r_free = 0.2470    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2470
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8907
moved from start:          0.1332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9244  Z= 0.109
  Angle     :  0.454   4.764  12561  Z= 0.236
  Chirality :  0.036   0.130   1427
  Planarity :  0.003   0.039   1550
  Dihedral  :  9.997  73.564   1481
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 20.17 %
    Favored  : 77.32 %
  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:  1.09 (0.26), residues: 1090
  helix:  2.22 (0.25), residues: 451
  sheet: -0.43 (0.46), residues: 125
  loop : -0.30 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 367 
 PHE   0.019   0.001   PHE B 407 
 TYR   0.010   0.001   TYR A 403 
 ARG   0.006   0.000   ARG A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03725 (  398)
  hydrogen bonds       : angle       3.81578 ( 1091)
  metal coordination   : bond        0.00059 (    4)
  metal coordination   : angle       0.60519 (    2)
  covalent geometry    : bond        0.00248 ( 9240)
  covalent geometry    : angle       0.45412 (12559)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 1.366 
Fit side-chains
   revert: symmetry clash
REVERT: A  323 ASP cc_start: 0.8413 (t0) cc_final: 0.8064 (t0)
REVERT: A  326 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8020 (tm-30)
REVERT: C  113 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8086 (t)
  outliers start: 24
  outliers final: 17
  residues processed: 121
  average time/residue: 2.6611
  time to fit residues: 346.5301
Evaluate side-chains
  117 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain B residue   57 GLN
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain C residue   83 ARG
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  396 GLU
Chi-restraints excluded: chain C residue  419 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 361 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.098396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.075195 restraints weight = 52609.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 2.29
r_work: 0.2652 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2535 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2522
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2522 r_free = 0.2522    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2522 r_free = 0.2522    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2522
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8908
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9244  Z= 0.111
  Angle     :  0.453   4.539  12561  Z= 0.235
  Chirality :  0.036   0.129   1427
  Planarity :  0.004   0.039   1550
  Dihedral  :  9.949  73.576   1481
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.77 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.79 %
    Favored  : 77.12 %
  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:  1.12 (0.26), residues: 1090
  helix:  2.25 (0.25), residues: 451
  sheet: -0.40 (0.46), residues: 125
  loop : -0.29 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 367 
 PHE   0.019   0.001   PHE B 407 
 TYR   0.009   0.001   TYR A 403 
 ARG   0.006   0.000   ARG A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03726 (  398)
  hydrogen bonds       : angle       3.78887 ( 1091)
  metal coordination   : bond        0.00077 (    4)
  metal coordination   : angle       0.64429 (    2)
  covalent geometry    : bond        0.00254 ( 9240)
  covalent geometry    : angle       0.45332 (12559)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 1.484 
Fit side-chains
   revert: symmetry clash
REVERT: A  323 ASP cc_start: 0.8537 (t0) cc_final: 0.8172 (t0)
REVERT: A  326 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8022 (tm-30)
REVERT: C  113 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8086 (t)
  outliers start: 20
  outliers final: 15
  residues processed: 116
  average time/residue: 2.6806
  time to fit residues: 332.3954
Evaluate side-chains
  115 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 1.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain B residue   57 GLN
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain C residue   83 ARG
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  419 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0980
   chunk 12 optimal weight:    0.9980
   chunk 89 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
B 361 GLN
C 124 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.097200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.073582 restraints weight = 59945.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.2736 rms_B_bonded: 2.42
r_work: 0.2619 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2501 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2501
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2435
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2435 r_free = 0.2435    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2435 r_free = 0.2435    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2435
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8933
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9244  Z= 0.152
  Angle     :  0.475   6.220  12561  Z= 0.247
  Chirality :  0.037   0.129   1427
  Planarity :  0.004   0.039   1550
  Dihedral  :  9.998  73.594   1481
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 20.90 %
    Favored  : 77.12 %
  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 (0.26), residues: 1090
  helix:  2.19 (0.25), residues: 450
  sheet: -0.44 (0.46), residues: 125
  loop : -0.32 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 
 PHE   0.020   0.001   PHE B 407 
 TYR   0.010   0.001   TYR A 403 
 ARG   0.005   0.000   ARG A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04107 (  398)
  hydrogen bonds       : angle       3.87113 ( 1091)
  metal coordination   : bond        0.00473 (    4)
  metal coordination   : angle       0.61105 (    2)
  covalent geometry    : bond        0.00353 ( 9240)
  covalent geometry    : angle       0.47462 (12559)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12075.69 seconds
wall clock time: 206 minutes 57.84 seconds (12417.84 seconds total)