Starting phenix.real_space_refine
on Sat Aug 23 03:23:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v9u_31827/08_2025/7v9u_31827.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v9u_31827/08_2025/7v9u_31827.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v9u_31827/08_2025/7v9u_31827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v9u_31827/08_2025/7v9u_31827.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v9u_31827/08_2025/7v9u_31827.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v9u_31827/08_2025/7v9u_31827.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.060
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: 5
    Type Number    sf(0)   Gaussians
     P     209      5.49       5
     S      18      5.16       5
     C    5183      2.51       5
     N    1687      2.21       5
     O    2257      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9354
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2478
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2478
          Classifications: {'peptide': 309}
          Link IDs: {'PTRANS': 11, 'TRANS': 297}
    Chain: "B"
      Number of atoms: 2478
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2478
          Classifications: {'peptide': 309}
          Link IDs: {'PTRANS': 11, 'TRANS': 297}
    Chain: "D"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 808
          Classifications: {'DNA': 39}
          Link IDs: {'rna3p': 38}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 1205
          Classifications: {'RNA': 57}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 8, 'rna3p_pur': 22, 'rna3p_pyr': 24}
          Link IDs: {'rna2p': 11, 'rna3p': 45}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 176
          Classifications: {'RNA': 8}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 7}
    Chain: "C"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 808
          Classifications: {'DNA': 39}
          Link IDs: {'rna3p': 38}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 1225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 1225
          Classifications: {'RNA': 58}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 10, 'rna3p_pur': 21, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 14, 'rna3p': 43}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 176
          Classifications: {'RNA': 8}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 7}
  Time building chain proxies: 1.83, per 1000 atoms: 0.20
  Number of scatterers: 9354
  At special positions: 0
  Unit cell: (123.25, 153, 93.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     P     209     15.00
     O    2257      8.00
     N    1687      7.00
     C    5183      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 115.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1160

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 8 sheets defined
      58.6% alpha, 9.4% beta
      65 base pairs and 115 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 16
      removed outlier: 3.725A  pdb=" N   ASN A   8 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 31
    Processing helix  chain 'A' and resid 33 through 42
      removed outlier: 3.674A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   TYR A  42 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 47
      removed outlier: 3.645A  pdb=" N   PHE A  46 " --> pdb=" O   THR A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 83
      removed outlier: 3.521A  pdb=" N   ALA A  74 " --> pdb=" O   ARG A  70 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL A  79 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 87
      removed outlier: 3.905A  pdb=" N   LEU A  87 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 84 through 87'
    Processing helix  chain 'A' and resid 102 through 107
    Processing helix  chain 'A' and resid 108 through 110
      No H-bonds generated for 'chain 'A' and resid 108 through 110'
    Processing helix  chain 'A' and resid 129 through 137
      removed outlier: 3.728A  pdb=" N   PHE A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL A 135 " --> pdb=" O   LYS A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 140
      No H-bonds generated for 'chain 'A' and resid 138 through 140'
    Processing helix  chain 'A' and resid 142 through 154
    Processing helix  chain 'A' and resid 165 through 174
      removed outlier: 3.662A  pdb=" N   LEU A 169 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 186
      removed outlier: 3.644A  pdb=" N   ASP A 178 " --> pdb=" O   CYS A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 224
      removed outlier: 3.588A  pdb=" N   VAL A 209 " --> pdb=" O   SER A 205 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ASP A 214 " --> pdb=" O   VAL A 210 " (cutoff:3.500A)
      Proline residue:  A 221  - end of helix
      removed outlier: 3.998A  pdb=" N   GLY A 224 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 272
      removed outlier: 3.813A  pdb=" N   ILE A 263 " --> pdb=" O   LYS A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 284 through 292
      removed outlier: 3.732A  pdb=" N   ILE A 288 " --> pdb=" O   TRP A 284 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A 289 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   SER A 290 " --> pdb=" O   SER A 286 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL A 291 " --> pdb=" O   PHE A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 310
      removed outlier: 3.812A  pdb=" N   HIS A 296 " --> pdb=" O   ASP A 292 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ARG A 297 " --> pdb=" O   SER A 293 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   ARG A 298 " --> pdb=" O   LYS A 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 16
      removed outlier: 3.706A  pdb=" N   LEU B  15 " --> pdb=" O   ARG B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 30
    Processing helix  chain 'B' and resid 33 through 42
    Processing helix  chain 'B' and resid 43 through 47
      removed outlier: 3.544A  pdb=" N   PHE B  46 " --> pdb=" O   THR B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 84
      removed outlier: 3.576A  pdb=" N   ALA B  74 " --> pdb=" O   ARG B  70 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 87
      No H-bonds generated for 'chain 'B' and resid 85 through 87'
    Processing helix  chain 'B' and resid 102 through 107
      removed outlier: 3.508A  pdb=" N   ALA B 106 " --> pdb=" O   ILE B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 110
      No H-bonds generated for 'chain 'B' and resid 108 through 110'
    Processing helix  chain 'B' and resid 129 through 139
      removed outlier: 3.735A  pdb=" N   PHE B 133 " --> pdb=" O   ALA B 129 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   SER B 138 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LEU B 139 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 154
    Processing helix  chain 'B' and resid 165 through 174
      removed outlier: 3.653A  pdb=" N   LEU B 169 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 186
      removed outlier: 3.633A  pdb=" N   ASP B 178 " --> pdb=" O   CYS B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 220
      removed outlier: 3.644A  pdb=" N   VAL B 209 " --> pdb=" O   SER B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 223
      No H-bonds generated for 'chain 'B' and resid 221 through 223'
    Processing helix  chain 'B' and resid 257 through 272
      removed outlier: 4.795A  pdb=" N   ILE B 263 " --> pdb=" O   LYS B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 281
      removed outlier: 4.146A  pdb=" N   HIS B 280 " --> pdb=" O   GLU B 277 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL B 281 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 277 through 281'
    Processing helix  chain 'B' and resid 284 through 292
      removed outlier: 4.025A  pdb=" N   ILE B 288 " --> pdb=" O   TRP B 284 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU B 289 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   SER B 290 " --> pdb=" O   SER B 286 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL B 291 " --> pdb=" O   PHE B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 310
      removed outlier: 3.641A  pdb=" N   HIS B 296 " --> pdb=" O   ASP B 292 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ARG B 297 " --> pdb=" O   SER B 293 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ARG B 298 " --> pdb=" O   LYS B 294 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ILE B 303 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 53
      removed outlier: 3.784A  pdb=" N   ARG A  63 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 195
    Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 121
      removed outlier: 4.733A  pdb=" N   VAL A 226 " --> pdb=" O   GLU A 121 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243
    Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 55
      removed outlier: 3.951A  pdb=" N   ARG B  61 " --> pdb=" O   LYS B  55 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 195
      removed outlier: 3.575A  pdb=" N   PHE B 114 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 121
      removed outlier: 4.761A  pdb=" N   VAL B 226 " --> pdb=" O   GLU B 121 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 243

    226 hydrogen bonds defined for protein.
    645 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      163 hydrogen bonds
      294 hydrogen bond angles
      0 basepair planarities
      65 basepair parallelities
      115 stacking parallelities
  Total time for adding SS restraints: 1.12

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1851
        1.33 -     1.45: 3295
        1.45 -     1.57: 4394
        1.57 -     1.69: 408
        1.69 -     1.81: 26
  Bond restraints: 9974
  Sorted by residual:
  bond pdb=" C3'  DG C  73 "
       pdb=" O3'  DG C  73 "
    ideal  model  delta    sigma   weight residual
    1.422  1.462 -0.040 3.00e-02 1.11e+03 1.79e+00
  bond pdb=" C3'  DG D  73 "
       pdb=" O3'  DG D  73 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.69e+00
  bond pdb=" C4'  DC C  83 "
       pdb=" C3'  DC C  83 "
    ideal  model  delta    sigma   weight residual
    1.523  1.500  0.023 2.00e-02 2.50e+03 1.30e+00
  bond pdb=" CG1 ILE B 145 "
       pdb=" CD1 ILE B 145 "
    ideal  model  delta    sigma   weight residual
    1.513  1.470  0.043 3.90e-02 6.57e+02 1.21e+00
  bond pdb=" C3'   A G  66 "
       pdb=" O3'   A G  66 "
    ideal  model  delta    sigma   weight residual
    1.417  1.432 -0.015 1.50e-02 4.44e+03 1.06e+00
  ... (remaining 9969 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 13932
        1.51 -     3.01: 391
        3.01 -     4.52: 71
        4.52 -     6.02: 18
        6.02 -     7.53: 4
  Bond angle restraints: 14416
  Sorted by residual:
  angle pdb=" N   ILE B 278 "
        pdb=" CA  ILE B 278 "
        pdb=" C   ILE B 278 "
      ideal   model   delta    sigma   weight residual
     111.91  108.84    3.07 8.90e-01 1.26e+00 1.19e+01
  angle pdb=" N   TYR B 260 "
        pdb=" CA  TYR B 260 "
        pdb=" C   TYR B 260 "
      ideal   model   delta    sigma   weight residual
     113.43  109.51    3.92 1.26e+00 6.30e-01 9.68e+00
  angle pdb=" C3'   A G  66 "
        pdb=" O3'   A G  66 "
        pdb=" P     U G  67 "
      ideal   model   delta    sigma   weight residual
     120.20  124.27   -4.07 1.50e+00 4.44e-01 7.35e+00
  angle pdb=" C   ALA B 196 "
        pdb=" CA  ALA B 196 "
        pdb=" CB  ALA B 196 "
      ideal   model   delta    sigma   weight residual
     110.42  115.76   -5.34 1.99e+00 2.53e-01 7.20e+00
  angle pdb=" C2'   C G  65 "
        pdb=" C1'   C G  65 "
        pdb=" N1    C G  65 "
      ideal   model   delta    sigma   weight residual
     112.00  116.00   -4.00 1.50e+00 4.44e-01 7.10e+00
  ... (remaining 14411 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.98: 5363
       35.98 -    71.96: 622
       71.96 -   107.93: 46
      107.93 -   143.91: 8
      143.91 -   179.89: 13
  Dihedral angle restraints: 6052
    sinusoidal: 4248
      harmonic: 1804
  Sorted by residual:
  dihedral pdb=" O4'   U E  52 "
           pdb=" C1'   U E  52 "
           pdb=" N1    U E  52 "
           pdb=" C2    U E  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   47.39  152.61     1      1.50e+01 4.44e-03 8.06e+01
  dihedral pdb=" O4'   C E  15 "
           pdb=" C1'   C E  15 "
           pdb=" N1    C E  15 "
           pdb=" C2    C E  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   48.83  151.17     1      1.50e+01 4.44e-03 8.00e+01
  dihedral pdb=" O4'   U E  68 "
           pdb=" C1'   U E  68 "
           pdb=" N1    U E  68 "
           pdb=" C2    U E  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -30.80 -129.20     1      1.50e+01 4.44e-03 6.96e+01
  ... (remaining 6049 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1338
       0.039 -    0.079: 305
       0.079 -    0.118: 69
       0.118 -    0.157: 15
       0.157 -    0.197: 4
  Chirality restraints: 1731
  Sorted by residual:
  chirality pdb=" C3'   A E  66 "
            pdb=" C4'   A E  66 "
            pdb=" O3'   A E  66 "
            pdb=" C2'   A E  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.28   -0.20 2.00e-01 2.50e+01 9.66e-01
  chirality pdb=" C3'   A G  66 "
            pdb=" C4'   A G  66 "
            pdb=" O3'   A G  66 "
            pdb=" C2'   A G  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.29   -0.18 2.00e-01 2.50e+01 8.51e-01
  chirality pdb=" C1'   C E  65 "
            pdb=" O4'   C E  65 "
            pdb=" C2'   C E  65 "
            pdb=" N1    C E  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.30    0.17 2.00e-01 2.50e+01 7.12e-01
  ... (remaining 1728 not shown)

  Planarity restraints: 1057
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 236 "   -0.035 5.00e-02 4.00e+02   5.31e-02 4.51e+00
        pdb=" N   PRO A 237 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 237 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 237 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 220 "   -0.032 5.00e-02 4.00e+02   4.90e-02 3.85e+00
        pdb=" N   PRO B 221 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B 221 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 221 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A E  13 "    0.021 2.00e-02 2.50e+03   9.76e-03 2.62e+00
        pdb=" N9    A E  13 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8    A E  13 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    A E  13 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    A E  13 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A E  13 "    0.004 2.00e-02 2.50e+03
        pdb=" N6    A E  13 "    0.007 2.00e-02 2.50e+03
        pdb=" N1    A E  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A E  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A E  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A E  13 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1054 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 737
        2.72 -     3.27: 8464
        3.27 -     3.81: 16545
        3.81 -     4.36: 20877
        4.36 -     4.90: 31372
  Nonbonded interactions: 77995
  Sorted by model distance:
  nonbonded pdb=" O   THR A 301 "
            pdb=" OG  SER A 304 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" O   ASN B 142 "
            pdb=" OG  SER B 146 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" O   THR B 301 "
            pdb=" OG  SER B 304 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OD2 ASP A 292 "
            pdb=" OG  SER A 295 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O   SER A 218 "
            pdb=" O2'   G F   1 "
     model   vdw
     2.197 3.040
  ... (remaining 77990 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = (chain 'G' and resid 9 through 81)
}
ncs_group {
  reference = chain 'F'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  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:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.840
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
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   0.043   9974  Z= 0.186
  Angle     :  0.633   7.531  14416  Z= 0.336
  Chirality :  0.037   0.197   1731
  Planarity :  0.005   0.053   1057
  Dihedral  : 25.349 179.890   4892
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.53 (0.32), residues: 614
  helix: -0.90 (0.29), residues: 308
  sheet:  0.62 (0.69), residues: 62
  loop : -1.46 (0.36), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 297 
 TYR   0.011   0.001   TYR A 179 
 PHE   0.025   0.002   PHE B  92 
 TRP   0.015   0.003   TRP B 284 
 HIS   0.009   0.001   HIS B 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 9974)
  covalent geometry    : angle       0.63324 (14416)
  hydrogen bonds       : bond        0.12549 (  389)
  hydrogen bonds       : angle       4.88678 (  939)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 LYS cc_start: 0.6634 (pttp) cc_final: 0.6325 (mtmm)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1097
  time to fit residues: 8.7961
Evaluate side-chains
  50 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0010
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    1.1788

-------------------------------------------------------------------------------
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 = 0.4426 r_free = 0.4426 target = 0.187650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.145377 restraints weight = 15069.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 1.67
r_work: 0.3688 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.0748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9974  Z= 0.157
  Angle     :  0.601   6.867  14416  Z= 0.314
  Chirality :  0.037   0.233   1731
  Planarity :  0.005   0.049   1057
  Dihedral  : 27.289 179.797   3650
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  8.51 %
    Favored  : 91.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.11 (0.32), residues: 614
  helix: -0.41 (0.29), residues: 312
  sheet:  0.73 (0.69), residues: 62
  loop : -1.47 (0.36), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 282 
 TYR   0.015   0.001   TYR A 302 
 PHE   0.016   0.002   PHE B  92 
 TRP   0.007   0.002   TRP B  78 
 HIS   0.006   0.001   HIS B 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9974)
  covalent geometry    : angle       0.60094 (14416)
  hydrogen bonds       : bond        0.04934 (  389)
  hydrogen bonds       : angle       3.59394 (  939)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: B   56 LYS cc_start: 0.7380 (pttp) cc_final: 0.6716 (tmtt)
REVERT: B  282 ARG cc_start: 0.7466 (mtm-85) cc_final: 0.7218 (mtm-85)
  outliers start: 2
  outliers final: 1
  residues processed: 57
  average time/residue: 0.1365
  time to fit residues: 10.1369
Evaluate side-chains
  50 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  202 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 52 optimal weight:    0.5980
   chunk 17 optimal weight:    3.9990
   chunk 51 optimal weight:    0.3980
   chunk 36 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.9584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.188005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.145252 restraints weight = 14881.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 1.60
r_work: 0.3708 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.1029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9974  Z= 0.139
  Angle     :  0.572   6.931  14416  Z= 0.299
  Chirality :  0.036   0.229   1731
  Planarity :  0.004   0.047   1057
  Dihedral  : 27.175 179.999   3650
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 12.14 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.81 (0.33), residues: 614
  helix: -0.08 (0.30), residues: 310
  sheet:  0.78 (0.69), residues: 62
  loop : -1.41 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  31 
 TYR   0.017   0.001   TYR A 302 
 PHE   0.013   0.001   PHE B  92 
 TRP   0.007   0.002   TRP A  78 
 HIS   0.006   0.001   HIS B 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9974)
  covalent geometry    : angle       0.57213 (14416)
  hydrogen bonds       : bond        0.04701 (  389)
  hydrogen bonds       : angle       3.41219 (  939)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 LYS cc_start: 0.7402 (pttp) cc_final: 0.6771 (tmtt)
  outliers start: 3
  outliers final: 3
  residues processed: 56
  average time/residue: 0.1347
  time to fit residues: 9.7243
Evaluate side-chains
  52 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue  202 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 67 optimal weight:    9.9990
   chunk 73 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   overall best weight:    2.1986

-------------------------------------------------------------------------------
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 = 0.4399 r_free = 0.4399 target = 0.185157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.141596 restraints weight = 15025.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3867 rms_B_bonded: 1.50
r_work: 0.3652 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9974  Z= 0.213
  Angle     :  0.638   7.291  14416  Z= 0.333
  Chirality :  0.039   0.232   1731
  Planarity :  0.005   0.052   1057
  Dihedral  : 27.148 179.265   3650
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 13.95 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.17 (0.32), residues: 614
  helix: -0.35 (0.29), residues: 310
  sheet:  0.58 (0.69), residues: 62
  loop : -1.61 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  31 
 TYR   0.012   0.002   TYR A 302 
 PHE   0.015   0.002   PHE B  92 
 TRP   0.009   0.002   TRP B 284 
 HIS   0.007   0.001   HIS B 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 9974)
  covalent geometry    : angle       0.63823 (14416)
  hydrogen bonds       : bond        0.05400 (  389)
  hydrogen bonds       : angle       3.61262 (  939)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 LYS cc_start: 0.7644 (pttp) cc_final: 0.6906 (tmtt)
  outliers start: 8
  outliers final: 5
  residues processed: 61
  average time/residue: 0.1354
  time to fit residues: 10.8634
Evaluate side-chains
  54 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue  202 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 66 optimal weight:    9.9990
   chunk 39 optimal weight:    0.6980
   chunk 64 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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 = 0.4406 r_free = 0.4406 target = 0.185787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.142524 restraints weight = 14928.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 1.45
r_work: 0.3671 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9974  Z= 0.181
  Angle     :  0.613   7.002  14416  Z= 0.319
  Chirality :  0.038   0.232   1731
  Planarity :  0.005   0.051   1057
  Dihedral  : 27.119 179.814   3650
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 16.49 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.12 (0.32), residues: 614
  helix: -0.30 (0.29), residues: 310
  sheet:  0.59 (0.69), residues: 62
  loop : -1.60 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  31 
 TYR   0.015   0.002   TYR A 302 
 PHE   0.012   0.002   PHE B  92 
 TRP   0.008   0.002   TRP A  78 
 HIS   0.007   0.001   HIS B 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 9974)
  covalent geometry    : angle       0.61306 (14416)
  hydrogen bonds       : bond        0.05129 (  389)
  hydrogen bonds       : angle       3.52968 (  939)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 LYS cc_start: 0.7632 (pttp) cc_final: 0.6950 (mtmm)
  outliers start: 9
  outliers final: 9
  residues processed: 58
  average time/residue: 0.1431
  time to fit residues: 10.7801
Evaluate side-chains
  62 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain B residue   11 ARG
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue  202 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 74 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0870
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.7360

-------------------------------------------------------------------------------
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 = 0.4435 r_free = 0.4435 target = 0.188552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.145867 restraints weight = 15013.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 1.49
r_work: 0.3731 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9974  Z= 0.129
  Angle     :  0.571   8.076  14416  Z= 0.297
  Chirality :  0.035   0.232   1731
  Planarity :  0.004   0.048   1057
  Dihedral  : 27.060 179.844   3650
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.67 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.33), residues: 614
  helix:  0.01 (0.30), residues: 314
  sheet:  0.81 (0.70), residues: 62
  loop : -1.41 (0.37), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B  31 
 TYR   0.011   0.001   TYR A 302 
 PHE   0.009   0.001   PHE B  92 
 TRP   0.008   0.001   TRP A  78 
 HIS   0.006   0.001   HIS B 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9974)
  covalent geometry    : angle       0.57097 (14416)
  hydrogen bonds       : bond        0.04623 (  389)
  hydrogen bonds       : angle       3.29810 (  939)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 LYS cc_start: 0.7613 (pttp) cc_final: 0.7003 (mtmm)
  outliers start: 12
  outliers final: 5
  residues processed: 60
  average time/residue: 0.1097
  time to fit residues: 8.8002
Evaluate side-chains
  53 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  226 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0030
   chunk 27 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 72 optimal weight:   20.0000
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 71 optimal weight:   10.0000
   chunk 26 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.8592

-------------------------------------------------------------------------------
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 = 0.4435 r_free = 0.4435 target = 0.188530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.145753 restraints weight = 15030.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 1.46
r_work: 0.3730 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3615 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9974  Z= 0.133
  Angle     :  0.567   7.034  14416  Z= 0.295
  Chirality :  0.035   0.231   1731
  Planarity :  0.004   0.047   1057
  Dihedral  : 27.015 179.936   3650
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.67 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.33), residues: 614
  helix:  0.09 (0.30), residues: 316
  sheet:  0.86 (0.69), residues: 62
  loop : -1.28 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  31 
 TYR   0.021   0.001   TYR B 260 
 PHE   0.009   0.001   PHE B  92 
 TRP   0.007   0.001   TRP A  78 
 HIS   0.006   0.001   HIS B 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9974)
  covalent geometry    : angle       0.56679 (14416)
  hydrogen bonds       : bond        0.04618 (  389)
  hydrogen bonds       : angle       3.28321 (  939)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 LYS cc_start: 0.7741 (pttp) cc_final: 0.7041 (mtmm)
  outliers start: 13
  outliers final: 12
  residues processed: 61
  average time/residue: 0.1119
  time to fit residues: 8.9266
Evaluate side-chains
  62 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain B residue   11 ARG
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  226 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 73 optimal weight:    9.9990
   chunk 75 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 50 optimal weight:    0.4980
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 = 0.4429 r_free = 0.4429 target = 0.188067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.145160 restraints weight = 14939.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3909 rms_B_bonded: 1.49
r_work: 0.3718 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9974  Z= 0.143
  Angle     :  0.579   7.507  14416  Z= 0.300
  Chirality :  0.036   0.231   1731
  Planarity :  0.004   0.047   1057
  Dihedral  : 26.995 179.816   3650
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 17.57 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.33), residues: 614
  helix:  0.10 (0.30), residues: 316
  sheet:  0.84 (0.69), residues: 62
  loop : -1.28 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  31 
 TYR   0.019   0.001   TYR B 260 
 PHE   0.010   0.001   PHE B  92 
 TRP   0.007   0.002   TRP A  78 
 HIS   0.006   0.001   HIS B 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9974)
  covalent geometry    : angle       0.57922 (14416)
  hydrogen bonds       : bond        0.04720 (  389)
  hydrogen bonds       : angle       3.30831 (  939)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 LYS cc_start: 0.7636 (pttp) cc_final: 0.7018 (mtmm)
  outliers start: 11
  outliers final: 10
  residues processed: 57
  average time/residue: 0.1329
  time to fit residues: 9.9303
Evaluate side-chains
  58 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  226 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 67 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.4406 r_free = 0.4406 target = 0.185913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.142625 restraints weight = 14848.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 1.44
r_work: 0.3681 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3566 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9974  Z= 0.183
  Angle     :  0.623   8.546  14416  Z= 0.323
  Chirality :  0.038   0.232   1731
  Planarity :  0.004   0.050   1057
  Dihedral  : 27.023 179.432   3650
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.21 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.85 (0.33), residues: 614
  helix: -0.09 (0.29), residues: 312
  sheet:  0.66 (0.69), residues: 62
  loop : -1.45 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  31 
 TYR   0.019   0.002   TYR B 260 
 PHE   0.012   0.002   PHE B 215 
 TRP   0.010   0.002   TRP B 284 
 HIS   0.007   0.001   HIS B 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 9974)
  covalent geometry    : angle       0.62323 (14416)
  hydrogen bonds       : bond        0.05201 (  389)
  hydrogen bonds       : angle       3.48608 (  939)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 LYS cc_start: 0.7662 (pttp) cc_final: 0.6861 (tmtt)
  outliers start: 12
  outliers final: 11
  residues processed: 63
  average time/residue: 0.1068
  time to fit residues: 9.0266
Evaluate side-chains
  63 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain B residue   11 ARG
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  226 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 67 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0970
   chunk 41 optimal weight:    1.9990
   chunk 54 optimal weight:    0.4980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.4448 r_free = 0.4448 target = 0.189780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.147302 restraints weight = 15011.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 1.49
r_work: 0.3721 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9974  Z= 0.124
  Angle     :  0.564   8.006  14416  Z= 0.292
  Chirality :  0.035   0.233   1731
  Planarity :  0.004   0.047   1057
  Dihedral  : 26.997 179.982   3650
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 17.39 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.34), residues: 614
  helix:  0.15 (0.30), residues: 316
  sheet:  0.92 (0.69), residues: 62
  loop : -1.21 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  31 
 TYR   0.018   0.001   TYR B 260 
 PHE   0.010   0.001   PHE B  92 
 TRP   0.008   0.001   TRP A  78 
 HIS   0.006   0.001   HIS B 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 9974)
  covalent geometry    : angle       0.56430 (14416)
  hydrogen bonds       : bond        0.04581 (  389)
  hydrogen bonds       : angle       3.24142 (  939)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 LYS cc_start: 0.7566 (pttp) cc_final: 0.6906 (tmtt)
REVERT: B  302 TYR cc_start: 0.6725 (t80) cc_final: 0.6204 (t80)
  outliers start: 9
  outliers final: 9
  residues processed: 61
  average time/residue: 0.1381
  time to fit residues: 11.1409
Evaluate side-chains
  58 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  226 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 69 optimal weight:    7.9990
   chunk 15 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0980
   chunk 43 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   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 280 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.189265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.146617 restraints weight = 14748.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 1.66
r_work: 0.3716 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9974  Z= 0.126
  Angle     :  0.563   8.041  14416  Z= 0.294
  Chirality :  0.035   0.232   1731
  Planarity :  0.004   0.047   1057
  Dihedral  : 26.971 179.922   3650
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 17.93 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.34), residues: 614
  helix:  0.23 (0.30), residues: 316
  sheet:  0.98 (0.69), residues: 62
  loop : -1.16 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 298 
 TYR   0.021   0.001   TYR B 260 
 PHE   0.008   0.001   PHE B  92 
 TRP   0.007   0.001   TRP B  78 
 HIS   0.006   0.001   HIS B 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9974)
  covalent geometry    : angle       0.56307 (14416)
  hydrogen bonds       : bond        0.04546 (  389)
  hydrogen bonds       : angle       3.24590 (  939)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2212.48 seconds
wall clock time: 38 minutes 33.39 seconds (2313.39 seconds total)