Starting phenix.real_space_refine
on Fri Aug 22 22:23:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sxe_40849/08_2025/8sxe_40849.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxe_40849/08_2025/8sxe_40849.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sxe_40849/08_2025/8sxe_40849.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxe_40849/08_2025/8sxe_40849.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxe_40849/08_2025/8sxe_40849.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxe_40849/08_2025/8sxe_40849.cif"
  }
  resolution = 3.55
  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=  -0.000 sd=   0.051
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      11      5.16       5
     C    5193      2.51       5
     N    1457      2.21       5
     O    1624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 8285
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 358, 2680
          Classifications: {'peptide': 358}
          Link IDs: {'PTRANS': 19, 'TRANS': 338}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2708
          Classifications: {'peptide': 361}
          Link IDs: {'PTRANS': 20, 'TRANS': 340}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1100
          Classifications: {'peptide': 140}
          Link IDs: {'PTRANS': 3, 'TRANS': 136}
    Chain: "D"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 35
          Classifications: {'peptide': 7}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'UNK:plan-1': 7}
          Unresolved non-hydrogen planarities: 7
    Chain: "E"
      Number of atoms: 1619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1619
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 10, 'TRANS': 205}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 143
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 143
          Classifications: {'peptide': 19}
          Link IDs: {'TRANS': 18}
  Time building chain proxies: 1.87, per 1000 atoms: 0.23
  Number of scatterers: 8285
  At special positions: 0
  Unit cell: (86.94, 132.894, 144.072, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      11     16.00
     O    1624      8.00
     N    1457      7.00
     C    5193      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: 0.67
  Conformation dependent library (CDL) restraints added in 401.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1996

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 14 sheets defined
      42.7% alpha, 16.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 60
    Processing helix  chain 'A' and resid 65 through 80
      removed outlier: 3.547A  pdb=" N   LEU A  69 " --> pdb=" O   ASP A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 101
    Processing helix  chain 'A' and resid 127 through 133
      removed outlier: 4.097A  pdb=" N   ALA A 132 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 161
    Processing helix  chain 'A' and resid 214 through 230
      removed outlier: 3.686A  pdb=" N   ASN A 230 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 259
      removed outlier: 3.539A  pdb=" N   ALA A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 314
      removed outlier: 3.515A  pdb=" N   GLN A 314 " --> pdb=" O   ALA A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 435
    Processing helix  chain 'B' and resid 42 through 59
    Processing helix  chain 'B' and resid 65 through 82
    Processing helix  chain 'B' and resid 89 through 98
      removed outlier: 3.538A  pdb=" N   GLU B  98 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 132
    Processing helix  chain 'B' and resid 152 through 161
    Processing helix  chain 'B' and resid 214 through 230
    Processing helix  chain 'B' and resid 248 through 259
      removed outlier: 3.632A  pdb=" N   PHE B 259 " --> pdb=" O   VAL B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 276
      removed outlier: 4.276A  pdb=" N   GLU B 276 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 314
    Processing helix  chain 'B' and resid 356 through 361
    Processing helix  chain 'B' and resid 417 through 434
    Processing helix  chain 'C' and resid 49 through 65
    Processing helix  chain 'C' and resid 67 through 83
      removed outlier: 3.630A  pdb=" N   ALA C  71 " --> pdb=" O   ARG C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 84 through 99
      removed outlier: 3.511A  pdb=" N   SER C  88 " --> pdb=" O   ASP C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 115
    Processing helix  chain 'C' and resid 118 through 132
      removed outlier: 3.621A  pdb=" N   ALA C 132 " --> pdb=" O   GLN C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 148
      removed outlier: 4.195A  pdb=" N   GLY C 148 " --> pdb=" O   LYS C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 162
    Processing helix  chain 'C' and resid 165 through 182
    Processing helix  chain 'E' and resid 214 through 230
      removed outlier: 4.284A  pdb=" N   VAL E 220 " --> pdb=" O   GLY E 216 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 260
    Processing helix  chain 'E' and resid 302 through 315
      removed outlier: 3.778A  pdb=" N   LEU E 311 " --> pdb=" O   VAL E 307 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 412 through 417
    Processing helix  chain 'E' and resid 417 through 434
    Processing helix  chain 'F' and resid 419 through 435
      removed outlier: 3.521A  pdb=" N   LEU F 430 " --> pdb=" O   LEU F 426 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   SER F 431 " --> pdb=" O   LEU F 427 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88
      removed outlier: 5.502A  pdb=" N   LYS A 343 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   LEU A 334 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 5.793A  pdb=" N   THR A 345 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   THR A 332 " --> pdb=" O   THR A 345 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 106
    Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 114
      removed outlier: 6.830A  pdb=" N   GLU A 110 " --> pdb=" O   VAL A 121 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147
    Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 200
      removed outlier: 5.523A  pdb=" N   SER A 196 " --> pdb=" O   ARG A 207 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ARG A 207 " --> pdb=" O   SER A 196 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   VAL A 198 " --> pdb=" O   TYR A 205 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   TYR A 205 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLU A 200 " --> pdb=" O   TYR A 203 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   ALA A 204 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   ASP A 240 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LEU A 206 " --> pdb=" O   ASP A 240 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU A 237 " --> pdb=" O   VAL A 293 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   LEU A 295 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   LEU A 239 " --> pdb=" O   LEU A 295 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE A 296 " --> pdb=" O   MET A 320 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 371 through 373
    Processing sheet with id=AA8, first strand: chain 'B' and resid 86 through 88
      removed outlier: 4.520A  pdb=" N   VAL B 266 " --> pdb=" O   PHE B 279 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 86 through 88
      removed outlier: 5.675A  pdb=" N   LYS B 343 " --> pdb=" O   LEU B 334 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   LEU B 334 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 5.680A  pdb=" N   THR B 345 " --> pdb=" O   THR B 332 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   THR B 332 " --> pdb=" O   THR B 345 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 112
      removed outlier: 6.770A  pdb=" N   GLU B 110 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE B 118 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 110 through 112
      removed outlier: 6.770A  pdb=" N   GLU B 110 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE B 118 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 5.570A  pdb=" N   ILE B 140 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   VAL B 173 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN B 142 " --> pdb=" O   THR B 171 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 194 through 200
      removed outlier: 5.365A  pdb=" N   SER B 196 " --> pdb=" O   ARG B 207 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   ARG B 207 " --> pdb=" O   SER B 196 " (cutoff:3.500A)
      removed outlier: 5.322A  pdb=" N   VAL B 198 " --> pdb=" O   TYR B 205 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   TYR B 205 " --> pdb=" O   VAL B 198 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLU B 200 " --> pdb=" O   TYR B 203 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   ALA B 204 " --> pdb=" O   VAL B 238 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ASP B 240 " --> pdb=" O   ALA B 204 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   LEU B 206 " --> pdb=" O   ASP B 240 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   LEU B 295 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   LEU B 239 " --> pdb=" O   LEU B 295 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 198 through 200
      removed outlier: 6.566A  pdb=" N   TYR E 203 " --> pdb=" O   LEU E 199 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 237 through 239
      removed outlier: 6.901A  pdb=" N   LEU E 237 " --> pdb=" O   VAL E 293 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5

    391 hydrogen bonds defined for protein.
    1101 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.84

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2846
        1.34 -     1.46: 1105
        1.46 -     1.57: 4421
        1.57 -     1.69: 0
        1.69 -     1.80: 22
  Bond restraints: 8394
  Sorted by residual:
  bond pdb=" CA  ILE B 118 "
       pdb=" CB  ILE B 118 "
    ideal  model  delta    sigma   weight residual
    1.540  1.529  0.011 1.36e-02 5.41e+03 6.31e-01
  bond pdb=" C   ARG C  83 "
       pdb=" N   ASP C  84 "
    ideal  model  delta    sigma   weight residual
    1.330  1.340 -0.010 1.47e-02 4.63e+03 4.64e-01
  bond pdb=" CA  ARG C  67 "
       pdb=" C   ARG C  67 "
    ideal  model  delta    sigma   weight residual
    1.530  1.522  0.007 1.10e-02 8.26e+03 4.44e-01
  bond pdb=" CG  PRO B 123 "
       pdb=" CD  PRO B 123 "
    ideal  model  delta    sigma   weight residual
    1.503  1.481  0.022 3.40e-02 8.65e+02 4.25e-01
  bond pdb=" CA  ARG C  67 "
       pdb=" CB  ARG C  67 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 1.32e-02 5.74e+03 3.80e-01
  ... (remaining 8389 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.82: 10666
        0.82 -     1.64: 542
        1.64 -     2.46: 81
        2.46 -     3.29: 34
        3.29 -     4.11: 30
  Bond angle restraints: 11353
  Sorted by residual:
  angle pdb=" CA  TYR A 349 "
        pdb=" CB  TYR A 349 "
        pdb=" CG  TYR A 349 "
      ideal   model   delta    sigma   weight residual
     113.90  117.05   -3.15 1.80e+00 3.09e-01 3.05e+00
  angle pdb=" N   ALA A  59 "
        pdb=" CA  ALA A  59 "
        pdb=" C   ALA A  59 "
      ideal   model   delta    sigma   weight residual
     114.04  112.01    2.03 1.24e+00 6.50e-01 2.67e+00
  angle pdb=" CA  ARG C  67 "
        pdb=" C   ARG C  67 "
        pdb=" N   PHE C  68 "
      ideal   model   delta    sigma   weight residual
     114.76  116.54   -1.78 1.14e+00 7.69e-01 2.43e+00
  angle pdb=" CA  ARG C  67 "
        pdb=" C   ARG C  67 "
        pdb=" O   ARG C  67 "
      ideal   model   delta    sigma   weight residual
     122.64  120.75    1.89 1.25e+00 6.40e-01 2.28e+00
  angle pdb=" N   ALA A 302 "
        pdb=" CA  ALA A 302 "
        pdb=" C   ALA A 302 "
      ideal   model   delta    sigma   weight residual
     111.02  112.77   -1.75 1.22e+00 6.72e-01 2.05e+00
  ... (remaining 11348 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 4584
       17.80 -    35.60: 477
       35.60 -    53.40: 67
       53.40 -    71.20: 8
       71.20 -    89.00: 13
  Dihedral angle restraints: 5149
    sinusoidal: 2032
      harmonic: 3117
  Sorted by residual:
  dihedral pdb=" CA  PHE C  48 "
           pdb=" C   PHE C  48 "
           pdb=" N   SER C  49 "
           pdb=" CA  SER C  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.29   18.71     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  ASP E 323 "
           pdb=" CB  ASP E 323 "
           pdb=" CG  ASP E 323 "
           pdb=" OD1 ASP E 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.92   58.92     1      2.00e+01 2.50e-03 1.16e+01
  dihedral pdb=" CB  GLU A 218 "
           pdb=" CG  GLU A 218 "
           pdb=" CD  GLU A 218 "
           pdb=" OE1 GLU A 218 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.69  -87.69     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 5146 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 822
       0.026 -    0.052: 298
       0.052 -    0.079: 87
       0.079 -    0.105: 70
       0.105 -    0.131: 40
  Chirality restraints: 1317
  Sorted by residual:
  chirality pdb=" CA  VAL B 363 "
            pdb=" N   VAL B 363 "
            pdb=" C   VAL B 363 "
            pdb=" CB  VAL B 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.29e-01
  chirality pdb=" CA  ILE B 318 "
            pdb=" N   ILE B 318 "
            pdb=" C   ILE B 318 "
            pdb=" CB  ILE B 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CA  ILE E 366 "
            pdb=" N   ILE E 366 "
            pdb=" C   ILE E 366 "
            pdb=" CB  ILE E 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 1314 not shown)

  Planarity restraints: 1501
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 285 "    0.025 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO B 286 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 286 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 286 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 222 "   -0.007 2.00e-02 2.50e+03   1.32e-02 1.74e+00
        pdb=" C   ALA A 222 "    0.023 2.00e-02 2.50e+03
        pdb=" O   ALA A 222 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   LEU A 223 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 166 "    0.021 5.00e-02 4.00e+02   3.17e-02 1.61e+00
        pdb=" N   PRO B 167 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO B 167 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 167 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1498 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 151
        2.65 -     3.21: 8324
        3.21 -     3.78: 12562
        3.78 -     4.34: 16938
        4.34 -     4.90: 28377
  Nonbonded interactions: 66352
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E 351 "
            pdb=" O   ARG E 355 "
     model   vdw
     2.089 3.040
  nonbonded pdb=" O   ARG C  83 "
            pdb=" OG  SER C 114 "
     model   vdw
     2.123 3.040
  nonbonded pdb=" O   LEU F 430 "
            pdb=" OG1 THR F 433 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" O   MET B 160 "
            pdb=" NH1 ARG B 186 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" OD1 ASP A 257 "
            pdb=" N   ASP A 282 "
     model   vdw
     2.255 3.120
  ... (remaining 66347 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 38 through 373 or resid 416 through 436))
  selection = (chain 'B' and (resid 38 through 373 or resid 416 through 436))
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.060
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.520
  Find NCS groups from input model:        0.070
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
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      :  0.002   0.028   8394  Z= 0.094
  Angle     :  0.468   4.108  11353  Z= 0.240
  Chirality :  0.040   0.131   1317
  Planarity :  0.003   0.037   1501
  Dihedral  : 14.582  89.003   3153
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  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:  0.44 (0.27), residues: 1076
  helix:  1.76 (0.26), residues: 432
  sheet: -1.22 (0.42), residues: 170
  loop : -0.43 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 242 
 TYR   0.014   0.001   TYR A 349 
 PHE   0.010   0.001   PHE C  48 
 TRP   0.004   0.001   TRP C 111 
 HIS   0.002   0.001   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 8394)
  covalent geometry    : angle       0.46809 (11353)
  hydrogen bonds       : bond        0.15024 (  379)
  hydrogen bonds       : angle       6.80084 ( 1101)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  142 GLN cc_start: 0.7760 (mt0) cc_final: 0.7426 (mt0)
REVERT: B  149 LYS cc_start: 0.8107 (mttp) cc_final: 0.7340 (tptt)
REVERT: B  153 MET cc_start: 0.7844 (ttp) cc_final: 0.7588 (ttt)
REVERT: B  237 LEU cc_start: 0.8707 (tt) cc_final: 0.8462 (tt)
REVERT: B  266 VAL cc_start: 0.8564 (p) cc_final: 0.8350 (p)
REVERT: C  134 ARG cc_start: 0.6130 (mpp80) cc_final: 0.5483 (mmm160)
REVERT: C  139 MET cc_start: 0.8181 (ttm) cc_final: 0.7835 (ttp)
REVERT: E  320 MET cc_start: 0.8513 (ttm) cc_final: 0.8228 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0939
  time to fit residues: 16.1318
Evaluate side-chains
  80 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0980
   chunk 100 optimal weight:    9.9990
   chunk 106 optimal weight:    0.1980
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.4175 r_free = 0.4175 target = 0.168647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.139452 restraints weight = 13872.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.140061 restraints weight = 9817.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.141878 restraints weight = 8836.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.142199 restraints weight = 6456.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.142864 restraints weight = 5965.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8394  Z= 0.160
  Angle     :  0.589   7.886  11353  Z= 0.307
  Chirality :  0.043   0.156   1317
  Planarity :  0.005   0.042   1501
  Dihedral  :  4.035  18.836   1182
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.24 %
    Favored  : 87.51 %
  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:  0.41 (0.26), residues: 1076
  helix:  1.73 (0.24), residues: 439
  sheet: -0.98 (0.43), residues: 160
  loop : -0.61 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 186 
 TYR   0.014   0.002   TYR A 349 
 PHE   0.011   0.001   PHE C  48 
 TRP   0.005   0.003   TRP C 111 
 HIS   0.002   0.000   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 8394)
  covalent geometry    : angle       0.58922 (11353)
  hydrogen bonds       : bond        0.04678 (  379)
  hydrogen bonds       : angle       4.96407 ( 1101)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   43 LEU cc_start: 0.8583 (tp) cc_final: 0.8369 (tp)
REVERT: B  142 GLN cc_start: 0.7937 (mt0) cc_final: 0.7722 (mt0)
REVERT: B  153 MET cc_start: 0.7668 (ttp) cc_final: 0.7444 (ttt)
REVERT: C   68 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.7103 (t80)
REVERT: C   72 LEU cc_start: 0.8446 (tp) cc_final: 0.8171 (tp)
REVERT: C  113 ARG cc_start: 0.7946 (tpt90) cc_final: 0.7705 (tpt90)
REVERT: C  134 ARG cc_start: 0.6254 (mpp80) cc_final: 0.5508 (mmm160)
REVERT: C  143 GLU cc_start: 0.7413 (tp30) cc_final: 0.7130 (tp30)
  outliers start: 11
  outliers final: 8
  residues processed: 102
  average time/residue: 0.0709
  time to fit residues: 10.3137
Evaluate side-chains
  80 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain C residue   68 PHE
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  260 LEU
Chi-restraints excluded: chain E residue  305 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 100 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0370
   chunk 21 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
E 243 ASN
F 422 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.168215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.138037 restraints weight = 13799.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.140038 restraints weight = 10354.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.142137 restraints weight = 7634.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.142280 restraints weight = 5656.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.142561 restraints weight = 5453.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8394  Z= 0.144
  Angle     :  0.551   5.942  11353  Z= 0.286
  Chirality :  0.042   0.140   1317
  Planarity :  0.004   0.050   1501
  Dihedral  :  3.973  18.536   1182
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 14.19 %
    Favored  : 84.45 %
  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:  0.39 (0.26), residues: 1076
  helix:  1.77 (0.25), residues: 440
  sheet: -1.26 (0.41), residues: 167
  loop : -0.55 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 186 
 TYR   0.014   0.001   TYR A 349 
 PHE   0.012   0.001   PHE A 104 
 TRP   0.006   0.002   TRP C 111 
 HIS   0.002   0.000   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8394)
  covalent geometry    : angle       0.55080 (11353)
  hydrogen bonds       : bond        0.04236 (  379)
  hydrogen bonds       : angle       4.60850 ( 1101)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   43 LEU cc_start: 0.8561 (tp) cc_final: 0.8330 (tp)
REVERT: C   68 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.7039 (t80)
REVERT: C   72 LEU cc_start: 0.8456 (tp) cc_final: 0.8222 (tp)
REVERT: C  113 ARG cc_start: 0.7781 (tpt90) cc_final: 0.7510 (tpt90)
REVERT: C  134 ARG cc_start: 0.6212 (mpp80) cc_final: 0.5497 (mmm160)
  outliers start: 12
  outliers final: 6
  residues processed: 90
  average time/residue: 0.0718
  time to fit residues: 9.1053
Evaluate side-chains
  82 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain C residue   68 PHE
Chi-restraints excluded: chain E residue  260 LEU
Chi-restraints excluded: chain E residue  320 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 106 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 70 optimal weight:    0.3980
   chunk 17 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 122 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.167792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.138574 restraints weight = 14159.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.141026 restraints weight = 9994.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.142519 restraints weight = 7308.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.142937 restraints weight = 5552.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.143136 restraints weight = 5277.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8394  Z= 0.155
  Angle     :  0.558   6.298  11353  Z= 0.290
  Chirality :  0.042   0.136   1317
  Planarity :  0.004   0.048   1501
  Dihedral  :  4.000  18.571   1182
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 14.87 %
    Favored  : 83.20 %
  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:  0.39 (0.26), residues: 1076
  helix:  1.73 (0.25), residues: 440
  sheet: -1.12 (0.43), residues: 152
  loop : -0.61 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 186 
 TYR   0.015   0.001   TYR A 349 
 PHE   0.009   0.001   PHE E 380 
 TRP   0.007   0.002   TRP C 111 
 HIS   0.002   0.000   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 8394)
  covalent geometry    : angle       0.55817 (11353)
  hydrogen bonds       : bond        0.04100 (  379)
  hydrogen bonds       : angle       4.52908 ( 1101)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   68 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7106 (t80)
REVERT: C   72 LEU cc_start: 0.8456 (tp) cc_final: 0.8252 (tp)
REVERT: C   84 ASP cc_start: 0.7322 (t0) cc_final: 0.6926 (t0)
REVERT: C  134 ARG cc_start: 0.6120 (mpp80) cc_final: 0.5350 (mmm160)
  outliers start: 17
  outliers final: 12
  residues processed: 96
  average time/residue: 0.0713
  time to fit residues: 9.7966
Evaluate side-chains
  86 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain C residue   68 PHE
Chi-restraints excluded: chain E residue  209 THR
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  260 LEU
Chi-restraints excluded: chain E residue  351 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 87 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.4155 r_free = 0.4155 target = 0.166091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.135864 restraints weight = 13986.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.136980 restraints weight = 10256.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.138567 restraints weight = 8972.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.138860 restraints weight = 6765.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.139397 restraints weight = 6201.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8394  Z= 0.183
  Angle     :  0.598   8.854  11353  Z= 0.307
  Chirality :  0.043   0.163   1317
  Planarity :  0.005   0.050   1501
  Dihedral  :  4.077  18.333   1182
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.46 %
    Favored  : 81.50 %
  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:  0.26 (0.26), residues: 1076
  helix:  1.63 (0.25), residues: 439
  sheet: -1.22 (0.43), residues: 155
  loop : -0.67 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 113 
 TYR   0.016   0.002   TYR A 349 
 PHE   0.009   0.001   PHE C 156 
 TRP   0.008   0.003   TRP C 111 
 HIS   0.003   0.000   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 8394)
  covalent geometry    : angle       0.59765 (11353)
  hydrogen bonds       : bond        0.04200 (  379)
  hydrogen bonds       : angle       4.59035 ( 1101)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   68 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7157 (t80)
REVERT: C  134 ARG cc_start: 0.6287 (mpp80) cc_final: 0.5465 (mmm160)
  outliers start: 18
  outliers final: 15
  residues processed: 92
  average time/residue: 0.0834
  time to fit residues: 10.9031
Evaluate side-chains
  87 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain C residue   68 PHE
Chi-restraints excluded: chain E residue  209 THR
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  260 LEU
Chi-restraints excluded: chain E residue  305 GLU
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain F residue  430 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0270
   chunk 17 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0980
   overall best weight:    0.5842

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

Flipped N/Q/H residues before XYZ refinement:
** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.168369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.138300 restraints weight = 13886.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.140551 restraints weight = 9801.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.142049 restraints weight = 7653.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.142302 restraints weight = 5862.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.142623 restraints weight = 5558.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8394  Z= 0.142
  Angle     :  0.561   8.095  11353  Z= 0.287
  Chirality :  0.042   0.139   1317
  Planarity :  0.004   0.047   1501
  Dihedral  :  3.962  18.193   1182
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.48 %
    Favored  : 80.02 %
  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:  0.31 (0.26), residues: 1076
  helix:  1.70 (0.25), residues: 438
  sheet: -1.24 (0.42), residues: 154
  loop : -0.65 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 113 
 TYR   0.016   0.001   TYR A 349 
 PHE   0.007   0.001   PHE C  48 
 TRP   0.008   0.002   TRP C 111 
 HIS   0.002   0.000   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8394)
  covalent geometry    : angle       0.56112 (11353)
  hydrogen bonds       : bond        0.03903 (  379)
  hydrogen bonds       : angle       4.42251 ( 1101)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  110 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8097 (mp0)
REVERT: C   68 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7118 (t80)
REVERT: C  134 ARG cc_start: 0.6285 (mpp80) cc_final: 0.5457 (mmm160)
REVERT: E  422 GLN cc_start: 0.8690 (mm110) cc_final: 0.8311 (tp40)
  outliers start: 22
  outliers final: 15
  residues processed: 102
  average time/residue: 0.0696
  time to fit residues: 10.1991
Evaluate side-chains
  89 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  110 GLU
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain C residue   68 PHE
Chi-restraints excluded: chain E residue  209 THR
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  260 LEU
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain F residue  430 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0870
   chunk 37 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 14 optimal weight:    9.9990
   chunk 98 optimal weight:    0.0970
   overall best weight:    0.5356

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

Flipped N/Q/H residues before XYZ refinement:
** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.162585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.133302 restraints weight = 14090.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.135344 restraints weight = 10373.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.137240 restraints weight = 7806.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.137427 restraints weight = 5813.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.137826 restraints weight = 5543.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8394  Z= 0.137
  Angle     :  0.559   7.704  11353  Z= 0.287
  Chirality :  0.042   0.179   1317
  Planarity :  0.004   0.048   1501
  Dihedral  :  3.928  18.099   1182
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.82 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.33 (0.26), residues: 1076
  helix:  1.68 (0.24), residues: 438
  sheet: -1.22 (0.45), residues: 143
  loop : -0.62 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 113 
 TYR   0.015   0.001   TYR A 349 
 PHE   0.010   0.001   PHE E 380 
 TRP   0.008   0.002   TRP C 111 
 HIS   0.002   0.000   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8394)
  covalent geometry    : angle       0.55892 (11353)
  hydrogen bonds       : bond        0.03818 (  379)
  hydrogen bonds       : angle       4.36697 ( 1101)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   68 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7187 (t80)
REVERT: C  134 ARG cc_start: 0.6129 (mpp80) cc_final: 0.5372 (mmm160)
REVERT: E  422 GLN cc_start: 0.8671 (mm110) cc_final: 0.8327 (tp40)
  outliers start: 25
  outliers final: 17
  residues processed: 100
  average time/residue: 0.0708
  time to fit residues: 10.3883
Evaluate side-chains
  92 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  257 ASP
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain C residue   68 PHE
Chi-restraints excluded: chain E residue  209 THR
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  260 LEU
Chi-restraints excluded: chain E residue  305 GLU
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain F residue  430 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 57 optimal weight:    0.1980
   chunk 27 optimal weight:    0.0570
   chunk 60 optimal weight:    0.4980
   chunk 75 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0770
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.3056

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
C 122 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.170117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.140438 restraints weight = 13930.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.142650 restraints weight = 10305.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.144627 restraints weight = 7641.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.144905 restraints weight = 5702.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.145200 restraints weight = 5379.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8394  Z= 0.114
  Angle     :  0.541   6.717  11353  Z= 0.279
  Chirality :  0.041   0.149   1317
  Planarity :  0.004   0.051   1501
  Dihedral  :  3.786  18.039   1182
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.07 %
    Favored  : 78.66 %
  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 (0.26), residues: 1076
  helix:  1.84 (0.25), residues: 439
  sheet: -1.18 (0.45), residues: 143
  loop : -0.58 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 113 
 TYR   0.014   0.001   TYR A 349 
 PHE   0.011   0.001   PHE E 380 
 TRP   0.008   0.003   TRP C 111 
 HIS   0.001   0.000   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8394)
  covalent geometry    : angle       0.54073 (11353)
  hydrogen bonds       : bond        0.03561 (  379)
  hydrogen bonds       : angle       4.24680 ( 1101)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 LYS cc_start: 0.8047 (ptpp) cc_final: 0.7745 (ptpp)
REVERT: B  305 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7726 (mt-10)
REVERT: C   68 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7124 (t80)
REVERT: C  134 ARG cc_start: 0.6171 (mpp80) cc_final: 0.5375 (mmm160)
  outliers start: 20
  outliers final: 15
  residues processed: 99
  average time/residue: 0.0677
  time to fit residues: 9.7581
Evaluate side-chains
  89 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  257 ASP
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain C residue   68 PHE
Chi-restraints excluded: chain E residue  209 THR
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  260 LEU
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain F residue  430 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0770
   chunk 5 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 13 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9990
   chunk 22 optimal weight:    0.3980
   overall best weight:    0.5740

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

Flipped N/Q/H residues before XYZ refinement:
** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.167571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.140185 restraints weight = 14063.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.139513 restraints weight = 14380.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.141295 restraints weight = 12284.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.142043 restraints weight = 8840.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.142353 restraints weight = 7936.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8394  Z= 0.141
  Angle     :  0.572   8.161  11353  Z= 0.293
  Chirality :  0.042   0.138   1317
  Planarity :  0.004   0.051   1501
  Dihedral  :  3.867  17.738   1182
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.30 %
    Favored  : 78.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.46 (0.26), residues: 1076
  helix:  1.83 (0.25), residues: 437
  sheet: -1.25 (0.44), residues: 148
  loop : -0.55 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 113 
 TYR   0.015   0.001   TYR A 349 
 PHE   0.012   0.001   PHE E 380 
 TRP   0.011   0.003   TRP C 111 
 HIS   0.002   0.000   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8394)
  covalent geometry    : angle       0.57167 (11353)
  hydrogen bonds       : bond        0.03722 (  379)
  hydrogen bonds       : angle       4.24737 ( 1101)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  305 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7785 (mt-10)
REVERT: C   68 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7254 (t80)
REVERT: C  134 ARG cc_start: 0.6053 (mpp80) cc_final: 0.5297 (mmm160)
  outliers start: 19
  outliers final: 16
  residues processed: 92
  average time/residue: 0.0627
  time to fit residues: 8.2879
Evaluate side-chains
  92 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  257 ASP
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain C residue   68 PHE
Chi-restraints excluded: chain E residue  209 THR
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  260 LEU
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain F residue  430 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 69 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0030
   chunk 93 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.167440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.137697 restraints weight = 13936.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.139872 restraints weight = 10118.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.141540 restraints weight = 7803.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.141775 restraints weight = 6025.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.142031 restraints weight = 5624.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8394  Z= 0.150
  Angle     :  0.589   9.259  11353  Z= 0.299
  Chirality :  0.042   0.139   1317
  Planarity :  0.004   0.052   1501
  Dihedral  :  3.881  17.721   1182
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 19.64 %
    Favored  : 78.43 %
  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:  0.41 (0.26), residues: 1076
  helix:  1.80 (0.25), residues: 438
  sheet: -1.27 (0.44), residues: 147
  loop : -0.59 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 113 
 TYR   0.015   0.001   TYR A 349 
 PHE   0.014   0.001   PHE E 380 
 TRP   0.008   0.003   TRP C 111 
 HIS   0.002   0.001   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8394)
  covalent geometry    : angle       0.58871 (11353)
  hydrogen bonds       : bond        0.03815 (  379)
  hydrogen bonds       : angle       4.27599 ( 1101)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  305 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7763 (mt-10)
REVERT: C   68 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7220 (t80)
REVERT: C  134 ARG cc_start: 0.6210 (mpp80) cc_final: 0.5345 (mmm160)
REVERT: F  428 LYS cc_start: 0.6294 (mmmt) cc_final: 0.5375 (mptt)
  outliers start: 17
  outliers final: 16
  residues processed: 92
  average time/residue: 0.0652
  time to fit residues: 8.6128
Evaluate side-chains
  92 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  257 ASP
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain C residue   68 PHE
Chi-restraints excluded: chain E residue  209 THR
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  260 LEU
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain F residue  430 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 42 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9990
   chunk 64 optimal weight:    0.4980
   chunk 30 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 11 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4163 r_free = 0.4163 target = 0.164277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.135173 restraints weight = 14412.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.136115 restraints weight = 14305.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.137619 restraints weight = 10549.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.138439 restraints weight = 7442.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.138813 restraints weight = 6574.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8394  Z= 0.149
  Angle     :  0.584   9.214  11353  Z= 0.297
  Chirality :  0.042   0.146   1317
  Planarity :  0.004   0.052   1501
  Dihedral  :  3.895  17.744   1182
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 19.86 %
    Favored  : 78.09 %
  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:  0.39 (0.26), residues: 1076
  helix:  1.76 (0.25), residues: 439
  sheet: -1.31 (0.44), residues: 148
  loop : -0.58 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 113 
 TYR   0.015   0.001   TYR A 349 
 PHE   0.014   0.001   PHE E 380 
 TRP   0.015   0.005   TRP C 111 
 HIS   0.002   0.000   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8394)
  covalent geometry    : angle       0.58351 (11353)
  hydrogen bonds       : bond        0.03830 (  379)
  hydrogen bonds       : angle       4.29433 ( 1101)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1200.56 seconds
wall clock time: 21 minutes 29.09 seconds (1289.09 seconds total)