Starting phenix.real_space_refine
on Wed Mar 12 21:06:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sxe_40849/03_2025/8sxe_40849.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxe_40849/03_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_40849/03_2025/8sxe_40849.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxe_40849/03_2025/8sxe_40849.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxe_40849/03_2025/8sxe_40849.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxe_40849/03_2025/8sxe_40849.cif"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.051
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.03, per 1000 atoms: 0.61
  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: 2.27
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.00
  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: 2.30

  Time building geometry restraints manager: 2.63 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:             1.490
  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:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.050
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.250
-------------------------------------------------------------------------------
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= 0.132
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (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
 TRP   0.004   0.001   TRP C 111 
 HIS   0.002   0.001   HIS A  84 
 PHE   0.010   0.001   PHE C  48 
 TYR   0.014   0.001   TYR A 349 
 ARG   0.002   0.000   ARG B 242 

*********************** 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  : 0.876 
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: 0.2221
  time to fit residues: 37.8604
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  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 45 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 83 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0870
   chunk 50 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   overall best weight:    0.4958

-------------------------------------------------------------------------------
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 = 0.4182 r_free = 0.4182 target = 0.167659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.138036 restraints weight = 13679.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.139972 restraints weight = 9854.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.141768 restraints weight = 7580.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.1550

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= 0.220
  Angle     :  0.573   7.702  11353  Z= 0.299
  Chirality :  0.043   0.150   1317
  Planarity :  0.004   0.043   1501
  Dihedral  :  3.972  18.285   1182
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 11.12 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.26), residues: 1076
  helix:  1.84 (0.25), residues: 437
  sheet: -1.09 (0.41), residues: 172
  loop : -0.55 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C 111 
 HIS   0.002   0.000   HIS A  84 
 PHE   0.011   0.001   PHE C  48 
 TYR   0.014   0.001   TYR C  54 
 ARG   0.005   0.000   ARG B 186 

*********************** 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: 9
    poor density    : 96
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   43 LEU cc_start: 0.8558 (tp) cc_final: 0.8353 (tp)
REVERT: B   77 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7696 (ttt)
REVERT: B  142 GLN cc_start: 0.7953 (mt0) cc_final: 0.7747 (mt0)
REVERT: B  153 MET cc_start: 0.7456 (ttp) cc_final: 0.7248 (ttt)
REVERT: C   68 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.7081 (t80)
REVERT: C   72 LEU cc_start: 0.8373 (tp) cc_final: 0.8165 (tp)
REVERT: C  134 ARG cc_start: 0.6180 (mpp80) cc_final: 0.5503 (mmm160)
REVERT: C  143 GLU cc_start: 0.7586 (tp30) cc_final: 0.7362 (tp30)
  outliers start: 9
  outliers final: 4
  residues processed: 102
  average time/residue: 0.2077
  time to fit residues: 29.6088
Evaluate side-chains
  76 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
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 C residue   68 PHE
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  260 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0010
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 29 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.1590

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

Flipped N/Q/H residues before XYZ refinement:
** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 422 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.164710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.134386 restraints weight = 14139.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.134871 restraints weight = 10659.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.136974 restraints weight = 9298.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8394  Z= 0.353
  Angle     :  0.628   7.190  11353  Z= 0.325
  Chirality :  0.044   0.140   1317
  Planarity :  0.005   0.043   1501
  Dihedral  :  4.265  18.348   1182
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 14.30 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.26), residues: 1076
  helix:  1.60 (0.25), residues: 439
  sheet: -1.26 (0.42), residues: 156
  loop : -0.68 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.003   TRP C 111 
 HIS   0.002   0.000   HIS A  84 
 PHE   0.011   0.001   PHE A 104 
 TYR   0.016   0.002   TYR A 349 
 ARG   0.007   0.000   ARG C 113 

*********************** 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
  98 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   68 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.7272 (t80)
REVERT: C  113 ARG cc_start: 0.7631 (tpt90) cc_final: 0.7393 (tpt90)
REVERT: C  134 ARG cc_start: 0.6313 (mpp80) cc_final: 0.5547 (mmm160)
REVERT: C  143 GLU cc_start: 0.7759 (tp30) cc_final: 0.7419 (tp30)
  outliers start: 15
  outliers final: 9
  residues processed: 94
  average time/residue: 0.2035
  time to fit residues: 27.4977
Evaluate side-chains
  80 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
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  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  219 VAL
Chi-restraints excluded: chain E residue  260 LEU
Chi-restraints excluded: chain E residue  305 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0570
   chunk 60 optimal weight:    0.4980
   chunk 100 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.4152 r_free = 0.4152 target = 0.162329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.133089 restraints weight = 13943.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.135572 restraints weight = 10533.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.137132 restraints weight = 7526.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.1989

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= 0.221
  Angle     :  0.558   6.396  11353  Z= 0.289
  Chirality :  0.042   0.146   1317
  Planarity :  0.004   0.047   1501
  Dihedral  :  4.048  18.974   1182
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.64 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.26), residues: 1076
  helix:  1.68 (0.25), residues: 439
  sheet: -1.20 (0.42), residues: 156
  loop : -0.65 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C 111 
 HIS   0.002   0.000   HIS A  84 
 PHE   0.008   0.001   PHE A 104 
 TYR   0.024   0.002   TYR A 267 
 ARG   0.003   0.000   ARG B 186 

*********************** 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
  104 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   68 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7104 (t80)
REVERT: C  113 ARG cc_start: 0.7818 (tpt90) cc_final: 0.7596 (tpt90)
REVERT: C  134 ARG cc_start: 0.5996 (mpp80) cc_final: 0.5475 (mmm160)
  outliers start: 19
  outliers final: 15
  residues processed: 99
  average time/residue: 0.1953
  time to fit residues: 27.5414
Evaluate side-chains
  88 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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   77 MET
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 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  320 MET
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain F residue  430 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 92 optimal weight:    0.0670
   chunk 84 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0980
   chunk 88 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.4718

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.165518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.136326 restraints weight = 14081.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.136230 restraints weight = 13786.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.138174 restraints weight = 11056.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8394  Z= 0.204
  Angle     :  0.548   7.897  11353  Z= 0.282
  Chirality :  0.042   0.146   1317
  Planarity :  0.004   0.048   1501
  Dihedral  :  3.927  18.675   1182
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.89 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.26), residues: 1076
  helix:  1.81 (0.25), residues: 439
  sheet: -1.29 (0.42), residues: 161
  loop : -0.59 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C 111 
 HIS   0.002   0.000   HIS A  84 
 PHE   0.007   0.001   PHE C 156 
 TYR   0.019   0.001   TYR A 267 
 ARG   0.004   0.000   ARG E 242 

*********************** 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
  110 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  110 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7948 (mp0)
REVERT: C   68 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.7227 (t80)
REVERT: C  134 ARG cc_start: 0.6064 (mpp80) cc_final: 0.5375 (mmm160)
  outliers start: 23
  outliers final: 15
  residues processed: 105
  average time/residue: 0.1913
  time to fit residues: 28.8126
Evaluate side-chains
  90 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
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  110 GLU
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 E residue  356 SER
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 55 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 89 optimal weight:    0.4980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4159 r_free = 0.4159 target = 0.163535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.134117 restraints weight = 14082.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.134267 restraints weight = 13299.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.136124 restraints weight = 10645.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8394  Z= 0.258
  Angle     :  0.570   6.953  11353  Z= 0.293
  Chirality :  0.042   0.144   1317
  Planarity :  0.004   0.046   1501
  Dihedral  :  4.013  18.292   1182
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.14 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.26), residues: 1076
  helix:  1.73 (0.25), residues: 439
  sheet: -1.27 (0.44), residues: 148
  loop : -0.59 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.003   TRP C 111 
 HIS   0.002   0.000   HIS A  84 
 PHE   0.010   0.001   PHE E 380 
 TYR   0.017   0.002   TYR A 267 
 ARG   0.003   0.000   ARG E 355 

*********************** 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
  103 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   68 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7294 (t80)
REVERT: C  134 ARG cc_start: 0.6118 (mpp80) cc_final: 0.5374 (mmm160)
REVERT: E  380 PHE cc_start: 0.6517 (p90) cc_final: 0.6185 (p90)
  outliers start: 23
  outliers final: 17
  residues processed: 97
  average time/residue: 0.1866
  time to fit residues: 25.9007
Evaluate side-chains
  90 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
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  153 MET
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  248 VAL
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  320 MET
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  356 SER
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 53 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    6.9990
   chunk 28 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9990
   chunk 104 optimal weight:    0.0270
   chunk 81 optimal weight:    0.0770
   chunk 25 optimal weight:    0.0970
   chunk 37 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.2194

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.170976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.141314 restraints weight = 13824.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.143575 restraints weight = 10415.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.145961 restraints weight = 7511.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.2469

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= 0.159
  Angle     :  0.531   7.173  11353  Z= 0.273
  Chirality :  0.041   0.138   1317
  Planarity :  0.004   0.046   1501
  Dihedral  :  3.731  18.312   1182
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 18.16 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.26), residues: 1076
  helix:  2.00 (0.25), residues: 433
  sheet: -1.42 (0.43), residues: 156
  loop : -0.43 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C 111 
 HIS   0.001   0.000   HIS E 391 
 PHE   0.010   0.001   PHE C  48 
 TYR   0.027   0.001   TYR A 267 
 ARG   0.003   0.000   ARG C 113 

*********************** 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
  104 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 LYS cc_start: 0.8044 (ptpp) cc_final: 0.7737 (ptpp)
REVERT: B  305 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7748 (mt-10)
REVERT: C   68 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7121 (t80)
REVERT: C  134 ARG cc_start: 0.6111 (mpp80) cc_final: 0.5308 (mmm160)
REVERT: E  196 SER cc_start: 0.7629 (t) cc_final: 0.7043 (p)
  outliers start: 18
  outliers final: 10
  residues processed: 100
  average time/residue: 0.2144
  time to fit residues: 29.8804
Evaluate side-chains
  86 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  257 ASP
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 E residue  356 SER
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 8 optimal weight:    5.9990
   chunk 57 optimal weight:    0.1980
   chunk 11 optimal weight:    0.1980
   chunk 21 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 92 optimal weight:    0.5980
   chunk 88 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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**
E 230 ASN
** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.170334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.141379 restraints weight = 13993.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.143737 restraints weight = 10313.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.145731 restraints weight = 7255.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8394  Z= 0.198
  Angle     :  0.547   8.093  11353  Z= 0.280
  Chirality :  0.041   0.137   1317
  Planarity :  0.004   0.046   1501
  Dihedral  :  3.797  18.068   1182
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 18.73 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.26), residues: 1076
  helix:  1.95 (0.25), residues: 438
  sheet: -1.30 (0.43), residues: 155
  loop : -0.54 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.003   TRP C 111 
 HIS   0.001   0.000   HIS A  84 
 PHE   0.010   0.001   PHE E 380 
 TYR   0.024   0.001   TYR A 267 
 ARG   0.005   0.000   ARG C 113 

*********************** 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
  92 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  305 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7727 (mt-10)
REVERT: C   68 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.7159 (t80)
REVERT: C  113 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7697 (tpt90)
REVERT: C  134 ARG cc_start: 0.6084 (mpp80) cc_final: 0.5312 (mmm160)
  outliers start: 15
  outliers final: 12
  residues processed: 89
  average time/residue: 0.1966
  time to fit residues: 25.1062
Evaluate side-chains
  87 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
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 B residue  153 MET
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  257 ASP
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0060
   chunk 45 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.6596

-------------------------------------------------------------------------------
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 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.162575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.133594 restraints weight = 14057.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.136081 restraints weight = 10303.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.137628 restraints weight = 7467.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.2532

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= 0.238
  Angle     :  0.562   7.688  11353  Z= 0.287
  Chirality :  0.042   0.140   1317
  Planarity :  0.004   0.052   1501
  Dihedral  :  3.858  17.883   1182
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.73 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.26), residues: 1076
  helix:  1.90 (0.25), residues: 438
  sheet: -1.41 (0.42), residues: 160
  loop : -0.53 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.003   TRP C 111 
 HIS   0.002   0.001   HIS A  84 
 PHE   0.012   0.001   PHE E 380 
 TYR   0.022   0.001   TYR A 267 
 ARG   0.004   0.000   ARG C 113 

*********************** 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
  96 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  305 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7738 (mt-10)
REVERT: C   68 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7227 (t80)
REVERT: C  113 ARG cc_start: 0.8005 (tpp80) cc_final: 0.7732 (tpt90)
REVERT: C  134 ARG cc_start: 0.6100 (mpp80) cc_final: 0.5314 (mmm160)
REVERT: F  428 LYS cc_start: 0.6253 (mmmt) cc_final: 0.5458 (mptt)
  outliers start: 16
  outliers final: 13
  residues processed: 92
  average time/residue: 0.2034
  time to fit residues: 26.5708
Evaluate side-chains
  90 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
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 B residue  153 MET
Chi-restraints excluded: chain B residue  160 MET
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 66 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.167283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.137436 restraints weight = 13850.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.139994 restraints weight = 10425.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.141738 restraints weight = 7398.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.2539

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= 0.269
  Angle     :  0.589   8.255  11353  Z= 0.301
  Chirality :  0.042   0.144   1317
  Planarity :  0.004   0.051   1501
  Dihedral  :  3.986  17.922   1182
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 19.41 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.26), residues: 1076
  helix:  1.77 (0.25), residues: 439
  sheet: -1.50 (0.41), residues: 160
  loop : -0.55 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.006   TRP C 111 
 HIS   0.002   0.001   HIS A  84 
 PHE   0.013   0.001   PHE E 380 
 TYR   0.022   0.002   TYR A 267 
 ARG   0.003   0.000   ARG C  65 

********************** 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
  93 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  305 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7754 (mt-10)
REVERT: C   68 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7269 (t80)
REVERT: C  134 ARG cc_start: 0.6248 (mpp80) cc_final: 0.5318 (mmm160)
REVERT: F  428 LYS cc_start: 0.6248 (mmmt) cc_final: 0.5438 (mptt)
  outliers start: 15
  outliers final: 13
  residues processed: 90
  average time/residue: 0.2122
  time to fit residues: 27.5245
Evaluate side-chains
  86 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
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 B residue  153 MET
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  248 VAL
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 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0040
   chunk 54 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    0.2980
   chunk 74 optimal weight:    0.9990
   chunk 64 optimal weight:    0.3980
   chunk 97 optimal weight:    2.9990
   chunk 55 optimal weight:    0.2980
   chunk 68 optimal weight:    0.3980
   overall best weight:    0.2792

-------------------------------------------------------------------------------
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 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.171357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.142599 restraints weight = 14091.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.145731 restraints weight = 10590.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.146680 restraints weight = 7461.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.2661

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= 0.177
  Angle     :  0.548   7.618  11353  Z= 0.281
  Chirality :  0.041   0.137   1317
  Planarity :  0.004   0.053   1501
  Dihedral  :  3.752  18.202   1182
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 20.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.26), residues: 1076
  helix:  1.95 (0.25), residues: 438
  sheet: -1.38 (0.43), residues: 155
  loop : -0.49 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.003   TRP C 111 
 HIS   0.001   0.000   HIS A  84 
 PHE   0.014   0.001   PHE E 380 
 TYR   0.022   0.001   TYR A 267 
 ARG   0.006   0.000   ARG C 113 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2678.56 seconds
wall clock time: 47 minutes 15.43 seconds (2835.43 seconds total)