Starting phenix.real_space_refine
on Sat Jun  7 17:33:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w8b_37351/06_2025/8w8b_37351.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w8b_37351/06_2025/8w8b_37351.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w8b_37351/06_2025/8w8b_37351.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w8b_37351/06_2025/8w8b_37351.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w8b_37351/06_2025/8w8b_37351.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w8b_37351/06_2025/8w8b_37351.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.152
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      64      5.16       5
     C    5613      2.51       5
     N    1459      2.21       5
     O    1598      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8734
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1751
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2513
          Classifications: {'peptide': 328}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 322}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "E"
      Number of atoms: 1756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1756
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 10, 'TRANS': 217}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 347
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 4, 'TRANS': 40}
    Chain: "R"
      Number of atoms: 2197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2197
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 11, 'TRANS': 266}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 170
          Unusual residues: {'CLR': 5, 'PLM': 1, 'UJL': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
  Time building chain proxies: 5.77, per 1000 atoms: 0.66
  Number of scatterers: 8734
  At special positions: 0
  Unit cell: (86.52, 115.36, 128.544, 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      64     16.00
     O    1598      8.00
     N    1459      7.00
     C    5613      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: 2.45
  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:  2046

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      40.6% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.585A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A  13 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.569A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 327 through 352
      removed outlier: 4.182A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 4.177A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'E' and resid 220 through 224
      removed outlier: 3.567A  pdb=" N   VAL E 224 " --> pdb=" O   ALA E 221 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 19 through 23
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'R' and resid 36 through 64
    Processing helix  chain 'R' and resid 65 through 68
      removed outlier: 3.509A  pdb=" N   GLN R  68 " --> pdb=" O   ARG R  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 65 through 68'
    Processing helix  chain 'R' and resid 69 through 100
      removed outlier: 4.402A  pdb=" N   LEU R  90 " --> pdb=" O   SER R  86 " (cutoff:3.500A)
      Proline residue:  R  91  - end of helix
    Processing helix  chain 'R' and resid 104 through 140
      removed outlier: 4.092A  pdb=" N   THR R 108 " --> pdb=" O   LEU R 104 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 147
    Processing helix  chain 'R' and resid 149 through 174
      removed outlier: 3.905A  pdb=" N   ALA R 153 " --> pdb=" O   THR R 149 " (cutoff:3.500A)
      Proline residue:  R 170  - end of helix
    Processing helix  chain 'R' and resid 192 through 204
    Processing helix  chain 'R' and resid 204 through 228
    Processing helix  chain 'R' and resid 325 through 371
      Proline residue:  R 360  - end of helix
      Proline residue:  R 369  - end of helix
    Processing helix  chain 'R' and resid 378 through 401
      removed outlier: 3.800A  pdb=" N   ASN R 392 " --> pdb=" O   LEU R 388 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   SER R 393 " --> pdb=" O   GLY R 389 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   LEU R 394 " --> pdb=" O   TYR R 390 " (cutoff:3.500A)
      Proline residue:  R 397  - end of helix
    Processing helix  chain 'R' and resid 404 through 415
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.905A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 4.279A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.053A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.782A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.011A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.604A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   MET B 217 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.578A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.769A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.811A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142
    Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.345A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)

    466 hydrogen bonds defined for protein.
    1314 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: 2.66

  Time building geometry restraints manager: 2.84 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: 2760
        1.34 -     1.46: 1943
        1.46 -     1.58: 4132
        1.58 -     1.69: 1
        1.69 -     1.81: 90
  Bond restraints: 8926
  Sorted by residual:
  bond pdb=" C8  UJL R 507 "
       pdb=" S1  UJL R 507 "
    ideal  model  delta    sigma   weight residual
    1.725  1.522  0.203 2.00e-02 2.50e+03 1.03e+02
  bond pdb=" C9  UJL R 507 "
       pdb=" S1  UJL R 507 "
    ideal  model  delta    sigma   weight residual
    1.730  1.536  0.194 2.00e-02 2.50e+03 9.44e+01
  bond pdb=" C6  UJL R 507 "
       pdb=" C7  UJL R 507 "
    ideal  model  delta    sigma   weight residual
    1.428  1.600 -0.172 2.00e-02 2.50e+03 7.36e+01
  bond pdb=" C7  UJL R 507 "
       pdb=" C8  UJL R 507 "
    ideal  model  delta    sigma   weight residual
    1.364  1.419 -0.055 2.00e-02 2.50e+03 7.54e+00
  bond pdb=" N   TYR R  35 "
       pdb=" CA  TYR R  35 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.09e+00
  ... (remaining 8921 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.25: 12064
        3.25 -     6.50: 42
        6.50 -     9.74: 3
        9.74 -    12.99: 0
       12.99 -    16.24: 1
  Bond angle restraints: 12110
  Sorted by residual:
  angle pdb=" C8  UJL R 507 "
        pdb=" S1  UJL R 507 "
        pdb=" C9  UJL R 507 "
      ideal   model   delta    sigma   weight residual
      91.70  107.94  -16.24 3.00e+00 1.11e-01 2.93e+01
  angle pdb=" N   ARG A 242 "
        pdb=" CA  ARG A 242 "
        pdb=" C   ARG A 242 "
      ideal   model   delta    sigma   weight residual
     112.89  108.28    4.61 1.24e+00 6.50e-01 1.38e+01
  angle pdb=" N   THR B 128 "
        pdb=" CA  THR B 128 "
        pdb=" CB  THR B 128 "
      ideal   model   delta    sigma   weight residual
     109.97  115.34   -5.37 1.47e+00 4.63e-01 1.33e+01
  angle pdb=" N   ASP B 291 "
        pdb=" CA  ASP B 291 "
        pdb=" C   ASP B 291 "
      ideal   model   delta    sigma   weight residual
     113.21  109.45    3.76 1.15e+00 7.56e-01 1.07e+01
  angle pdb=" N   SER B 245 "
        pdb=" CA  SER B 245 "
        pdb=" C   SER B 245 "
      ideal   model   delta    sigma   weight residual
     109.69  114.17   -4.48 1.44e+00 4.82e-01 9.69e+00
  ... (remaining 12105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4992
       17.94 -    35.87: 409
       35.87 -    53.80: 105
       53.80 -    71.74: 22
       71.74 -    89.67: 7
  Dihedral angle restraints: 5535
    sinusoidal: 2362
      harmonic: 3173
  Sorted by residual:
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.72   18.28     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  LEU B 117 "
           pdb=" C   LEU B 117 "
           pdb=" N   ASP B 118 "
           pdb=" CA  ASP B 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.30   17.70     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CG  ARG G  62 "
           pdb=" CD  ARG G  62 "
           pdb=" NE  ARG G  62 "
           pdb=" CZ  ARG G  62 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.43   48.57     2      1.50e+01 4.44e-03 1.20e+01
  ... (remaining 5532 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1070
       0.040 -    0.080: 221
       0.080 -    0.120: 80
       0.120 -    0.159: 14
       0.159 -    0.199: 1
  Chirality restraints: 1386
  Sorted by residual:
  chirality pdb=" CA  THR B 128 "
            pdb=" N   THR B 128 "
            pdb=" C   THR B 128 "
            pdb=" CB  THR B 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.33    0.20 2.00e-01 2.50e+01 9.92e-01
  chirality pdb=" CB  VAL R  98 "
            pdb=" CA  VAL R  98 "
            pdb=" CG1 VAL R  98 "
            pdb=" CG2 VAL R  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.93e-01
  chirality pdb=" C3  UJL R 507 "
            pdb=" C2  UJL R 507 "
            pdb=" C9  UJL R 507 "
            pdb=" O1  UJL R 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.32   -0.14 2.00e-01 2.50e+01 4.84e-01
  ... (remaining 1383 not shown)

  Planarity restraints: 1492
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  62 "    0.172 9.50e-02 1.11e+02   7.74e-02 4.24e+00
        pdb=" NE  ARG G  62 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  62 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  62 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  62 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 235 "    0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO E 236 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO E 236 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO E 236 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 219 "    0.112 9.50e-02 1.11e+02   5.02e-02 1.84e+00
        pdb=" NE  ARG B 219 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 219 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 219 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 219 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1489 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 109
        2.63 -     3.20: 7774
        3.20 -     3.77: 13188
        3.77 -     4.33: 19297
        4.33 -     4.90: 32905
  Nonbonded interactions: 73273
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  57 "
            pdb=" OE1 GLU G  58 "
     model   vdw
     2.063 3.040
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" O   ARG B 314 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   SER E  85 "
            pdb=" OG  SER E  85 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OG1 THR B  29 "
            pdb=" OE1 GLN B  32 "
     model   vdw
     2.232 3.040
  ... (remaining 73268 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.060
  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:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.950
  Find NCS groups from input model:        0.110
  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:             0.010
  Load rotamer database and sin/cos tables:13.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
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      :  0.005   0.203   8926  Z= 0.229
  Angle     :  0.576  16.239  12110  Z= 0.314
  Chirality :  0.040   0.199   1386
  Planarity :  0.004   0.077   1492
  Dihedral  : 14.501  89.673   3489
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 14.72 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.26), residues: 1076
  helix:  2.56 (0.27), residues: 375
  sheet:  0.50 (0.31), residues: 275
  loop : -0.32 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  47 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.020   0.001   PHE B 292 
 TYR   0.010   0.001   TYR E 190 
 ARG   0.013   0.001   ARG G  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17407 (  466)
  hydrogen bonds       : angle       6.46289 ( 1314)
  covalent geometry    : bond        0.00465 ( 8926)
  covalent geometry    : angle       0.57572 (12110)

*********************** 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
  113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.929 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.8761 (pt0) cc_final: 0.8298 (pt0)
REVERT: A  275 GLU cc_start: 0.7322 (tp30) cc_final: 0.7075 (tp30)
REVERT: E   18 ARG cc_start: 0.8008 (ttt180) cc_final: 0.7770 (tpt170)
  outliers start: 5
  outliers final: 3
  residues processed: 112
  average time/residue: 1.3634
  time to fit residues: 162.1405
Evaluate side-chains
  101 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain R residue   61 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 54 optimal weight:    8.9990
   chunk 42 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 50 optimal weight:    8.9990
   chunk 61 optimal weight:    0.9990
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
E  82 GLN
R  72 ASN
R 408 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.147074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.109975 restraints weight = 9671.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 1.81
r_work: 0.2997 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.1082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8926  Z= 0.133
  Angle     :  0.537   9.226  12110  Z= 0.289
  Chirality :  0.042   0.138   1386
  Planarity :  0.004   0.048   1492
  Dihedral  :  5.511  57.700   1542
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.43 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.26), residues: 1076
  helix:  2.66 (0.27), residues: 378
  sheet:  0.66 (0.30), residues: 278
  loop : -0.29 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  82 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.012   0.001   PHE R 362 
 TYR   0.015   0.001   TYR E 190 
 ARG   0.006   0.000   ARG G  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04457 (  466)
  hydrogen bonds       : angle       4.84100 ( 1314)
  covalent geometry    : bond        0.00300 ( 8926)
  covalent geometry    : angle       0.53680 (12110)

*********************** 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
  117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.890 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.9029 (m-80) cc_final: 0.8791 (m-80)
REVERT: B  134 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7827 (ptp90)
REVERT: B  217 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7218 (pp-130)
REVERT: B  270 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7815 (pp)
REVERT: B  333 ASP cc_start: 0.7808 (t0) cc_final: 0.7551 (t0)
REVERT: G   38 MET cc_start: 0.7677 (mtp) cc_final: 0.7323 (mtp)
  outliers start: 18
  outliers final: 4
  residues processed: 109
  average time/residue: 1.4018
  time to fit residues: 162.2065
Evaluate side-chains
  99 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0770
   chunk 77 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0980
   chunk 71 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0470
   chunk 52 optimal weight:    8.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 239 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.149275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.112300 restraints weight = 9807.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 1.83
r_work: 0.3050 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8926  Z= 0.107
  Angle     :  0.486   6.460  12110  Z= 0.262
  Chirality :  0.041   0.129   1386
  Planarity :  0.003   0.039   1492
  Dihedral  :  5.144  57.436   1537
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.72 %
    Favored  : 83.57 %
  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:  1.57 (0.26), residues: 1076
  helix:  2.74 (0.27), residues: 381
  sheet:  0.51 (0.31), residues: 271
  loop : -0.14 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.010   0.001   PHE R 362 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.005   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03873 (  466)
  hydrogen bonds       : angle       4.53415 ( 1314)
  covalent geometry    : bond        0.00236 ( 8926)
  covalent geometry    : angle       0.48554 (12110)

*********************** 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
  118 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 1.187 
Fit side-chains
REVERT: A  205 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7451 (mpp80)
REVERT: B   59 TYR cc_start: 0.9021 (m-80) cc_final: 0.8798 (m-80)
REVERT: B  134 ARG cc_start: 0.8124 (mtm110) cc_final: 0.7599 (ptt-90)
REVERT: B  270 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7885 (pp)
REVERT: G   38 MET cc_start: 0.7681 (mtp) cc_final: 0.7303 (mtp)
REVERT: R  227 ARG cc_start: 0.7196 (mmt90) cc_final: 0.6900 (mmt180)
  outliers start: 16
  outliers final: 6
  residues processed: 114
  average time/residue: 1.4192
  time to fit residues: 171.8328
Evaluate side-chains
  102 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 73 optimal weight:    0.0040
   chunk 71 optimal weight:    8.9990
   chunk 57 optimal weight:    0.0870
   chunk 82 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.5570

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
B 266 HIS
E  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.150332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.115846 restraints weight = 9707.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 1.67
r_work: 0.3071 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8926  Z= 0.102
  Angle     :  0.471   6.453  12110  Z= 0.254
  Chirality :  0.040   0.125   1386
  Planarity :  0.003   0.039   1492
  Dihedral  :  5.016  56.139   1537
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.79 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.26), residues: 1076
  helix:  2.74 (0.27), residues: 383
  sheet:  0.45 (0.31), residues: 267
  loop : -0.14 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.002   0.000   HIS E  35 
 PHE   0.009   0.001   PHE E  29 
 TYR   0.013   0.001   TYR E 190 
 ARG   0.006   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03609 (  466)
  hydrogen bonds       : angle       4.36447 ( 1314)
  covalent geometry    : bond        0.00222 ( 8926)
  covalent geometry    : angle       0.47079 (12110)

*********************** 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
  118 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.951 
Fit side-chains
REVERT: A  205 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7466 (mpp80)
REVERT: B  134 ARG cc_start: 0.8092 (mtm110) cc_final: 0.7671 (ptt-90)
REVERT: B  270 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8007 (pp)
REVERT: G   38 MET cc_start: 0.7703 (mtp) cc_final: 0.7361 (mtp)
REVERT: G   58 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8135 (pm20)
  outliers start: 15
  outliers final: 5
  residues processed: 114
  average time/residue: 1.5900
  time to fit residues: 193.9905
Evaluate side-chains
  102 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 102 optimal weight:    0.0970
   chunk 58 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9980
   chunk 78 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 61 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.146223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.109339 restraints weight = 9780.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 1.81
r_work: 0.3006 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8926  Z= 0.150
  Angle     :  0.520   7.414  12110  Z= 0.278
  Chirality :  0.042   0.132   1386
  Planarity :  0.004   0.040   1492
  Dihedral  :  5.350  52.095   1537
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.43 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.26), residues: 1076
  helix:  2.64 (0.27), residues: 381
  sheet:  0.32 (0.30), residues: 283
  loop : -0.23 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E  47 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.013   0.001   PHE A 196 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.006   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04116 (  466)
  hydrogen bonds       : angle       4.51517 ( 1314)
  covalent geometry    : bond        0.00356 ( 8926)
  covalent geometry    : angle       0.52009 (12110)

*********************** 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
  119 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.861 
Fit side-chains
REVERT: A  205 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7684 (mtm180)
REVERT: B  134 ARG cc_start: 0.8184 (mtm110) cc_final: 0.7874 (ptp90)
REVERT: B  146 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8569 (tp)
REVERT: B  270 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8036 (pp)
REVERT: E   38 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8517 (ptt180)
REVERT: E   87 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6523 (mtt180)
REVERT: E  194 ASN cc_start: 0.8981 (m110) cc_final: 0.8720 (m110)
REVERT: G   38 MET cc_start: 0.7705 (mtp) cc_final: 0.7331 (mtp)
REVERT: G   58 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8215 (pm20)
  outliers start: 23
  outliers final: 10
  residues processed: 112
  average time/residue: 1.2129
  time to fit residues: 145.3558
Evaluate side-chains
  105 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 14 optimal weight:    0.1980
   chunk 82 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 92 optimal weight:    4.9990
   chunk 67 optimal weight:    0.1980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.152229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.116008 restraints weight = 9517.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 1.77
r_work: 0.3148 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8926  Z= 0.114
  Angle     :  0.489   6.431  12110  Z= 0.262
  Chirality :  0.041   0.129   1386
  Planarity :  0.003   0.039   1492
  Dihedral  :  5.160  47.072   1537
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.94 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.26), residues: 1076
  helix:  2.74 (0.27), residues: 381
  sheet:  0.34 (0.30), residues: 268
  loop : -0.26 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 213 
 PHE   0.009   0.001   PHE A 196 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.006   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03694 (  466)
  hydrogen bonds       : angle       4.38813 ( 1314)
  covalent geometry    : bond        0.00260 ( 8926)
  covalent geometry    : angle       0.48929 (12110)

*********************** 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
  112 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 1.088 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.8983 (m-80) cc_final: 0.8775 (m-80)
REVERT: B  134 ARG cc_start: 0.8092 (mtm110) cc_final: 0.7490 (ptt-90)
REVERT: B  146 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8508 (tp)
REVERT: B  270 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8009 (pp)
REVERT: E   87 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.6345 (mtt180)
REVERT: G   38 MET cc_start: 0.7534 (mtp) cc_final: 0.7118 (mtp)
REVERT: G   58 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7991 (pm20)
  outliers start: 15
  outliers final: 7
  residues processed: 108
  average time/residue: 1.2776
  time to fit residues: 147.1837
Evaluate side-chains
  106 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 104 optimal weight:    0.7980
   chunk 88 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
E  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.153343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.117887 restraints weight = 9627.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.70
r_work: 0.3152 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8926  Z= 0.122
  Angle     :  0.494   6.846  12110  Z= 0.263
  Chirality :  0.041   0.129   1386
  Planarity :  0.003   0.039   1492
  Dihedral  :  5.170  45.445   1537
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.76 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.26), residues: 1076
  helix:  2.72 (0.27), residues: 382
  sheet:  0.33 (0.30), residues: 268
  loop : -0.27 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 213 
 PHE   0.011   0.001   PHE A 196 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.007   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03758 (  466)
  hydrogen bonds       : angle       4.39201 ( 1314)
  covalent geometry    : bond        0.00281 ( 8926)
  covalent geometry    : angle       0.49357 (12110)

*********************** 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
  121 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 1.025 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.9056 (m-80) cc_final: 0.8840 (m-80)
REVERT: B  134 ARG cc_start: 0.8056 (mtm110) cc_final: 0.7451 (ptt-90)
REVERT: B  146 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8478 (tp)
REVERT: B  153 ASP cc_start: 0.8220 (m-30) cc_final: 0.7983 (m-30)
REVERT: B  197 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8219 (ttp-110)
REVERT: B  270 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8092 (pp)
REVERT: E   38 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8465 (ptt180)
REVERT: E   87 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6453 (mtt180)
REVERT: G   38 MET cc_start: 0.7594 (mtp) cc_final: 0.7207 (mtp)
REVERT: G   58 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7896 (pm20)
  outliers start: 24
  outliers final: 8
  residues processed: 112
  average time/residue: 1.3684
  time to fit residues: 164.0487
Evaluate side-chains
  105 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0030
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.154323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.118801 restraints weight = 9642.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.71
r_work: 0.3167 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8926  Z= 0.110
  Angle     :  0.488   6.582  12110  Z= 0.260
  Chirality :  0.040   0.133   1386
  Planarity :  0.003   0.039   1492
  Dihedral  :  5.040  44.901   1537
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 17.62 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.26), residues: 1076
  helix:  2.76 (0.27), residues: 383
  sheet:  0.32 (0.30), residues: 268
  loop : -0.26 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.009   0.001   PHE A 196 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.007   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03587 (  466)
  hydrogen bonds       : angle       4.32569 ( 1314)
  covalent geometry    : bond        0.00250 ( 8926)
  covalent geometry    : angle       0.48846 (12110)

*********************** 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
  119 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.993 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.9025 (m-80) cc_final: 0.8819 (m-80)
REVERT: B  134 ARG cc_start: 0.8070 (mtm110) cc_final: 0.7493 (ptt-90)
REVERT: B  146 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8496 (tp)
REVERT: B  197 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8118 (ttp-110)
REVERT: B  270 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8106 (pp)
REVERT: E   38 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8453 (ptt180)
REVERT: E   87 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6454 (mtt180)
REVERT: G   38 MET cc_start: 0.7565 (mtp) cc_final: 0.7180 (mtp)
REVERT: G   58 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7928 (pm20)
  outliers start: 17
  outliers final: 6
  residues processed: 113
  average time/residue: 1.2073
  time to fit residues: 146.2666
Evaluate side-chains
  105 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 39 optimal weight:    0.1980
   chunk 27 optimal weight:    0.7980
   chunk 50 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.153955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.118514 restraints weight = 9600.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.70
r_work: 0.3163 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8926  Z= 0.115
  Angle     :  0.497   6.633  12110  Z= 0.264
  Chirality :  0.041   0.132   1386
  Planarity :  0.003   0.039   1492
  Dihedral  :  5.048  45.374   1537
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 18.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.26), residues: 1076
  helix:  2.74 (0.27), residues: 383
  sheet:  0.32 (0.30), residues: 268
  loop : -0.29 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.010   0.001   PHE A 196 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.007   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  466)
  hydrogen bonds       : angle       4.34051 ( 1314)
  covalent geometry    : bond        0.00263 ( 8926)
  covalent geometry    : angle       0.49684 (12110)

*********************** 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
  115 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.872 
Fit side-chains
REVERT: B  134 ARG cc_start: 0.8054 (mtm110) cc_final: 0.7450 (ptt-90)
REVERT: B  153 ASP cc_start: 0.8276 (m-30) cc_final: 0.7903 (m-30)
REVERT: B  197 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8146 (ttp-110)
REVERT: B  270 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8114 (pp)
REVERT: E   38 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8462 (ptt180)
REVERT: E   87 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6491 (mtt180)
REVERT: G   38 MET cc_start: 0.7583 (mtp) cc_final: 0.7196 (mtp)
REVERT: G   58 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7961 (pm20)
  outliers start: 17
  outliers final: 7
  residues processed: 110
  average time/residue: 1.1481
  time to fit residues: 135.2031
Evaluate side-chains
  107 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 5 optimal weight:    0.0060
   chunk 71 optimal weight:    0.0670
   chunk 70 optimal weight:    0.0570
   chunk 21 optimal weight:    7.9990
   chunk 101 optimal weight:    0.9980
   chunk 81 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 105 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.3452

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
R 193 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.157257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.122450 restraints weight = 9590.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.70
r_work: 0.3216 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8926  Z= 0.091
  Angle     :  0.475   7.002  12110  Z= 0.252
  Chirality :  0.040   0.126   1386
  Planarity :  0.003   0.038   1492
  Dihedral  :  4.731  42.777   1537
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 19.01 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.26), residues: 1076
  helix:  2.81 (0.27), residues: 385
  sheet:  0.47 (0.31), residues: 262
  loop : -0.26 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.002   0.000   HIS B 142 
 PHE   0.008   0.001   PHE A 189 
 TYR   0.013   0.001   TYR E 190 
 ARG   0.007   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03236 (  466)
  hydrogen bonds       : angle       4.19239 ( 1314)
  covalent geometry    : bond        0.00191 ( 8926)
  covalent geometry    : angle       0.47525 (12110)

********************** 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
  113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.948 
Fit side-chains
REVERT: B  134 ARG cc_start: 0.8045 (mtm110) cc_final: 0.7542 (ptt-90)
REVERT: B  197 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8116 (ttp-110)
REVERT: B  270 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8087 (pp)
REVERT: E   18 ARG cc_start: 0.7867 (ttt180) cc_final: 0.7649 (tpp-160)
REVERT: E  204 SER cc_start: 0.8544 (p) cc_final: 0.8287 (t)
REVERT: G   38 MET cc_start: 0.7502 (mtp) cc_final: 0.7111 (mtp)
REVERT: G   58 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7904 (mp0)
  outliers start: 12
  outliers final: 6
  residues processed: 109
  average time/residue: 1.1324
  time to fit residues: 132.6242
Evaluate side-chains
  110 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 75 optimal weight:    9.9990
   chunk 76 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0010
   chunk 42 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 30 optimal weight:    0.4980
   overall best weight:    1.0188

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
E  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.153522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.117850 restraints weight = 9615.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 1.72
r_work: 0.3151 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8926  Z= 0.132
  Angle     :  0.522   7.095  12110  Z= 0.276
  Chirality :  0.041   0.145   1386
  Planarity :  0.003   0.039   1492
  Dihedral  :  5.060  45.987   1537
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 19.01 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.26), residues: 1076
  helix:  2.75 (0.27), residues: 383
  sheet:  0.36 (0.29), residues: 279
  loop : -0.32 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.011   0.001   PHE A 196 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.007   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03752 (  466)
  hydrogen bonds       : angle       4.33447 ( 1314)
  covalent geometry    : bond        0.00310 ( 8926)
  covalent geometry    : angle       0.52248 (12110)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6822.53 seconds
wall clock time: 119 minutes 13.11 seconds (7153.11 seconds total)