Starting phenix.real_space_refine
on Thu Feb 13 11:22:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7c2e_30274/02_2025/7c2e_30274_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7c2e_30274/02_2025/7c2e_30274.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7c2e_30274/02_2025/7c2e_30274.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7c2e_30274/02_2025/7c2e_30274.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7c2e_30274/02_2025/7c2e_30274_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7c2e_30274/02_2025/7c2e_30274_neut.cif"
  }
  resolution = 4.2
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    5632      2.51       5
     N    1529      2.21       5
     O    1613      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8828
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1637
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 6, 'TRANS': 186}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 3152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3152
          Classifications: {'peptide': 380}
          Link IDs: {'PTRANS': 14, 'TRANS': 365}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 41
          Unusual residues: {'FFR': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ALA R 209 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA R 209 " occ=0.00
  Time building chain proxies: 5.31, per 1000 atoms: 0.60
  Number of scatterers: 8828
  At special positions: 0
  Unit cell: (82.555, 154.66, 121.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      53     16.00
     F       1      9.00
     O    1613      8.00
     N    1529      7.00
     C    5632      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  62 " - pdb=" SG  CYS R 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " distance=2.04

  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: 2.50
  Conformation dependent library (CDL) restraints added in 980.2 milliseconds
  

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2064

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 11 sheets defined
      39.7% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 39
      removed outlier: 4.000A  pdb=" N   GLU A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 238
      removed outlier: 3.831A  pdb=" N   LYS A 233 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
      removed outlier: 5.037A  pdb=" N   ILE A 235 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.506A  pdb=" N   PHE A 315 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 312 through 318'
    Processing helix  chain 'A' and resid 331 through 351
    Processing helix  chain 'A' and resid 372 through 391
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.622A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.626A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'R' and resid 31 through 52
    Processing helix  chain 'R' and resid 138 through 169
    Processing helix  chain 'R' and resid 174 through 198
    Processing helix  chain 'R' and resid 206 through 211
      removed outlier: 3.947A  pdb=" N   GLN R 210 " --> pdb=" O   SER R 206 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 211 through 222
      removed outlier: 3.569A  pdb=" N   ASP R 215 " --> pdb=" O   GLN R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 223 through 256
    Processing helix  chain 'R' and resid 261 through 274
    Processing helix  chain 'R' and resid 275 through 292
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 303 through 337
      removed outlier: 4.311A  pdb=" N   ILE R 309 " --> pdb=" O   TYR R 305 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
    Processing helix  chain 'R' and resid 345 through 360
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 362 through 369
    Processing helix  chain 'R' and resid 380 through 391
      removed outlier: 4.279A  pdb=" N   GLU R 387 " --> pdb=" O   LYS R 383 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 393 through 405
    Processing helix  chain 'R' and resid 406 through 423
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.707A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.392A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.819A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63
      removed outlier: 3.755A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.602A  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: 3.582A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.521A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG B 150 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL B 158 " --> pdb=" O   ARG B 150 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.573A  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: 3.973A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.394A  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 277
      removed outlier: 6.383A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ALA B 287 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 5
      removed outlier: 3.750A  pdb=" N   LEU N  18 " --> pdb=" O   MET N  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.142A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   THR N 122 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TYR N  94 " --> pdb=" O   THR N 122 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 83 through 84
      removed outlier: 3.617A  pdb=" N   VAL R  83 " --> pdb=" O   VAL R 100 " (cutoff:3.500A)

    401 hydrogen bonds defined for protein.
    1170 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: 2.12

  Time building geometry restraints manager: 2.76 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1426
        1.29 -     1.43: 2516
        1.43 -     1.57: 5024
        1.57 -     1.70: 0
        1.70 -     1.84: 71
  Bond restraints: 9037
  Sorted by residual:
  bond pdb=" C21 FFR R 501 "
       pdb=" N20 FFR R 501 "
    ideal  model  delta    sigma   weight residual
    1.306  1.364 -0.058 2.00e-02 2.50e+03 8.43e+00
  bond pdb=" C36 FFR R 501 "
       pdb=" O39 FFR R 501 "
    ideal  model  delta    sigma   weight residual
    1.433  1.489 -0.056 2.00e-02 2.50e+03 7.88e+00
  bond pdb=" C38 FFR R 501 "
       pdb=" O39 FFR R 501 "
    ideal  model  delta    sigma   weight residual
    1.436  1.490 -0.054 2.00e-02 2.50e+03 7.16e+00
  bond pdb=" C   LEU R 118 "
       pdb=" N   PRO R 119 "
    ideal  model  delta    sigma   weight residual
    1.331  1.359 -0.028 1.20e-02 6.94e+03 5.49e+00
  bond pdb=" C21 FFR R 501 "
       pdb=" O22 FFR R 501 "
    ideal  model  delta    sigma   weight residual
    1.341  1.382 -0.041 2.00e-02 2.50e+03 4.14e+00
  ... (remaining 9032 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 11890
        1.92 -     3.83: 288
        3.83 -     5.75: 47
        5.75 -     7.66: 16
        7.66 -     9.58: 11
  Bond angle restraints: 12252
  Sorted by residual:
  angle pdb=" C   ASN R 302 "
        pdb=" N   MET R 303 "
        pdb=" CA  MET R 303 "
      ideal   model   delta    sigma   weight residual
     121.54  131.12   -9.58 1.91e+00 2.74e-01 2.52e+01
  angle pdb=" N   GLY R 361 "
        pdb=" CA  GLY R 361 "
        pdb=" C   GLY R 361 "
      ideal   model   delta    sigma   weight residual
     111.03  117.91   -6.88 1.40e+00 5.10e-01 2.42e+01
  angle pdb=" CA  TYR R 148 "
        pdb=" CB  TYR R 148 "
        pdb=" CG  TYR R 148 "
      ideal   model   delta    sigma   weight residual
     113.90  122.47   -8.57 1.80e+00 3.09e-01 2.27e+01
  angle pdb=" C   LYS N  76 "
        pdb=" N   ASN N  77 "
        pdb=" CA  ASN N  77 "
      ideal   model   delta    sigma   weight residual
     121.54  130.57   -9.03 1.91e+00 2.74e-01 2.23e+01
  angle pdb=" C   THR B  86 "
        pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
      ideal   model   delta    sigma   weight residual
     121.54  129.72   -8.18 1.91e+00 2.74e-01 1.84e+01
  ... (remaining 12247 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.00: 5079
       15.00 -    30.00: 189
       30.00 -    45.00: 59
       45.00 -    60.00: 6
       60.00 -    75.00: 3
  Dihedral angle restraints: 5336
    sinusoidal: 2146
      harmonic: 3190
  Sorted by residual:
  dihedral pdb=" CA  SER R 261 "
           pdb=" C   SER R 261 "
           pdb=" N   GLU R 262 "
           pdb=" CA  GLU R 262 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.27  -28.73     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CA  ARG R 299 "
           pdb=" C   ARG R 299 "
           pdb=" N   ASN R 300 "
           pdb=" CA  ASN R 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.99  -27.01     0      5.00e+00 4.00e-02 2.92e+01
  dihedral pdb=" CA  ARG A 228 "
           pdb=" C   ARG A 228 "
           pdb=" N   ASP A 229 "
           pdb=" CA  ASP A 229 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.21  -22.79     0      5.00e+00 4.00e-02 2.08e+01
  ... (remaining 5333 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 932
       0.044 -    0.089: 296
       0.089 -    0.133: 92
       0.133 -    0.177: 15
       0.177 -    0.222: 3
  Chirality restraints: 1338
  Sorted by residual:
  chirality pdb=" CB  THR R 378 "
            pdb=" CA  THR R 378 "
            pdb=" OG1 THR R 378 "
            pdb=" CG2 THR R 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  ASN N  77 "
            pdb=" N   ASN N  77 "
            pdb=" C   ASN N  77 "
            pdb=" CB  ASN N  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  THR B  87 "
            pdb=" N   THR B  87 "
            pdb=" C   THR B  87 "
            pdb=" CB  THR B  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.33e-01
  ... (remaining 1335 not shown)

  Planarity restraints: 1556
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C02 FFR R 501 "   -0.146 2.00e-02 2.50e+03   8.09e-02 1.96e+02
        pdb=" C04 FFR R 501 "   -0.018 2.00e-02 2.50e+03
        pdb=" C06 FFR R 501 "    0.033 2.00e-02 2.50e+03
        pdb=" C07 FFR R 501 "    0.038 2.00e-02 2.50e+03
        pdb=" C08 FFR R 501 "    0.060 2.00e-02 2.50e+03
        pdb=" C09 FFR R 501 "    0.040 2.00e-02 2.50e+03
        pdb=" C11 FFR R 501 "   -0.025 2.00e-02 2.50e+03
        pdb=" C12 FFR R 501 "   -0.177 2.00e-02 2.50e+03
        pdb=" C35 FFR R 501 "    0.120 2.00e-02 2.50e+03
        pdb=" N1  FFR R 501 "    0.010 2.00e-02 2.50e+03
        pdb=" N10 FFR R 501 "    0.014 2.00e-02 2.50e+03
        pdb=" N34 FFR R 501 "    0.051 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  FFR R 501 "   -0.020 2.00e-02 2.50e+03   5.18e-02 6.72e+01
        pdb=" C23 FFR R 501 "   -0.118 2.00e-02 2.50e+03
        pdb=" C24 FFR R 501 "    0.011 2.00e-02 2.50e+03
        pdb=" C25 FFR R 501 "    0.042 2.00e-02 2.50e+03
        pdb=" C26 FFR R 501 "    0.052 2.00e-02 2.50e+03
        pdb=" C28 FFR R 501 "    0.030 2.00e-02 2.50e+03
        pdb=" C29 FFR R 501 "    0.025 2.00e-02 2.50e+03
        pdb=" C30 FFR R 501 "    0.027 2.00e-02 2.50e+03
        pdb=" F1  FFR R 501 "    0.022 2.00e-02 2.50e+03
        pdb=" N2  FFR R 501 "   -0.072 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R 303 "    0.016 2.00e-02 2.50e+03   3.23e-02 1.04e+01
        pdb=" C   MET R 303 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   MET R 303 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ASN R 304 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1553 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 91
        2.64 -     3.20: 7226
        3.20 -     3.77: 13439
        3.77 -     4.33: 17709
        4.33 -     4.90: 29444
  Nonbonded interactions: 67909
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.071 3.040
  nonbonded pdb=" ND1 HIS G  44 "
            pdb=" OE2 GLU G  47 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" OD2 ASP R  67 "
            pdb=" NH2 ARG R 102 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" OG1 THR B 184 "
            pdb=" OD2 ASP B 205 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" NZ  LYS A 233 "
            pdb=" OD2 ASP B 228 "
     model   vdw
     2.261 3.120
  ... (remaining 67904 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             0.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     21.900
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.050
  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:2.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9037  Z= 0.226
  Angle     :  0.797   9.579  12252  Z= 0.450
  Chirality :  0.049   0.222   1338
  Planarity :  0.007   0.081   1556
  Dihedral  :  9.286  75.003   3254
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  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: -3.36 (0.21), residues: 1072
  helix: -1.26 (0.19), residues: 396
  sheet: -2.87 (0.33), residues: 169
  loop : -2.79 (0.23), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 274 
 HIS   0.006   0.001   HIS R 171 
 PHE   0.023   0.002   PHE R 413 
 TYR   0.030   0.002   TYR R 178 
 ARG   0.004   0.000   ARG A  20 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  488 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 488
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8144 (tp40) cc_final: 0.7787 (tp40)
REVERT: A  270 LEU cc_start: 0.9027 (mt) cc_final: 0.8824 (mt)
REVERT: A  272 LEU cc_start: 0.9148 (tp) cc_final: 0.8748 (tp)
REVERT: A  279 ASN cc_start: 0.7763 (t0) cc_final: 0.7495 (t0)
REVERT: A  386 MET cc_start: 0.8142 (tmt) cc_final: 0.7368 (tmm)
REVERT: A  390 GLN cc_start: 0.8595 (mt0) cc_final: 0.7657 (mm-40)
REVERT: B   16 ASN cc_start: 0.8537 (m-40) cc_final: 0.8285 (m-40)
REVERT: B   75 GLN cc_start: 0.8596 (mp-120) cc_final: 0.8366 (mp10)
REVERT: B   76 ASP cc_start: 0.7059 (p0) cc_final: 0.6645 (t0)
REVERT: B  101 MET cc_start: 0.7700 (mtp) cc_final: 0.7389 (mtm)
REVERT: B  253 PHE cc_start: 0.8089 (m-80) cc_final: 0.7773 (m-80)
REVERT: B  276 VAL cc_start: 0.9110 (m) cc_final: 0.8642 (m)
REVERT: B  308 LEU cc_start: 0.8689 (mt) cc_final: 0.8349 (mp)
REVERT: N  122 THR cc_start: 0.5617 (p) cc_final: 0.4983 (p)
REVERT: R   34 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8118 (tp30)
REVERT: R   37 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8448 (tm-30)
REVERT: R   38 LYS cc_start: 0.9182 (mttt) cc_final: 0.8912 (mttt)
REVERT: R   67 ASP cc_start: 0.7810 (p0) cc_final: 0.7156 (p0)
REVERT: R   69 TYR cc_start: 0.7985 (t80) cc_final: 0.7562 (t80)
REVERT: R  163 SER cc_start: 0.9229 (m) cc_final: 0.8883 (p)
REVERT: R  179 ILE cc_start: 0.9293 (mm) cc_final: 0.8930 (mm)
REVERT: R  230 PHE cc_start: 0.7746 (t80) cc_final: 0.7087 (t80)
REVERT: R  303 MET cc_start: 0.6550 (tpp) cc_final: 0.5964 (tpp)
REVERT: R  387 GLU cc_start: 0.8467 (tm-30) cc_final: 0.7954 (mt-10)
REVERT: R  393 PHE cc_start: 0.7554 (m-10) cc_final: 0.6919 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 488
  average time/residue: 0.2613
  time to fit residues: 166.5915
Evaluate side-chains
  264 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 45 optimal weight:   10.0000
   chunk 27 optimal weight:    7.9990
   chunk 54 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 97 optimal weight:    0.8980
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 292 ASN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B  75 GLN
B 142 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
N  74 ASN
R 171 HIS
R 177 ASN
R 180 HIS
R 240 ASN
R 394 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.117335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.097791 restraints weight = 30582.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.100247 restraints weight = 20430.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.102165 restraints weight = 15096.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.4697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9037  Z= 0.227
  Angle     :  0.655  11.929  12252  Z= 0.343
  Chirality :  0.044   0.166   1338
  Planarity :  0.005   0.045   1556
  Dihedral  :  5.246  45.378   1220
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.59 %
    Favored  : 96.20 %
  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: -1.80 (0.24), residues: 1072
  helix:  0.60 (0.25), residues: 409
  sheet: -2.38 (0.34), residues: 190
  loop : -2.31 (0.26), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP R 284 
 HIS   0.009   0.002   HIS R 173 
 PHE   0.019   0.001   PHE R 367 
 TYR   0.019   0.002   TYR A  37 
 ARG   0.010   0.001   ARG A 265 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 326
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7937 (pp20)
REVERT: A   35 GLN cc_start: 0.8528 (pt0) cc_final: 0.8224 (tp40)
REVERT: A  270 LEU cc_start: 0.9058 (mt) cc_final: 0.8857 (mt)
REVERT: A  389 ARG cc_start: 0.7810 (ppt170) cc_final: 0.7153 (ppt170)
REVERT: A  390 GLN cc_start: 0.8902 (mt0) cc_final: 0.7926 (mm-40)
REVERT: B   75 GLN cc_start: 0.8825 (mp10) cc_final: 0.8588 (mm110)
REVERT: B  127 LYS cc_start: 0.8686 (mmtm) cc_final: 0.8330 (mmtm)
REVERT: B  146 LEU cc_start: 0.8646 (mp) cc_final: 0.7843 (mp)
REVERT: B  254 ASP cc_start: 0.7618 (t0) cc_final: 0.7289 (t0)
REVERT: B  262 MET cc_start: 0.7927 (ttm) cc_final: 0.7486 (ttp)
REVERT: B  276 VAL cc_start: 0.9200 (m) cc_final: 0.8871 (m)
REVERT: B  308 LEU cc_start: 0.8973 (mt) cc_final: 0.8284 (mt)
REVERT: B  337 LYS cc_start: 0.8877 (mptt) cc_final: 0.8336 (mptt)
REVERT: B  339 TRP cc_start: 0.7107 (m100) cc_final: 0.6874 (m100)
REVERT: G   20 LYS cc_start: 0.7496 (pptt) cc_final: 0.6946 (tptt)
REVERT: G   36 ASP cc_start: 0.8942 (m-30) cc_final: 0.8740 (m-30)
REVERT: G   37 LEU cc_start: 0.8886 (mt) cc_final: 0.8369 (pp)
REVERT: N   18 LEU cc_start: 0.8345 (tp) cc_final: 0.7846 (tp)
REVERT: N   20 LEU cc_start: 0.8504 (mt) cc_final: 0.8223 (mt)
REVERT: N   33 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8409 (ptmm)
REVERT: N   83 MET cc_start: 0.7824 (mtm) cc_final: 0.7372 (mtm)
REVERT: R   37 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8537 (tm-30)
REVERT: R   44 ARG cc_start: 0.9024 (tmt170) cc_final: 0.8786 (tpt90)
REVERT: R   67 ASP cc_start: 0.7874 (p0) cc_final: 0.7149 (p0)
REVERT: R  163 SER cc_start: 0.9325 (m) cc_final: 0.8933 (p)
REVERT: R  184 PHE cc_start: 0.8331 (m-10) cc_final: 0.7979 (m-10)
REVERT: R  230 PHE cc_start: 0.8192 (t80) cc_final: 0.7607 (t80)
REVERT: R  246 VAL cc_start: 0.9342 (t) cc_final: 0.9101 (p)
REVERT: R  303 MET cc_start: 0.6808 (tpp) cc_final: 0.6308 (tpp)
  outliers start: 2
  outliers final: 1
  residues processed: 326
  average time/residue: 0.2276
  time to fit residues: 99.3749
Evaluate side-chains
  230 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 228
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 78 optimal weight:    9.9990
   chunk 59 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   chunk 90 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A 220 HIS
A 236 GLN
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 171 HIS
R 173 HIS
R 177 ASN
R 240 ASN
R 304 ASN
R 407 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.107674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.088337 restraints weight = 32130.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.090559 restraints weight = 21639.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.092171 restraints weight = 16213.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.6020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   9037  Z= 0.361
  Angle     :  0.750  11.519  12252  Z= 0.395
  Chirality :  0.046   0.171   1338
  Planarity :  0.005   0.043   1556
  Dihedral  :  5.932  48.025   1220
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 18.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.75 %
    Favored  : 95.14 %
  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: -1.60 (0.25), residues: 1072
  helix:  0.61 (0.25), residues: 409
  sheet: -2.28 (0.37), residues: 178
  loop : -2.05 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP R 284 
 HIS   0.011   0.002   HIS B 225 
 PHE   0.015   0.002   PHE B 151 
 TYR   0.017   0.002   TYR R 220 
 ARG   0.007   0.001   ARG R 421 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 291
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8631 (pt0) cc_final: 0.8401 (tp40)
REVERT: A  237 CYS cc_start: 0.8311 (p) cc_final: 0.8072 (p)
REVERT: A  386 MET cc_start: 0.8147 (tmm) cc_final: 0.7943 (tmm)
REVERT: B   76 ASP cc_start: 0.8060 (p0) cc_final: 0.7642 (p0)
REVERT: B  101 MET cc_start: 0.8086 (mtp) cc_final: 0.7692 (mtm)
REVERT: B  127 LYS cc_start: 0.8691 (mmtm) cc_final: 0.8471 (mmtm)
REVERT: B  254 ASP cc_start: 0.7532 (t0) cc_final: 0.7156 (t0)
REVERT: B  262 MET cc_start: 0.8109 (ttm) cc_final: 0.7828 (ttp)
REVERT: B  308 LEU cc_start: 0.8910 (mt) cc_final: 0.8451 (mp)
REVERT: B  311 HIS cc_start: 0.6461 (m-70) cc_final: 0.5956 (m-70)
REVERT: B  337 LYS cc_start: 0.9019 (mptt) cc_final: 0.8489 (mptt)
REVERT: N   18 LEU cc_start: 0.8461 (tp) cc_final: 0.8143 (tp)
REVERT: N   33 LYS cc_start: 0.8756 (ttpp) cc_final: 0.8400 (ptmm)
REVERT: N   83 MET cc_start: 0.8012 (mtm) cc_final: 0.7630 (mtm)
REVERT: N  120 GLN cc_start: 0.7385 (pp30) cc_final: 0.6997 (pp30)
REVERT: R   37 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8648 (tm-30)
REVERT: R  163 SER cc_start: 0.9339 (m) cc_final: 0.9028 (p)
REVERT: R  181 LEU cc_start: 0.9270 (tp) cc_final: 0.9051 (tp)
REVERT: R  182 ASN cc_start: 0.8930 (m-40) cc_final: 0.8593 (m-40)
REVERT: R  184 PHE cc_start: 0.8450 (m-10) cc_final: 0.8123 (m-80)
REVERT: R  230 PHE cc_start: 0.8292 (t80) cc_final: 0.7988 (t80)
REVERT: R  376 ARG cc_start: 0.5874 (ptt-90) cc_final: 0.5561 (ptt-90)
  outliers start: 1
  outliers final: 0
  residues processed: 292
  average time/residue: 0.2117
  time to fit residues: 84.6438
Evaluate side-chains
  217 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B 142 HIS
B 268 ASN
** N  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 171 HIS
R 173 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.109560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.090366 restraints weight = 31519.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.092562 restraints weight = 21275.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.094219 restraints weight = 15851.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.6322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9037  Z= 0.229
  Angle     :  0.643  11.968  12252  Z= 0.340
  Chirality :  0.043   0.154   1338
  Planarity :  0.004   0.042   1556
  Dihedral  :  5.521  43.070   1220
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  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: -1.30 (0.25), residues: 1072
  helix:  0.86 (0.25), residues: 409
  sheet: -2.06 (0.38), residues: 175
  loop : -1.91 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 284 
 HIS   0.011   0.002   HIS B 225 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.016   0.002   TYR A  37 
 ARG   0.006   0.001   ARG R 170 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8133 (pm20) cc_final: 0.7697 (pp20)
REVERT: A   35 GLN cc_start: 0.8615 (pt0) cc_final: 0.8406 (tp40)
REVERT: A  272 LEU cc_start: 0.9311 (tp) cc_final: 0.9110 (tp)
REVERT: A  284 ASP cc_start: 0.7453 (m-30) cc_final: 0.7243 (m-30)
REVERT: A  346 LEU cc_start: 0.8900 (mt) cc_final: 0.8545 (mt)
REVERT: B   50 THR cc_start: 0.8321 (m) cc_final: 0.8028 (p)
REVERT: B   76 ASP cc_start: 0.7952 (p0) cc_final: 0.7023 (t0)
REVERT: B  127 LYS cc_start: 0.8651 (mmtm) cc_final: 0.8438 (mmtm)
REVERT: B  254 ASP cc_start: 0.7374 (t0) cc_final: 0.7015 (t70)
REVERT: B  308 LEU cc_start: 0.8912 (mt) cc_final: 0.8576 (mp)
REVERT: B  337 LYS cc_start: 0.8943 (mptt) cc_final: 0.8534 (mmtt)
REVERT: G   20 LYS cc_start: 0.7652 (pptt) cc_final: 0.7187 (tptt)
REVERT: G   37 LEU cc_start: 0.9064 (mt) cc_final: 0.8587 (pp)
REVERT: N   18 LEU cc_start: 0.8440 (tp) cc_final: 0.8072 (tp)
REVERT: N   20 LEU cc_start: 0.8519 (mt) cc_final: 0.8305 (mt)
REVERT: N   34 MET cc_start: 0.8807 (mpp) cc_final: 0.7962 (mpp)
REVERT: N   77 ASN cc_start: 0.7973 (t0) cc_final: 0.7316 (t0)
REVERT: N   83 MET cc_start: 0.8006 (mtm) cc_final: 0.7636 (mtm)
REVERT: N   94 TYR cc_start: 0.7849 (m-80) cc_final: 0.7615 (m-80)
REVERT: N  120 GLN cc_start: 0.7036 (pp30) cc_final: 0.6697 (pp30)
REVERT: R   37 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8633 (tm-30)
REVERT: R   38 LYS cc_start: 0.9133 (pttm) cc_final: 0.8537 (pttm)
REVERT: R  163 SER cc_start: 0.9299 (m) cc_final: 0.9037 (p)
REVERT: R  182 ASN cc_start: 0.8882 (m-40) cc_final: 0.8325 (m-40)
REVERT: R  184 PHE cc_start: 0.8354 (m-10) cc_final: 0.8040 (m-80)
REVERT: R  230 PHE cc_start: 0.8419 (t80) cc_final: 0.8013 (t80)
REVERT: R  415 LYS cc_start: 0.9244 (ptpp) cc_final: 0.8920 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.2094
  time to fit residues: 81.2674
Evaluate side-chains
  210 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 94 optimal weight:   30.0000
   chunk 3 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 43 optimal weight:    0.7980
   chunk 20 optimal weight:    9.9990
   chunk 88 optimal weight:    4.9990
   chunk 96 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 103 optimal weight:    7.9990
   chunk 8 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  39 GLN
N  82 GLN
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 363 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.107795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.088682 restraints weight = 31628.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.090910 restraints weight = 21306.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.092518 restraints weight = 15868.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.6714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9037  Z= 0.262
  Angle     :  0.655   8.176  12252  Z= 0.345
  Chirality :  0.044   0.137   1338
  Planarity :  0.004   0.032   1556
  Dihedral  :  5.724  46.851   1220
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  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: -1.21 (0.25), residues: 1072
  helix:  0.81 (0.25), residues: 412
  sheet: -1.96 (0.36), residues: 186
  loop : -1.75 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R  39 
 HIS   0.009   0.002   HIS B 225 
 PHE   0.015   0.002   PHE A 219 
 TYR   0.021   0.002   TYR R 220 
 ARG   0.008   0.001   ARG R 170 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8634 (pt0) cc_final: 0.8396 (tp40)
REVERT: A  272 LEU cc_start: 0.9362 (tp) cc_final: 0.9152 (tp)
REVERT: A  346 LEU cc_start: 0.8970 (mt) cc_final: 0.8751 (mt)
REVERT: B   16 ASN cc_start: 0.8683 (m-40) cc_final: 0.8469 (m-40)
REVERT: B   76 ASP cc_start: 0.7821 (p0) cc_final: 0.6676 (t0)
REVERT: B  254 ASP cc_start: 0.7339 (t0) cc_final: 0.6938 (t0)
REVERT: B  308 LEU cc_start: 0.8871 (mt) cc_final: 0.8494 (mp)
REVERT: N   18 LEU cc_start: 0.8434 (tp) cc_final: 0.8100 (tp)
REVERT: N   34 MET cc_start: 0.8746 (mpp) cc_final: 0.7877 (mpp)
REVERT: N   77 ASN cc_start: 0.7982 (t0) cc_final: 0.7293 (t0)
REVERT: N   83 MET cc_start: 0.8021 (mtm) cc_final: 0.7645 (mtm)
REVERT: N  120 GLN cc_start: 0.6932 (pp30) cc_final: 0.6556 (pp30)
REVERT: R   37 GLN cc_start: 0.9120 (mm-40) cc_final: 0.8585 (tm-30)
REVERT: R   69 TYR cc_start: 0.8424 (t80) cc_final: 0.8114 (t80)
REVERT: R  163 SER cc_start: 0.9219 (m) cc_final: 0.8971 (p)
REVERT: R  177 ASN cc_start: 0.9225 (m110) cc_final: 0.8982 (m-40)
REVERT: R  184 PHE cc_start: 0.8325 (m-10) cc_final: 0.8109 (m-10)
REVERT: R  230 PHE cc_start: 0.8409 (t80) cc_final: 0.8105 (t80)
REVERT: R  415 LYS cc_start: 0.9280 (ptpp) cc_final: 0.8804 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.2182
  time to fit residues: 86.2075
Evaluate side-chains
  208 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0040
   chunk 72 optimal weight:   30.0000
   chunk 70 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   overall best weight:    1.9798

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A  41 HIS
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B  54 HIS
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  74 ASN
R 171 HIS
** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 407 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.109204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.090693 restraints weight = 31437.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.092807 restraints weight = 21340.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.094221 restraints weight = 16017.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.6830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9037  Z= 0.203
  Angle     :  0.635   8.245  12252  Z= 0.335
  Chirality :  0.044   0.151   1338
  Planarity :  0.004   0.044   1556
  Dihedral  :  5.573  42.320   1220
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.53 %
    Favored  : 97.36 %
  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: -1.07 (0.25), residues: 1072
  helix:  1.03 (0.25), residues: 402
  sheet: -1.88 (0.37), residues: 175
  loop : -1.73 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R 284 
 HIS   0.009   0.002   HIS B  54 
 PHE   0.018   0.001   PHE R 315 
 TYR   0.020   0.002   TYR R 220 
 ARG   0.006   0.000   ARG R  48 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 284
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8618 (pt0) cc_final: 0.8359 (tp40)
REVERT: A  270 LEU cc_start: 0.9077 (mt) cc_final: 0.8869 (mt)
REVERT: B   76 ASP cc_start: 0.7842 (p0) cc_final: 0.7308 (p0)
REVERT: B  254 ASP cc_start: 0.7320 (t0) cc_final: 0.7030 (t70)
REVERT: B  308 LEU cc_start: 0.8799 (mt) cc_final: 0.7926 (mp)
REVERT: B  337 LYS cc_start: 0.8777 (mptt) cc_final: 0.8350 (mmtm)
REVERT: B  339 TRP cc_start: 0.7516 (m100) cc_final: 0.7302 (m-10)
REVERT: N   18 LEU cc_start: 0.8372 (tp) cc_final: 0.8029 (tp)
REVERT: N   32 TYR cc_start: 0.8583 (m-80) cc_final: 0.8257 (m-80)
REVERT: N   34 MET cc_start: 0.8771 (mpp) cc_final: 0.7858 (mpp)
REVERT: N   77 ASN cc_start: 0.8027 (t0) cc_final: 0.7346 (t0)
REVERT: N   83 MET cc_start: 0.8118 (mtm) cc_final: 0.7713 (mtm)
REVERT: N  120 GLN cc_start: 0.6908 (pp30) cc_final: 0.6651 (pp30)
REVERT: R   37 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8660 (tm-30)
REVERT: R   38 LYS cc_start: 0.9115 (pttt) cc_final: 0.8822 (pttt)
REVERT: R   69 TYR cc_start: 0.8545 (t80) cc_final: 0.8276 (t80)
REVERT: R  163 SER cc_start: 0.9229 (m) cc_final: 0.8988 (p)
REVERT: R  177 ASN cc_start: 0.9214 (m110) cc_final: 0.8959 (m-40)
REVERT: R  184 PHE cc_start: 0.8330 (m-10) cc_final: 0.8113 (m-10)
REVERT: R  230 PHE cc_start: 0.8416 (t80) cc_final: 0.8162 (t80)
REVERT: R  414 ARG cc_start: 0.8102 (mmt180) cc_final: 0.7800 (mmt-90)
  outliers start: 1
  outliers final: 0
  residues processed: 284
  average time/residue: 0.1918
  time to fit residues: 76.7134
Evaluate side-chains
  211 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 93 optimal weight:    0.5980
   chunk 17 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 102 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 73 optimal weight:   20.0000
   chunk 49 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 387 HIS
B   6 GLN
B  54 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.108446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.089661 restraints weight = 32081.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.091809 restraints weight = 21797.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.093191 restraints weight = 16379.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.7023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9037  Z= 0.220
  Angle     :  0.653   8.708  12252  Z= 0.342
  Chirality :  0.045   0.159   1338
  Planarity :  0.004   0.037   1556
  Dihedral  :  5.606  44.469   1220
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.25), residues: 1072
  helix:  1.04 (0.25), residues: 402
  sheet: -1.83 (0.36), residues: 177
  loop : -1.69 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP R 297 
 HIS   0.011   0.001   HIS B 225 
 PHE   0.020   0.001   PHE A 238 
 TYR   0.021   0.002   TYR R 220 
 ARG   0.004   0.000   ARG R 176 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8588 (pt0) cc_final: 0.8291 (tp40)
REVERT: A  272 LEU cc_start: 0.9371 (tp) cc_final: 0.9106 (tp)
REVERT: A  346 LEU cc_start: 0.8927 (mt) cc_final: 0.8672 (mt)
REVERT: A  387 HIS cc_start: 0.8479 (m-70) cc_final: 0.8141 (m-70)
REVERT: B   76 ASP cc_start: 0.7839 (p0) cc_final: 0.6641 (t0)
REVERT: B  186 ASP cc_start: 0.7079 (m-30) cc_final: 0.6875 (m-30)
REVERT: B  209 LYS cc_start: 0.9149 (mptt) cc_final: 0.8819 (mptt)
REVERT: B  254 ASP cc_start: 0.7438 (t0) cc_final: 0.7007 (t0)
REVERT: B  308 LEU cc_start: 0.8839 (mt) cc_final: 0.8607 (mp)
REVERT: B  337 LYS cc_start: 0.8749 (mptt) cc_final: 0.8545 (mmtt)
REVERT: G   37 LEU cc_start: 0.9118 (mt) cc_final: 0.8666 (pp)
REVERT: N   18 LEU cc_start: 0.8382 (tp) cc_final: 0.7984 (tp)
REVERT: N   20 LEU cc_start: 0.8583 (mm) cc_final: 0.8194 (mm)
REVERT: N   32 TYR cc_start: 0.8666 (m-80) cc_final: 0.8215 (m-80)
REVERT: N   34 MET cc_start: 0.8751 (mpp) cc_final: 0.7824 (mpp)
REVERT: N   77 ASN cc_start: 0.7914 (t0) cc_final: 0.7106 (t0)
REVERT: N   83 MET cc_start: 0.8220 (mtm) cc_final: 0.7773 (mtm)
REVERT: N  120 GLN cc_start: 0.6783 (pp30) cc_final: 0.6394 (pp30)
REVERT: N  122 THR cc_start: 0.4840 (p) cc_final: 0.4386 (p)
REVERT: R   37 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8650 (tm-30)
REVERT: R   38 LYS cc_start: 0.9103 (pttt) cc_final: 0.8740 (pttt)
REVERT: R   69 TYR cc_start: 0.8619 (t80) cc_final: 0.8321 (t80)
REVERT: R  204 MET cc_start: 0.8255 (mpp) cc_final: 0.8044 (mpp)
REVERT: R  230 PHE cc_start: 0.8357 (t80) cc_final: 0.8154 (t80)
REVERT: R  231 LEU cc_start: 0.9242 (tt) cc_final: 0.8946 (tt)
REVERT: R  284 TRP cc_start: 0.7576 (t60) cc_final: 0.7017 (t60)
REVERT: R  414 ARG cc_start: 0.8076 (mmt180) cc_final: 0.7814 (mmt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 267
  average time/residue: 0.1973
  time to fit residues: 74.1934
Evaluate side-chains
  215 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 41 optimal weight:   20.0000
   chunk 52 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 100 optimal weight:    7.9990
   chunk 89 optimal weight:    0.9990
   chunk 57 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 82 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B 110 ASN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 374 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.108781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.090029 restraints weight = 32231.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.092176 restraints weight = 21955.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.093704 restraints weight = 16482.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.7112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9037  Z= 0.205
  Angle     :  0.636   8.791  12252  Z= 0.336
  Chirality :  0.044   0.167   1338
  Planarity :  0.004   0.031   1556
  Dihedral  :  5.532  44.083   1220
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 15.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  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: -0.94 (0.25), residues: 1072
  helix:  1.07 (0.25), residues: 403
  sheet: -1.73 (0.37), residues: 171
  loop : -1.65 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP R 284 
 HIS   0.010   0.001   HIS B 225 
 PHE   0.017   0.002   PHE B 234 
 TYR   0.021   0.002   TYR R 220 
 ARG   0.007   0.000   ARG R 176 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 272
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8629 (pt0) cc_final: 0.8316 (tp40)
REVERT: A  272 LEU cc_start: 0.9367 (tp) cc_final: 0.9087 (tp)
REVERT: A  346 LEU cc_start: 0.8969 (mt) cc_final: 0.8696 (mt)
REVERT: A  386 MET cc_start: 0.8102 (tmm) cc_final: 0.7849 (tmm)
REVERT: A  387 HIS cc_start: 0.8468 (m-70) cc_final: 0.8187 (m-70)
REVERT: B   76 ASP cc_start: 0.7700 (p0) cc_final: 0.7056 (p0)
REVERT: B  235 PHE cc_start: 0.8470 (t80) cc_final: 0.8175 (t80)
REVERT: B  254 ASP cc_start: 0.7281 (t0) cc_final: 0.6956 (t0)
REVERT: B  308 LEU cc_start: 0.8849 (mt) cc_final: 0.8627 (mp)
REVERT: B  337 LYS cc_start: 0.8754 (mptt) cc_final: 0.8253 (mmtm)
REVERT: G   36 ASP cc_start: 0.8994 (m-30) cc_final: 0.8766 (m-30)
REVERT: G   37 LEU cc_start: 0.9145 (mt) cc_final: 0.8728 (pp)
REVERT: N   18 LEU cc_start: 0.8354 (tp) cc_final: 0.7944 (tp)
REVERT: N   20 LEU cc_start: 0.8444 (mm) cc_final: 0.8204 (mm)
REVERT: N   32 TYR cc_start: 0.8620 (m-80) cc_final: 0.8198 (m-80)
REVERT: N   34 MET cc_start: 0.8733 (mpp) cc_final: 0.7748 (mpp)
REVERT: N   50 ASP cc_start: 0.8967 (p0) cc_final: 0.8766 (p0)
REVERT: N   77 ASN cc_start: 0.7926 (t0) cc_final: 0.7136 (t0)
REVERT: N   83 MET cc_start: 0.8203 (mtm) cc_final: 0.7828 (mtm)
REVERT: N  120 GLN cc_start: 0.6801 (pp30) cc_final: 0.6318 (pp30)
REVERT: N  122 THR cc_start: 0.4953 (p) cc_final: 0.4676 (p)
REVERT: R   37 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8651 (tm-30)
REVERT: R   38 LYS cc_start: 0.9104 (pttt) cc_final: 0.8751 (pttt)
REVERT: R   69 TYR cc_start: 0.8626 (t80) cc_final: 0.8376 (t80)
REVERT: R  231 LEU cc_start: 0.9217 (tt) cc_final: 0.8964 (tt)
REVERT: R  284 TRP cc_start: 0.7686 (t60) cc_final: 0.7369 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 272
  average time/residue: 0.1962
  time to fit residues: 74.7607
Evaluate side-chains
  215 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 4 optimal weight:    0.6980
   chunk 15 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 84 optimal weight:    7.9990
   chunk 101 optimal weight:    4.9990
   chunk 74 optimal weight:    9.9990
   chunk 52 optimal weight:    0.0060
   chunk 70 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 102 optimal weight:    0.0070
   overall best weight:    1.5418

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B  54 HIS
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
R 210 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.109675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.090961 restraints weight = 31955.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.093148 restraints weight = 21678.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.094657 restraints weight = 16216.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.7207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9037  Z= 0.185
  Angle     :  0.648   8.854  12252  Z= 0.338
  Chirality :  0.045   0.144   1338
  Planarity :  0.004   0.030   1556
  Dihedral  :  5.418  42.558   1220
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.74 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.79 (0.25), residues: 1072
  helix:  1.26 (0.25), residues: 397
  sheet: -1.56 (0.37), residues: 170
  loop : -1.62 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP R 284 
 HIS   0.009   0.001   HIS B 225 
 PHE   0.029   0.002   PHE R 367 
 TYR   0.022   0.002   TYR R 220 
 ARG   0.006   0.000   ARG A 389 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 279
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8683 (pt0) cc_final: 0.8362 (tp40)
REVERT: A   40 THR cc_start: 0.8337 (m) cc_final: 0.8094 (m)
REVERT: A  223 ASP cc_start: 0.7396 (t0) cc_final: 0.7165 (t0)
REVERT: A  272 LEU cc_start: 0.9337 (tp) cc_final: 0.9054 (tp)
REVERT: A  278 ASN cc_start: 0.8739 (m-40) cc_final: 0.8221 (m-40)
REVERT: A  346 LEU cc_start: 0.8934 (mt) cc_final: 0.8677 (mt)
REVERT: A  386 MET cc_start: 0.8177 (tmm) cc_final: 0.7962 (tmm)
REVERT: A  387 HIS cc_start: 0.8460 (m-70) cc_final: 0.8129 (m-70)
REVERT: B   76 ASP cc_start: 0.7683 (p0) cc_final: 0.6424 (t0)
REVERT: B  159 THR cc_start: 0.8867 (p) cc_final: 0.8660 (p)
REVERT: B  235 PHE cc_start: 0.8452 (t80) cc_final: 0.8193 (t80)
REVERT: B  254 ASP cc_start: 0.7300 (t0) cc_final: 0.6993 (t0)
REVERT: B  308 LEU cc_start: 0.8522 (mt) cc_final: 0.8194 (mt)
REVERT: B  337 LYS cc_start: 0.8722 (mptt) cc_final: 0.8249 (mmtm)
REVERT: G   37 LEU cc_start: 0.9162 (mt) cc_final: 0.8735 (pp)
REVERT: G   40 TYR cc_start: 0.7521 (t80) cc_final: 0.7241 (t80)
REVERT: N    6 GLU cc_start: 0.6304 (tm-30) cc_final: 0.5812 (pp20)
REVERT: N   18 LEU cc_start: 0.8300 (tp) cc_final: 0.7499 (tt)
REVERT: N   20 LEU cc_start: 0.8403 (mm) cc_final: 0.7883 (mm)
REVERT: N   32 TYR cc_start: 0.8590 (m-80) cc_final: 0.8221 (m-80)
REVERT: N   34 MET cc_start: 0.8705 (mpp) cc_final: 0.7714 (mpp)
REVERT: N   50 ASP cc_start: 0.8887 (p0) cc_final: 0.8671 (p0)
REVERT: N   77 ASN cc_start: 0.7959 (t0) cc_final: 0.7294 (t0)
REVERT: N   83 MET cc_start: 0.8124 (mtm) cc_final: 0.7744 (mtm)
REVERT: N  105 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7899 (mpp80)
REVERT: N  122 THR cc_start: 0.4952 (p) cc_final: 0.4399 (p)
REVERT: R   37 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8651 (tm-30)
REVERT: R   38 LYS cc_start: 0.9108 (pttt) cc_final: 0.8791 (pttt)
  outliers start: 1
  outliers final: 0
  residues processed: 280
  average time/residue: 0.1939
  time to fit residues: 76.6913
Evaluate side-chains
  216 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0670
   chunk 75 optimal weight:    0.0970
   chunk 105 optimal weight:    0.9990
   chunk 21 optimal weight:    7.9990
   chunk 66 optimal weight:    0.7980
   chunk 69 optimal weight:    0.4980
   chunk 7 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.4916

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 210 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.113317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.094244 restraints weight = 31437.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.096636 restraints weight = 20546.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.098386 restraints weight = 15042.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.7184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9037  Z= 0.158
  Angle     :  0.656   9.317  12252  Z= 0.341
  Chirality :  0.045   0.158   1338
  Planarity :  0.004   0.030   1556
  Dihedral  :  5.062  38.400   1220
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.32 %
    Favored  : 99.58 %
  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: 1072
  helix:  1.43 (0.26), residues: 391
  sheet: -1.37 (0.36), residues: 185
  loop : -1.41 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP R 284 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.013   0.001   PHE R 367 
 TYR   0.021   0.001   TYR A  37 
 ARG   0.004   0.000   ARG R 176 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 293
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8649 (pt0) cc_final: 0.8340 (tp40)
REVERT: A  272 LEU cc_start: 0.9330 (tp) cc_final: 0.9060 (tp)
REVERT: A  278 ASN cc_start: 0.8654 (m-40) cc_final: 0.8321 (p0)
REVERT: A  358 TYR cc_start: 0.5869 (m-10) cc_final: 0.5510 (m-10)
REVERT: A  386 MET cc_start: 0.8054 (tmm) cc_final: 0.7547 (tmm)
REVERT: A  387 HIS cc_start: 0.8328 (m-70) cc_final: 0.8054 (m-70)
REVERT: A  390 GLN cc_start: 0.8606 (mt0) cc_final: 0.8148 (mt0)
REVERT: B   76 ASP cc_start: 0.7521 (p0) cc_final: 0.6116 (t0)
REVERT: B  121 CYS cc_start: 0.8570 (m) cc_final: 0.8367 (m)
REVERT: B  186 ASP cc_start: 0.7190 (m-30) cc_final: 0.6964 (m-30)
REVERT: B  235 PHE cc_start: 0.8188 (t80) cc_final: 0.7973 (t80)
REVERT: B  254 ASP cc_start: 0.7191 (t0) cc_final: 0.6863 (t0)
REVERT: B  332 TRP cc_start: 0.8877 (m-10) cc_final: 0.8667 (m-10)
REVERT: B  337 LYS cc_start: 0.8851 (mptt) cc_final: 0.8485 (mmpt)
REVERT: G   32 LYS cc_start: 0.8575 (ptpt) cc_final: 0.8251 (ptpp)
REVERT: G   37 LEU cc_start: 0.9101 (mt) cc_final: 0.8748 (pp)
REVERT: G   40 TYR cc_start: 0.7624 (t80) cc_final: 0.7068 (t80)
REVERT: N   18 LEU cc_start: 0.8114 (tp) cc_final: 0.6958 (tt)
REVERT: N   32 TYR cc_start: 0.8434 (m-80) cc_final: 0.8201 (m-80)
REVERT: N   34 MET cc_start: 0.8671 (mpp) cc_final: 0.7742 (mpp)
REVERT: N   77 ASN cc_start: 0.7937 (t0) cc_final: 0.7210 (t0)
REVERT: N   83 MET cc_start: 0.8053 (mtm) cc_final: 0.7689 (mtm)
REVERT: R   34 GLU cc_start: 0.8188 (tp30) cc_final: 0.7986 (tp30)
REVERT: R   37 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8747 (tm-30)
REVERT: R  183 LEU cc_start: 0.9255 (tp) cc_final: 0.9050 (tp)
REVERT: R  411 LEU cc_start: 0.9511 (tp) cc_final: 0.9125 (tp)
REVERT: R  412 GLU cc_start: 0.8180 (mp0) cc_final: 0.7859 (mp0)
REVERT: R  415 LYS cc_start: 0.9189 (ptpp) cc_final: 0.8941 (ptpp)
  outliers start: 1
  outliers final: 0
  residues processed: 294
  average time/residue: 0.1882
  time to fit residues: 77.1388
Evaluate side-chains
  225 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 58 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0870
   chunk 86 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0050
   chunk 97 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    3.0178

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A  41 HIS
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 210 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.107824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.088749 restraints weight = 31916.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.090945 restraints weight = 21611.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.092472 restraints weight = 16192.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.7484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9037  Z= 0.252
  Angle     :  0.685   7.543  12252  Z= 0.360
  Chirality :  0.046   0.161   1338
  Planarity :  0.004   0.034   1556
  Dihedral  :  5.662  51.210   1220
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.21 %
    Favored  : 99.58 %
  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: -0.74 (0.25), residues: 1072
  helix:  1.13 (0.25), residues: 401
  sheet: -1.25 (0.37), residues: 172
  loop : -1.57 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.003   TRP R 284 
 HIS   0.015   0.002   HIS R 363 
 PHE   0.025   0.002   PHE R 195 
 TYR   0.020   0.002   TYR R 252 
 ARG   0.007   0.001   ARG R 176 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3000.46 seconds
wall clock time: 54 minutes 28.67 seconds (3268.67 seconds total)