Starting phenix.real_space_refine
on Thu Mar 13 13:50:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7c2e_30274/03_2025/7c2e_30274_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7c2e_30274/03_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_30274/03_2025/7c2e_30274.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7c2e_30274/03_2025/7c2e_30274.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7c2e_30274/03_2025/7c2e_30274_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7c2e_30274/03_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.28, 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: 2.15
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.83
  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: 2.29

  Time building geometry restraints manager: 2.53 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:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.040
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.100
-------------------------------------------------------------------------------
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  : 0.924 
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: 0.2481
  time to fit residues: 157.4994
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  : 1.028 
-------------------------------------------------------------------------------
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 = 0.117336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.097809 restraints weight = 30582.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.100246 restraints weight = 20414.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.102151 restraints weight = 15100.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.4696

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  45.377   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  : 1.046 
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: 0.8235 (OUTLIER) cc_final: 0.7940 (pp20)
REVERT: A   35 GLN cc_start: 0.8527 (pt0) cc_final: 0.8223 (tp40)
REVERT: A  270 LEU cc_start: 0.9059 (mt) cc_final: 0.8858 (mt)
REVERT: A  389 ARG cc_start: 0.7814 (ppt170) cc_final: 0.7156 (ppt170)
REVERT: A  390 GLN cc_start: 0.8901 (mt0) cc_final: 0.7922 (mm-40)
REVERT: B   75 GLN cc_start: 0.8826 (mp10) cc_final: 0.8589 (mm110)
REVERT: B  127 LYS cc_start: 0.8685 (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: 0.7623 (t0) cc_final: 0.7294 (t0)
REVERT: B  262 MET cc_start: 0.7933 (ttm) cc_final: 0.7491 (ttp)
REVERT: B  276 VAL cc_start: 0.9202 (m) cc_final: 0.8873 (m)
REVERT: B  308 LEU cc_start: 0.8973 (mt) cc_final: 0.8285 (mt)
REVERT: B  337 LYS cc_start: 0.8877 (mptt) cc_final: 0.8336 (mptt)
REVERT: B  339 TRP cc_start: 0.7108 (m100) cc_final: 0.6874 (m100)
REVERT: G   20 LYS cc_start: 0.7495 (pptt) cc_final: 0.6945 (tptt)
REVERT: G   36 ASP cc_start: 0.8944 (m-30) cc_final: 0.8739 (m-30)
REVERT: G   37 LEU cc_start: 0.8887 (mt) cc_final: 0.8369 (pp)
REVERT: N   18 LEU cc_start: 0.8349 (tp) cc_final: 0.7849 (tp)
REVERT: N   20 LEU cc_start: 0.8506 (mt) cc_final: 0.8224 (mt)
REVERT: N   33 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8409 (ptmm)
REVERT: N   83 MET cc_start: 0.7831 (mtm) cc_final: 0.7374 (mtm)
REVERT: R   37 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8539 (tm-30)
REVERT: R   44 ARG cc_start: 0.9031 (tmt170) cc_final: 0.8789 (tpt90)
REVERT: R   67 ASP cc_start: 0.7880 (p0) cc_final: 0.7156 (p0)
REVERT: R  163 SER cc_start: 0.9326 (m) cc_final: 0.8933 (p)
REVERT: R  184 PHE cc_start: 0.8334 (m-10) cc_final: 0.7982 (m-10)
REVERT: R  230 PHE cc_start: 0.8195 (t80) cc_final: 0.7612 (t80)
REVERT: R  246 VAL cc_start: 0.9343 (t) cc_final: 0.9101 (p)
REVERT: R  303 MET cc_start: 0.6813 (tpp) cc_final: 0.6308 (tpp)
  outliers start: 2
  outliers final: 1
  residues processed: 326
  average time/residue: 0.2597
  time to fit residues: 113.6812
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  : 1.107 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 49 optimal weight:   10.0000
   chunk 15 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 88 optimal weight:    9.9990
   chunk 90 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 20 optimal weight:    8.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A 236 GLN
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 HIS
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 = 0.4011 r_free = 0.4011 target = 0.111612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.092149 restraints weight = 31595.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.094471 restraints weight = 21325.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.096201 restraints weight = 15901.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.5627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9037  Z= 0.263
  Angle     :  0.664  11.107  12252  Z= 0.350
  Chirality :  0.044   0.152   1338
  Planarity :  0.004   0.035   1556
  Dihedral  :  5.446  42.553   1220
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.25), residues: 1072
  helix:  0.90 (0.25), residues: 398
  sheet: -2.21 (0.37), residues: 178
  loop : -2.06 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP R 284 
 HIS   0.009   0.002   HIS B  54 
 PHE   0.013   0.002   PHE A 273 
 TYR   0.018   0.002   TYR R 305 
 ARG   0.005   0.001   ARG R 190 

*********************** 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
  307 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 307
  time to evaluate  : 0.927 
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   35 GLN cc_start: 0.8594 (pt0) cc_final: 0.8373 (tp40)
REVERT: A  266 LEU cc_start: 0.8947 (tp) cc_final: 0.8697 (tp)
REVERT: A  386 MET cc_start: 0.8130 (tmm) cc_final: 0.7414 (tmm)
REVERT: A  389 ARG cc_start: 0.7541 (ppt170) cc_final: 0.6946 (ppt170)
REVERT: A  390 GLN cc_start: 0.8936 (mt0) cc_final: 0.8356 (mm-40)
REVERT: B   76 ASP cc_start: 0.7885 (p0) cc_final: 0.7004 (t0)
REVERT: B   78 LYS cc_start: 0.8558 (tptt) cc_final: 0.8249 (mmmt)
REVERT: B  254 ASP cc_start: 0.7455 (t0) cc_final: 0.7122 (t70)
REVERT: B  262 MET cc_start: 0.8084 (ttm) cc_final: 0.7882 (ttp)
REVERT: B  308 LEU cc_start: 0.8936 (mt) cc_final: 0.8643 (mt)
REVERT: B  337 LYS cc_start: 0.8913 (mptt) cc_final: 0.8449 (mptt)
REVERT: G   20 LYS cc_start: 0.7537 (pptt) cc_final: 0.7045 (tptt)
REVERT: N   18 LEU cc_start: 0.8454 (tp) cc_final: 0.8118 (tp)
REVERT: N   33 LYS cc_start: 0.8712 (ttpp) cc_final: 0.8333 (ptmm)
REVERT: N   83 MET cc_start: 0.7961 (mtm) cc_final: 0.7588 (mtm)
REVERT: R   37 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8751 (tm-30)
REVERT: R   67 ASP cc_start: 0.8068 (p0) cc_final: 0.7754 (p0)
REVERT: R  163 SER cc_start: 0.9344 (m) cc_final: 0.9006 (p)
REVERT: R  184 PHE cc_start: 0.8352 (m-10) cc_final: 0.8065 (m-10)
REVERT: R  230 PHE cc_start: 0.8286 (t80) cc_final: 0.7888 (t80)
REVERT: R  246 VAL cc_start: 0.9335 (t) cc_final: 0.9128 (p)
REVERT: R  415 LYS cc_start: 0.9252 (ptpp) cc_final: 0.8947 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 307
  average time/residue: 0.1934
  time to fit residues: 82.8211
Evaluate side-chains
  221 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   chunk 41 optimal weight:    9.9990
   chunk 9 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
R 171 HIS
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.114878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.096051 restraints weight = 30874.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.098285 restraints weight = 21070.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.099951 restraints weight = 15807.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.5824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9037  Z= 0.159
  Angle     :  0.610  10.571  12252  Z= 0.317
  Chirality :  0.042   0.153   1338
  Planarity :  0.004   0.029   1556
  Dihedral  :  5.048  35.337   1220
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.90 %
    Favored  : 97.99 %
  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:  1.22 (0.25), residues: 400
  sheet: -1.73 (0.38), residues: 176
  loop : -1.77 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP R 284 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.017   0.002   TYR A  37 
 ARG   0.005   0.000   ARG R  48 

*********************** 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
  306 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 305
  time to evaluate  : 1.065 
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   27 GLU cc_start: 0.8097 (pm20) cc_final: 0.7808 (pp20)
REVERT: A   35 GLN cc_start: 0.8589 (pt0) cc_final: 0.8330 (tp40)
REVERT: A   46 LEU cc_start: 0.8501 (pt) cc_final: 0.7826 (tp)
REVERT: A  346 LEU cc_start: 0.8934 (mt) cc_final: 0.8544 (mt)
REVERT: A  386 MET cc_start: 0.8063 (tmm) cc_final: 0.7357 (tmm)
REVERT: A  389 ARG cc_start: 0.7471 (ppt170) cc_final: 0.6951 (ppt170)
REVERT: A  390 GLN cc_start: 0.9035 (mt0) cc_final: 0.8247 (mm-40)
REVERT: B   50 THR cc_start: 0.8247 (m) cc_final: 0.7942 (p)
REVERT: B  121 CYS cc_start: 0.8317 (m) cc_final: 0.8115 (m)
REVERT: B  160 SER cc_start: 0.8005 (p) cc_final: 0.7561 (p)
REVERT: B  175 GLN cc_start: 0.8072 (mp-120) cc_final: 0.7766 (mp10)
REVERT: B  254 ASP cc_start: 0.7417 (t0) cc_final: 0.7115 (t70)
REVERT: B  264 TYR cc_start: 0.6055 (m-80) cc_final: 0.5702 (m-80)
REVERT: B  276 VAL cc_start: 0.9370 (m) cc_final: 0.9052 (m)
REVERT: B  308 LEU cc_start: 0.9000 (mt) cc_final: 0.7525 (mt)
REVERT: B  337 LYS cc_start: 0.8620 (mptt) cc_final: 0.8247 (mptt)
REVERT: B  339 TRP cc_start: 0.7259 (m100) cc_final: 0.6684 (m-10)
REVERT: G   20 LYS cc_start: 0.7655 (pptt) cc_final: 0.7216 (tptt)
REVERT: N   18 LEU cc_start: 0.8271 (tp) cc_final: 0.7922 (tp)
REVERT: N   20 LEU cc_start: 0.8535 (mt) cc_final: 0.8276 (mt)
REVERT: N   33 LYS cc_start: 0.8658 (ttpp) cc_final: 0.8409 (pttt)
REVERT: N   34 MET cc_start: 0.8830 (mpp) cc_final: 0.8001 (mpp)
REVERT: N   77 ASN cc_start: 0.7940 (t0) cc_final: 0.7099 (t0)
REVERT: N   83 MET cc_start: 0.7950 (mtm) cc_final: 0.7552 (mtm)
REVERT: R   37 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8692 (tm-30)
REVERT: R   38 LYS cc_start: 0.9037 (pttm) cc_final: 0.8755 (pttm)
REVERT: R   67 ASP cc_start: 0.7949 (p0) cc_final: 0.7062 (p0)
REVERT: R  163 SER cc_start: 0.9333 (m) cc_final: 0.9014 (p)
REVERT: R  177 ASN cc_start: 0.9253 (m110) cc_final: 0.9025 (m110)
REVERT: R  184 PHE cc_start: 0.8276 (m-10) cc_final: 0.8066 (m-10)
REVERT: R  230 PHE cc_start: 0.8209 (t80) cc_final: 0.7932 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 305
  average time/residue: 0.2034
  time to fit residues: 85.7576
Evaluate side-chains
  234 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 3 optimal weight:    0.0870
   chunk 41 optimal weight:    0.5980
   chunk 43 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 88 optimal weight:    0.9990
   chunk 96 optimal weight:    7.9990
   chunk 69 optimal weight:    3.9990
   chunk 103 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0770
   overall best weight:    0.5520

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B  54 HIS
B 340 ASN
N  39 GLN
N  82 GLN
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 320 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.116073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.097355 restraints weight = 30537.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.099649 restraints weight = 20753.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.101361 restraints weight = 15506.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.5997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9037  Z= 0.146
  Angle     :  0.587   9.729  12252  Z= 0.306
  Chirality :  0.042   0.148   1338
  Planarity :  0.003   0.029   1556
  Dihedral  :  4.883  34.831   1220
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  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: -0.64 (0.26), residues: 1072
  helix:  1.44 (0.26), residues: 403
  sheet: -1.44 (0.37), residues: 182
  loop : -1.63 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 284 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.020   0.001   PHE R 367 
 TYR   0.020   0.002   TYR R 220 
 ARG   0.007   0.000   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
  295 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 295
  time to evaluate  : 0.938 
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   35 GLN cc_start: 0.8551 (pt0) cc_final: 0.8310 (tp40)
REVERT: A   46 LEU cc_start: 0.8364 (pt) cc_final: 0.7894 (tp)
REVERT: A  272 LEU cc_start: 0.9281 (tp) cc_final: 0.8983 (tp)
REVERT: A  346 LEU cc_start: 0.8925 (mt) cc_final: 0.8721 (mt)
REVERT: A  386 MET cc_start: 0.8080 (tmm) cc_final: 0.7497 (tmm)
REVERT: A  389 ARG cc_start: 0.7538 (ppt170) cc_final: 0.7273 (ppt170)
REVERT: A  390 GLN cc_start: 0.9040 (mt0) cc_final: 0.8208 (mt0)
REVERT: B   76 ASP cc_start: 0.7682 (p0) cc_final: 0.6855 (t0)
REVERT: B  101 MET cc_start: 0.8303 (mpp) cc_final: 0.7898 (mtm)
REVERT: B  125 ASN cc_start: 0.7129 (t0) cc_final: 0.6869 (t0)
REVERT: B  254 ASP cc_start: 0.7343 (t0) cc_final: 0.7028 (t70)
REVERT: B  276 VAL cc_start: 0.9346 (m) cc_final: 0.8988 (m)
REVERT: B  308 LEU cc_start: 0.8939 (mt) cc_final: 0.7719 (mp)
REVERT: B  337 LYS cc_start: 0.8761 (mptt) cc_final: 0.8522 (mmpt)
REVERT: B  339 TRP cc_start: 0.7139 (m100) cc_final: 0.6793 (m-10)
REVERT: G   20 LYS cc_start: 0.7707 (pptt) cc_final: 0.7349 (tptt)
REVERT: N   34 MET cc_start: 0.8754 (mpp) cc_final: 0.8081 (mpp)
REVERT: N   77 ASN cc_start: 0.7912 (t0) cc_final: 0.7052 (t0)
REVERT: N  122 THR cc_start: 0.4416 (p) cc_final: 0.4126 (p)
REVERT: R   37 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8677 (tm-30)
REVERT: R   38 LYS cc_start: 0.9039 (pttm) cc_final: 0.8640 (pttm)
REVERT: R  161 ILE cc_start: 0.9276 (mm) cc_final: 0.9072 (mt)
REVERT: R  163 SER cc_start: 0.9311 (m) cc_final: 0.8987 (p)
REVERT: R  179 ILE cc_start: 0.9321 (mm) cc_final: 0.8955 (mm)
REVERT: R  184 PHE cc_start: 0.8220 (m-10) cc_final: 0.7944 (m-10)
REVERT: R  230 PHE cc_start: 0.8214 (t80) cc_final: 0.7761 (t80)
REVERT: R  360 LEU cc_start: 0.8542 (mp) cc_final: 0.8340 (mp)
REVERT: R  411 LEU cc_start: 0.9534 (tp) cc_final: 0.8969 (tp)
REVERT: R  415 LYS cc_start: 0.9197 (ptpp) cc_final: 0.8898 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 295
  average time/residue: 0.2019
  time to fit residues: 82.7757
Evaluate side-chains
  228 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 99 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 72 optimal weight:    8.9990
   chunk 70 optimal weight:    8.9990
   chunk 90 optimal weight:    0.1980
   chunk 51 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   overall best weight:    3.8388

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B  54 HIS
B 230 ASN
N  82 GLN
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 304 ASN
R 363 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.109476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.090795 restraints weight = 31555.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.092986 restraints weight = 21442.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.094546 restraints weight = 16023.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.6562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   9037  Z= 0.302
  Angle     :  0.671   8.757  12252  Z= 0.358
  Chirality :  0.045   0.140   1338
  Planarity :  0.004   0.038   1556
  Dihedral  :  5.415  48.722   1220
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  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: -0.87 (0.25), residues: 1072
  helix:  1.09 (0.25), residues: 406
  sheet: -1.55 (0.39), residues: 170
  loop : -1.65 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 297 
 HIS   0.009   0.002   HIS B 225 
 PHE   0.020   0.002   PHE A 273 
 TYR   0.022   0.002   TYR R 220 
 ARG   0.008   0.001   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
  267 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 0.862 
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: A  223 ASP cc_start: 0.7485 (t0) cc_final: 0.7245 (t70)
REVERT: A  272 LEU cc_start: 0.9390 (tp) cc_final: 0.9128 (tp)
REVERT: A  346 LEU cc_start: 0.8968 (mt) cc_final: 0.8678 (mt)
REVERT: A  390 GLN cc_start: 0.9101 (mt0) cc_final: 0.8539 (mt0)
REVERT: B   76 ASP cc_start: 0.7810 (p0) cc_final: 0.6910 (t0)
REVERT: B  101 MET cc_start: 0.8310 (mpp) cc_final: 0.8036 (mtm)
REVERT: B  254 ASP cc_start: 0.7399 (t0) cc_final: 0.7044 (t70)
REVERT: B  276 VAL cc_start: 0.9503 (m) cc_final: 0.9203 (m)
REVERT: B  308 LEU cc_start: 0.9002 (mt) cc_final: 0.8520 (mt)
REVERT: B  337 LYS cc_start: 0.8873 (mptt) cc_final: 0.8576 (mmpt)
REVERT: N   77 ASN cc_start: 0.8015 (t0) cc_final: 0.7239 (t0)
REVERT: R   37 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8669 (tm-30)
REVERT: R   38 LYS cc_start: 0.9073 (pttm) cc_final: 0.8633 (pttm)
REVERT: R   41 GLU cc_start: 0.8904 (tp30) cc_final: 0.8660 (tp30)
REVERT: R   44 ARG cc_start: 0.9162 (ppt170) cc_final: 0.8808 (tmm160)
REVERT: R  163 SER cc_start: 0.9335 (m) cc_final: 0.9062 (p)
REVERT: R  184 PHE cc_start: 0.8347 (m-10) cc_final: 0.8091 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 267
  average time/residue: 0.2020
  time to fit residues: 74.9932
Evaluate side-chains
  213 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 102 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   chunk 73 optimal weight:   20.0000
   chunk 49 optimal weight:    4.9990
   chunk 96 optimal weight:    4.9990
   chunk 84 optimal weight:    0.7980
   chunk 85 optimal weight:    7.9990
   overall best weight:    3.1586

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B 268 ASN
N  39 GLN
N  74 ASN
N  82 GLN
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.108548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.090039 restraints weight = 31797.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.092270 restraints weight = 21236.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.093931 restraints weight = 15735.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.6898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9037  Z= 0.254
  Angle     :  0.652   8.412  12252  Z= 0.347
  Chirality :  0.045   0.153   1338
  Planarity :  0.004   0.035   1556
  Dihedral  :  5.465  46.837   1220
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.26), residues: 1072
  helix:  0.92 (0.25), residues: 406
  sheet: -1.64 (0.37), residues: 188
  loop : -1.56 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R 297 
 HIS   0.010   0.002   HIS B 225 
 PHE   0.018   0.002   PHE A 273 
 TYR   0.021   0.002   TYR B 124 
 ARG   0.003   0.001   ARG R  48 

*********************** 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
  271 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 0.928 
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: A  223 ASP cc_start: 0.7523 (t0) cc_final: 0.7150 (t70)
REVERT: A  237 CYS cc_start: 0.8244 (p) cc_final: 0.7923 (p)
REVERT: A  272 LEU cc_start: 0.9393 (tp) cc_final: 0.9142 (tp)
REVERT: A  346 LEU cc_start: 0.8981 (mt) cc_final: 0.8699 (mt)
REVERT: A  386 MET cc_start: 0.8122 (tmm) cc_final: 0.7921 (tmm)
REVERT: A  390 GLN cc_start: 0.9034 (mt0) cc_final: 0.8490 (mt0)
REVERT: B   76 ASP cc_start: 0.7762 (p0) cc_final: 0.6764 (t0)
REVERT: B  101 MET cc_start: 0.8488 (mpp) cc_final: 0.8044 (mtm)
REVERT: B  254 ASP cc_start: 0.7232 (t0) cc_final: 0.6838 (t0)
REVERT: B  276 VAL cc_start: 0.9472 (m) cc_final: 0.9199 (m)
REVERT: B  308 LEU cc_start: 0.8885 (mt) cc_final: 0.8568 (mp)
REVERT: B  337 LYS cc_start: 0.8948 (mptt) cc_final: 0.8699 (mmtt)
REVERT: N   20 LEU cc_start: 0.8668 (mt) cc_final: 0.8269 (mt)
REVERT: N   32 TYR cc_start: 0.8707 (m-80) cc_final: 0.8457 (m-80)
REVERT: N   34 MET cc_start: 0.8713 (mpp) cc_final: 0.7948 (mpp)
REVERT: N   77 ASN cc_start: 0.7899 (t0) cc_final: 0.7104 (t0)
REVERT: R   37 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8628 (tm-30)
REVERT: R   38 LYS cc_start: 0.8970 (pttm) cc_final: 0.8536 (pttm)
REVERT: R   44 ARG cc_start: 0.9064 (ppt170) cc_final: 0.8721 (ttp80)
REVERT: R   69 TYR cc_start: 0.8305 (t80) cc_final: 0.8008 (t80)
REVERT: R  163 SER cc_start: 0.9248 (m) cc_final: 0.8977 (p)
REVERT: R  179 ILE cc_start: 0.9367 (mm) cc_final: 0.8876 (mm)
REVERT: R  181 LEU cc_start: 0.9331 (tp) cc_final: 0.9099 (tp)
REVERT: R  184 PHE cc_start: 0.8296 (m-10) cc_final: 0.7973 (m-10)
REVERT: R  190 ARG cc_start: 0.8352 (tpp80) cc_final: 0.8068 (tpt-90)
REVERT: R  230 PHE cc_start: 0.8327 (t80) cc_final: 0.8036 (t80)
REVERT: R  360 LEU cc_start: 0.8705 (mp) cc_final: 0.8492 (mp)
REVERT: R  414 ARG cc_start: 0.8140 (mmt180) cc_final: 0.7791 (mmt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 271
  average time/residue: 0.1932
  time to fit residues: 73.0149
Evaluate side-chains
  207 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 52 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 57 optimal weight:   20.0000
   chunk 20 optimal weight:    8.9990
   chunk 82 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0070
   overall best weight:    1.5402

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B  54 HIS
B 268 ASN
N  39 GLN
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 374 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.110717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.092091 restraints weight = 31463.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.094408 restraints weight = 21079.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.096018 restraints weight = 15616.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.6963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9037  Z= 0.189
  Angle     :  0.642   8.803  12252  Z= 0.334
  Chirality :  0.044   0.155   1338
  Planarity :  0.004   0.034   1556
  Dihedral  :  5.292  42.185   1220
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  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 (0.26), residues: 1072
  helix:  1.24 (0.26), residues: 397
  sheet: -1.40 (0.39), residues: 177
  loop : -1.59 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP R 284 
 HIS   0.008   0.001   HIS B 225 
 PHE   0.016   0.001   PHE A 273 
 TYR   0.020   0.002   TYR R 220 
 ARG   0.006   0.000   ARG N 105 

*********************** 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
  279 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 0.925 
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: A   40 THR cc_start: 0.8461 (m) cc_final: 0.8223 (m)
REVERT: A  223 ASP cc_start: 0.7391 (t0) cc_final: 0.6945 (t0)
REVERT: A  237 CYS cc_start: 0.8221 (p) cc_final: 0.7778 (p)
REVERT: A  272 LEU cc_start: 0.9359 (tp) cc_final: 0.9101 (tp)
REVERT: A  346 LEU cc_start: 0.8957 (mt) cc_final: 0.8706 (mt)
REVERT: A  386 MET cc_start: 0.8011 (tmm) cc_final: 0.7365 (tmm)
REVERT: A  390 GLN cc_start: 0.8976 (mt0) cc_final: 0.8305 (mt0)
REVERT: B   76 ASP cc_start: 0.7595 (p0) cc_final: 0.6541 (t0)
REVERT: B  125 ASN cc_start: 0.7441 (t0) cc_final: 0.7194 (t0)
REVERT: B  186 ASP cc_start: 0.7155 (m-30) cc_final: 0.6917 (m-30)
REVERT: B  254 ASP cc_start: 0.7231 (t0) cc_final: 0.6834 (t0)
REVERT: B  262 MET cc_start: 0.8023 (ttp) cc_final: 0.7523 (ptm)
REVERT: B  276 VAL cc_start: 0.9431 (m) cc_final: 0.9149 (m)
REVERT: B  308 LEU cc_start: 0.8819 (mt) cc_final: 0.7705 (mp)
REVERT: B  337 LYS cc_start: 0.8870 (mptt) cc_final: 0.8455 (mmtt)
REVERT: B  339 TRP cc_start: 0.7522 (m100) cc_final: 0.7039 (m-10)
REVERT: N   34 MET cc_start: 0.8688 (mpp) cc_final: 0.7889 (mpp)
REVERT: N   77 ASN cc_start: 0.7958 (t0) cc_final: 0.7178 (t0)
REVERT: R   37 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8643 (tm-30)
REVERT: R   38 LYS cc_start: 0.8977 (pttm) cc_final: 0.8662 (pttt)
REVERT: R  177 ASN cc_start: 0.9159 (m110) cc_final: 0.8734 (m-40)
REVERT: R  230 PHE cc_start: 0.8289 (t80) cc_final: 0.8045 (t80)
REVERT: R  360 LEU cc_start: 0.8650 (mp) cc_final: 0.8443 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 279
  average time/residue: 0.1848
  time to fit residues: 72.5558
Evaluate side-chains
  221 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 84 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   chunk 74 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 70 optimal weight:    8.9990
   chunk 21 optimal weight:    7.9990
   chunk 102 optimal weight:   10.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 387 HIS
B   6 GLN
** G  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  39 GLN
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 304 ASN
R 374 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.105502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.086680 restraints weight = 32115.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.088913 restraints weight = 21242.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.090542 restraints weight = 15702.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.7501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9037  Z= 0.322
  Angle     :  0.741   8.603  12252  Z= 0.389
  Chirality :  0.048   0.206   1338
  Planarity :  0.004   0.039   1556
  Dihedral  :  5.872  50.949   1220
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 20.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  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: -1.08 (0.25), residues: 1072
  helix:  0.78 (0.25), residues: 403
  sheet: -1.49 (0.39), residues: 184
  loop : -1.67 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 339 
 HIS   0.014   0.002   HIS B 225 
 PHE   0.022   0.002   PHE R 195 
 TYR   0.023   0.002   TYR B 124 
 ARG   0.008   0.001   ARG R  43 

*********************** 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
  267 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 1.265 
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: A  272 LEU cc_start: 0.9380 (tp) cc_final: 0.9125 (tp)
REVERT: A  278 ASN cc_start: 0.8643 (m-40) cc_final: 0.7986 (m-40)
REVERT: A  346 LEU cc_start: 0.9095 (mt) cc_final: 0.8816 (mt)
REVERT: A  386 MET cc_start: 0.8047 (tmm) cc_final: 0.7169 (tmm)
REVERT: A  387 HIS cc_start: 0.8646 (m-70) cc_final: 0.8208 (m-70)
REVERT: A  390 GLN cc_start: 0.9111 (mt0) cc_final: 0.8323 (mt0)
REVERT: B   76 ASP cc_start: 0.7849 (p0) cc_final: 0.6583 (t0)
REVERT: B  101 MET cc_start: 0.8674 (mpp) cc_final: 0.8405 (mpp)
REVERT: B  254 ASP cc_start: 0.7485 (t0) cc_final: 0.7092 (t0)
REVERT: B  276 VAL cc_start: 0.9508 (m) cc_final: 0.9184 (m)
REVERT: B  308 LEU cc_start: 0.8757 (mt) cc_final: 0.7729 (mp)
REVERT: B  337 LYS cc_start: 0.8848 (mptt) cc_final: 0.8480 (mmtt)
REVERT: B  339 TRP cc_start: 0.7755 (m100) cc_final: 0.7452 (m-10)
REVERT: G   36 ASP cc_start: 0.8890 (m-30) cc_final: 0.8657 (m-30)
REVERT: N   77 ASN cc_start: 0.8190 (t0) cc_final: 0.7537 (t0)
REVERT: R   37 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8706 (tm-30)
REVERT: R   38 LYS cc_start: 0.9090 (pttm) cc_final: 0.8775 (pttm)
REVERT: R   41 GLU cc_start: 0.8553 (tp30) cc_final: 0.8288 (tp30)
REVERT: R   69 TYR cc_start: 0.8583 (t80) cc_final: 0.8179 (t80)
REVERT: R  182 ASN cc_start: 0.8950 (m-40) cc_final: 0.8746 (m-40)
REVERT: R  204 MET cc_start: 0.8328 (mpp) cc_final: 0.8110 (mpp)
REVERT: R  230 PHE cc_start: 0.8324 (t80) cc_final: 0.8032 (t80)
REVERT: R  237 VAL cc_start: 0.9015 (t) cc_final: 0.8213 (t)
REVERT: R  360 LEU cc_start: 0.8755 (mp) cc_final: 0.8519 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 267
  average time/residue: 0.1998
  time to fit residues: 74.9014
Evaluate side-chains
  202 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
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:    0.0270
   chunk 67 optimal weight:    0.8980
   chunk 75 optimal weight:   20.0000
   chunk 105 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 69 optimal weight:    0.4980
   chunk 7 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9990
   chunk 24 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.2842

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A  35 GLN
A 220 HIS
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B  54 HIS
B 142 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  39 GLN
N  74 ASN
** R 173 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: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.110026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.091325 restraints weight = 31504.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.093614 restraints weight = 20911.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.095339 restraints weight = 15416.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.7395

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= 0.193
  Angle     :  0.664   8.804  12252  Z= 0.351
  Chirality :  0.046   0.160   1338
  Planarity :  0.004   0.056   1556
  Dihedral  :  5.383  41.042   1220
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  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: -0.95 (0.25), residues: 1072
  helix:  0.91 (0.25), residues: 400
  sheet: -1.45 (0.38), residues: 178
  loop : -1.60 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 297 
 HIS   0.010   0.001   HIS B  54 
 PHE   0.015   0.001   PHE R 184 
 TYR   0.034   0.002   TYR G  40 
 ARG   0.014   0.001   ARG B 129 

********************** 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
  277 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 1.082 
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: A  223 ASP cc_start: 0.7537 (t0) cc_final: 0.7266 (t0)
REVERT: A  272 LEU cc_start: 0.9253 (tp) cc_final: 0.8943 (tp)
REVERT: A  346 LEU cc_start: 0.8910 (mt) cc_final: 0.8625 (mt)
REVERT: A  386 MET cc_start: 0.7867 (tmm) cc_final: 0.7195 (tmm)
REVERT: A  387 HIS cc_start: 0.8546 (m-70) cc_final: 0.8167 (m-70)
REVERT: A  390 GLN cc_start: 0.9134 (mt0) cc_final: 0.8276 (mt0)
REVERT: B   76 ASP cc_start: 0.7576 (p0) cc_final: 0.6290 (t0)
REVERT: B  125 ASN cc_start: 0.7502 (t0) cc_final: 0.7222 (t0)
REVERT: B  186 ASP cc_start: 0.7112 (m-30) cc_final: 0.6859 (m-30)
REVERT: B  254 ASP cc_start: 0.7204 (t0) cc_final: 0.6794 (t0)
REVERT: B  262 MET cc_start: 0.7888 (ttp) cc_final: 0.7272 (ptm)
REVERT: B  276 VAL cc_start: 0.9449 (m) cc_final: 0.9148 (m)
REVERT: B  308 LEU cc_start: 0.8828 (mt) cc_final: 0.7845 (mp)
REVERT: B  311 HIS cc_start: 0.6622 (m-70) cc_final: 0.6152 (m-70)
REVERT: B  337 LYS cc_start: 0.8696 (mptt) cc_final: 0.8043 (mmtm)
REVERT: B  339 TRP cc_start: 0.7416 (m100) cc_final: 0.7194 (m-10)
REVERT: N   18 LEU cc_start: 0.8488 (tp) cc_final: 0.8126 (tt)
REVERT: N   20 LEU cc_start: 0.8374 (mt) cc_final: 0.8117 (mt)
REVERT: N   34 MET cc_start: 0.8711 (mpp) cc_final: 0.7942 (mpp)
REVERT: N   45 LEU cc_start: 0.8305 (mp) cc_final: 0.7878 (mp)
REVERT: N   73 ASP cc_start: 0.7836 (m-30) cc_final: 0.6171 (m-30)
REVERT: N   77 ASN cc_start: 0.8077 (t0) cc_final: 0.7416 (t0)
REVERT: N   83 MET cc_start: 0.8413 (mpp) cc_final: 0.8203 (mpp)
REVERT: N  122 THR cc_start: 0.5783 (p) cc_final: 0.5553 (p)
REVERT: R   37 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8638 (tm-30)
REVERT: R   41 GLU cc_start: 0.8621 (tp30) cc_final: 0.8327 (tp30)
REVERT: R   69 TYR cc_start: 0.8500 (t80) cc_final: 0.8269 (t80)
REVERT: R  178 TYR cc_start: 0.7508 (m-10) cc_final: 0.7244 (m-80)
REVERT: R  182 ASN cc_start: 0.8784 (m-40) cc_final: 0.8569 (m-40)
REVERT: R  230 PHE cc_start: 0.8313 (t80) cc_final: 0.8071 (t80)
REVERT: R  411 LEU cc_start: 0.9450 (tp) cc_final: 0.9179 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 277
  average time/residue: 0.2028
  time to fit residues: 76.9708
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  : 0.973 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 41 optimal weight:    8.9990
   chunk 58 optimal weight:    9.9990
   chunk 60 optimal weight:    6.9990
   chunk 69 optimal weight:    0.5980
   chunk 86 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 73 optimal weight:    0.5980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A  35 GLN
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** 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  74 ASN
R 171 HIS
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.110583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.092011 restraints weight = 31308.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.094294 restraints weight = 21048.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.095900 restraints weight = 15615.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.7496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9037  Z= 0.193
  Angle     :  0.674   8.611  12252  Z= 0.353
  Chirality :  0.045   0.146   1338
  Planarity :  0.004   0.059   1556
  Dihedral  :  5.353  45.128   1220
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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: -0.82 (0.25), residues: 1072
  helix:  1.01 (0.26), residues: 400
  sheet: -1.42 (0.37), residues: 178
  loop : -1.50 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 306 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.038   0.002   PHE A 238 
 TYR   0.021   0.002   TYR N 117 
 ARG   0.014   0.000   ARG B 129 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3241.16 seconds
wall clock time: 57 minutes 47.79 seconds (3467.79 seconds total)