Starting phenix.real_space_refine
on Fri Nov 15 23:27:28 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/11_2024/8haf_34587.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/11_2024/8haf_34587.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/11_2024/8haf_34587.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/11_2024/8haf_34587.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/11_2024/8haf_34587.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/11_2024/8haf_34587.cif"
  }
  resolution = 3.25
  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=   0.001 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    6258      2.51       5
     N    1635      2.21       5
     O    1730      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 9681
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1950
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2616
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
    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: 983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 983
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
    Chain: "P"
      Number of atoms: 301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 301
          Classifications: {'peptide': 36}
          Link IDs: {'TRANS': 35}
    Chain: "R"
      Number of atoms: 3029
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 3029
          Classifications: {'peptide': 369}
          Link IDs: {'PTRANS': 11, 'TRANS': 357}
          Chain breaks: 3
    Chain: "R"
      Number of atoms: 366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 366
          Unusual residues: {'CLR': 6, 'PLM': 11}
          Classifications: {'undetermined': 17}
          Link IDs: {None: 16}
  Time building chain proxies: 6.45, per 1000 atoms: 0.67
  Number of scatterers: 9681
  At special positions: 0
  Unit cell: (103.824, 130.192, 140.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    1730      8.00
     N    1635      7.00
     C    6258      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  48 " - pdb=" SG  CYS R 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 131 " - pdb=" SG  CYS R 170 " distance=2.03

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.72
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2194

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      41.8% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 33
      removed outlier: 4.267A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLN A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 56
    Processing helix  chain 'A' and resid 235 through 241
      removed outlier: 4.311A  pdb=" N   ASP A 240 " --> pdb=" O   CYS A 237 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL A 241 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.525A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.539A  pdb=" N   ASN B  16 " --> pdb=" O   GLU B  12 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.544A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 4.217A  pdb=" N   GLN G  11 " --> pdb=" O   ALA G   7 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.643A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 5 through 32
    Processing helix  chain 'P' and resid 33 through 36
    Processing helix  chain 'R' and resid 33 through 51
      removed outlier: 3.596A  pdb=" N   PHE R  39 " --> pdb=" O   GLU R  35 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 167 through 172
      removed outlier: 3.758A  pdb=" N   VAL R 171 " --> pdb=" O   TYR R 167 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   LYS R 172 " --> pdb=" O   SER R 168 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 167 through 172'
    Processing helix  chain 'R' and resid 178 through 212
      removed outlier: 3.553A  pdb=" N   PHE R 212 " --> pdb=" O   ILE R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 244
      removed outlier: 3.735A  pdb=" N   ALA R 242 " --> pdb=" O   PHE R 238 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU R 244 " --> pdb=" O   LYS R 240 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 278 through 311
      removed outlier: 3.653A  pdb=" N   GLY R 303 " --> pdb=" O   ILE R 299 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 319
    Processing helix  chain 'R' and resid 320 through 347
      removed outlier: 4.052A  pdb=" N   LEU R 331 " --> pdb=" O   PHE R 327 " (cutoff:3.500A)
      Proline residue:  R 332  - end of helix
      removed outlier: 3.581A  pdb=" N   ALA R 347 " --> pdb=" O   ARG R 343 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 357 through 359
      No H-bonds generated for 'chain 'R' and resid 357 through 359'
    Processing helix  chain 'R' and resid 360 through 393
      Proline residue:  R 366  - end of helix
      removed outlier: 3.971A  pdb=" N   ILE R 371 " --> pdb=" O   ILE R 367 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   VAL R 372 " --> pdb=" O   LEU R 368 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 400 through 414
      removed outlier: 3.769A  pdb=" N   ARG R 404 " --> pdb=" O   ARG R 400 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 434 through 460
      removed outlier: 4.088A  pdb=" N   SER R 449 " --> pdb=" O   MET R 445 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   GLY R 452 " --> pdb=" O   ASN R 448 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   PHE R 453 " --> pdb=" O   SER R 449 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 463 through 480
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.711A  pdb=" N   PHE A 208 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   HIS A  34 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.646A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.772A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.684A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.306A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.004A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.999A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.583A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.632A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.507A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 6 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.526A  pdb=" N   THR N 125 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ARG N  38 " --> pdb=" O   GLU N  46 " (cutoff:3.500A)

    449 hydrogen bonds defined for protein.
    1284 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: 2.57

  Time building geometry restraints manager: 3.09 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3073
        1.35 -     1.46: 2394
        1.46 -     1.58: 4348
        1.58 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 9897
  Sorted by residual:
  bond pdb=" C1  PLM R1507 "
       pdb=" C2  PLM R1507 "
    ideal  model  delta    sigma   weight residual
    1.542  1.573 -0.031 2.00e-02 2.50e+03 2.38e+00
  bond pdb=" C1  PLM R1501 "
       pdb=" C2  PLM R1501 "
    ideal  model  delta    sigma   weight residual
    1.542  1.572 -0.030 2.00e-02 2.50e+03 2.18e+00
  bond pdb=" C1  PLM R1511 "
       pdb=" C2  PLM R1511 "
    ideal  model  delta    sigma   weight residual
    1.542  1.571 -0.029 2.00e-02 2.50e+03 2.09e+00
  bond pdb=" C1  PLM R1504 "
       pdb=" C2  PLM R1504 "
    ideal  model  delta    sigma   weight residual
    1.542  1.571 -0.029 2.00e-02 2.50e+03 2.08e+00
  bond pdb=" C1  PLM R1503 "
       pdb=" C2  PLM R1503 "
    ideal  model  delta    sigma   weight residual
    1.542  1.571 -0.029 2.00e-02 2.50e+03 2.05e+00
  ... (remaining 9892 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.48: 13355
        6.48 -    12.96: 7
       12.96 -    19.44: 5
       19.44 -    25.92: 0
       25.92 -    32.39: 2
  Bond angle restraints: 13369
  Sorted by residual:
  angle pdb=" C17 CLR R1515 "
        pdb=" C13 CLR R1515 "
        pdb=" C18 CLR R1515 "
      ideal   model   delta    sigma   weight residual
     110.18   77.79   32.39 3.00e+00 1.11e-01 1.17e+02
  angle pdb=" C12 CLR R1515 "
        pdb=" C13 CLR R1515 "
        pdb=" C18 CLR R1515 "
      ideal   model   delta    sigma   weight residual
     111.01   78.96   32.05 3.00e+00 1.11e-01 1.14e+02
  angle pdb=" C4  CLR R1512 "
        pdb=" C3  CLR R1512 "
        pdb=" O1  CLR R1512 "
      ideal   model   delta    sigma   weight residual
     111.96  130.39  -18.43 3.00e+00 1.11e-01 3.77e+01
  angle pdb=" C12 CLR R1515 "
        pdb=" C13 CLR R1515 "
        pdb=" C17 CLR R1515 "
      ideal   model   delta    sigma   weight residual
     116.52  133.93  -17.41 3.00e+00 1.11e-01 3.37e+01
  angle pdb=" C14 CLR R1515 "
        pdb=" C13 CLR R1515 "
        pdb=" C18 CLR R1515 "
      ideal   model   delta    sigma   weight residual
     112.24   95.10   17.14 3.00e+00 1.11e-01 3.27e+01
  ... (remaining 13364 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.92: 5993
       35.92 -    71.83: 176
       71.83 -   107.75: 2
      107.75 -   143.67: 2
      143.67 -   179.58: 5
  Dihedral angle restraints: 6178
    sinusoidal: 2782
      harmonic: 3396
  Sorted by residual:
  dihedral pdb=" CB  CYS R 131 "
           pdb=" SG  CYS R 131 "
           pdb=" SG  CYS R 170 "
           pdb=" CB  CYS R 170 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.39  -60.39     1      1.00e+01 1.00e-02 4.86e+01
  dihedral pdb=" C18 CLR R1515 "
           pdb=" C13 CLR R1515 "
           pdb=" C14 CLR R1515 "
           pdb=" C8  CLR R1515 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.65 -116.93  179.58     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C15 CLR R1515 "
           pdb=" C13 CLR R1515 "
           pdb=" C14 CLR R1515 "
           pdb=" C18 CLR R1515 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.18 -111.99 -178.83     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 6175 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.349: 1468
       0.349 -    0.699: 1
       0.699 -    1.048: 1
       1.048 -    1.397: 0
       1.397 -    1.746: 1
  Chirality restraints: 1471
  Sorted by residual:
  chirality pdb=" C13 CLR R1515 "
            pdb=" C12 CLR R1515 "
            pdb=" C14 CLR R1515 "
            pdb=" C17 CLR R1515 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -1.19   -1.75 2.00e-01 2.50e+01 7.62e+01
  chirality pdb=" C3  CLR R1512 "
            pdb=" C2  CLR R1512 "
            pdb=" C4  CLR R1512 "
            pdb=" O1  CLR R1512 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.46   -1.41   -1.05 2.00e-01 2.50e+01 2.74e+01
  chirality pdb=" C3  CLR R1515 "
            pdb=" C2  CLR R1515 "
            pdb=" C4  CLR R1515 "
            pdb=" O1  CLR R1515 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.46   -3.00    0.55 2.00e-01 2.50e+01 7.54e+00
  ... (remaining 1468 not shown)

  Planarity restraints: 1652
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 164 "   -0.024 2.00e-02 2.50e+03   2.15e-02 1.16e+01
        pdb=" CG  TRP R 164 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 164 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 164 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 164 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 164 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 164 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 164 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 164 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 164 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP R 137 "    0.012 2.00e-02 2.50e+03   2.32e-02 5.38e+00
        pdb=" C   ASP R 137 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ASP R 137 "    0.015 2.00e-02 2.50e+03
        pdb=" N   PHE R 138 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG P  21 "   -0.011 2.00e-02 2.50e+03   2.22e-02 4.92e+00
        pdb=" C   ARG P  21 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ARG P  21 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   PHE P  22 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1649 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.32: 8
        2.32 -     2.96: 4397
        2.96 -     3.61: 13918
        3.61 -     4.25: 21038
        4.25 -     4.90: 36186
  Nonbonded interactions: 75547
  Sorted by model distance:
  nonbonded pdb=" O1  CLR R1512 "
            pdb=" O1  CLR R1515 "
     model   vdw
     1.671 2.432
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.043 3.040
  nonbonded pdb=" O1  CLR R1512 "
            pdb=" C2  CLR R1515 "
     model   vdw
     2.061 2.752
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" C4  CLR R1512 "
            pdb=" O1  CLR R1515 "
     model   vdw
     2.236 2.752
  ... (remaining 75542 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.160
  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:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     25.230
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
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      :  0.003   0.040   9897  Z= 0.201
  Angle     :  0.821  32.394  13369  Z= 0.376
  Chirality :  0.068   1.746   1471
  Planarity :  0.004   0.052   1652
  Dihedral  : 16.056 179.584   3972
  Min Nonbonded Distance : 1.671

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 17.96 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.26), residues: 1147
  helix:  2.05 (0.25), residues: 460
  sheet:  0.92 (0.42), residues: 175
  loop : -1.03 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.001   TRP R 164 
 HIS   0.004   0.001   HIS R 420 
 PHE   0.017   0.001   PHE R  39 
 TYR   0.032   0.001   TYR R 191 
 ARG   0.012   0.001   ARG R  43 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 215
  time to evaluate  : 1.009 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6267 (tmm) cc_final: 0.5877 (tmm)
REVERT: A  208 PHE cc_start: 0.8405 (m-80) cc_final: 0.8202 (m-80)
REVERT: A  211 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7885 (mttt)
REVERT: A  283 ARG cc_start: 0.7362 (ptt180) cc_final: 0.6982 (ptp-170)
REVERT: A  342 ARG cc_start: 0.7316 (ttp-170) cc_final: 0.7096 (ttt-90)
REVERT: B  188 MET cc_start: 0.7690 (mmm) cc_final: 0.7372 (mmm)
REVERT: B  217 MET cc_start: 0.6992 (ppp) cc_final: 0.6234 (ppp)
REVERT: B  289 TYR cc_start: 0.7813 (m-80) cc_final: 0.6921 (m-80)
REVERT: B  295 ASN cc_start: 0.8242 (m-40) cc_final: 0.8003 (m-40)
REVERT: N   34 MET cc_start: 0.8015 (mmm) cc_final: 0.7501 (mmm)
REVERT: N   49 SER cc_start: 0.8222 (p) cc_final: 0.7787 (t)
REVERT: R  240 LYS cc_start: 0.7317 (tmmt) cc_final: 0.7086 (ttpt)
REVERT: R  342 VAL cc_start: 0.7439 (t) cc_final: 0.7113 (p)
REVERT: R  404 ARG cc_start: 0.7230 (mtt90) cc_final: 0.7021 (mtt90)
REVERT: R  413 LEU cc_start: 0.7112 (tp) cc_final: 0.6834 (tp)
  outliers start: 4
  outliers final: 3
  residues processed: 217
  average time/residue: 0.3137
  time to fit residues: 87.7403
Evaluate side-chains
  192 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 189
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue  135 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    0.8980
   chunk 85 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
A 271 ASN
A 362 HIS
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 HIS
B 220 GLN
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9897  Z= 0.279
  Angle     :  0.810  32.582  13369  Z= 0.356
  Chirality :  0.069   1.665   1471
  Planarity :  0.004   0.045   1652
  Dihedral  : 12.629 179.938   1833
  Min Nonbonded Distance : 1.672

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 16.87 %
    Favored  : 81.04 %
  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:  1.04 (0.26), residues: 1147
  helix:  2.31 (0.25), residues: 454
  sheet:  0.81 (0.38), residues: 205
  loop : -0.97 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 164 
 HIS   0.008   0.001   HIS A 362 
 PHE   0.020   0.002   PHE R 335 
 TYR   0.025   0.002   TYR R 191 
 ARG   0.008   0.001   ARG A  31 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 203
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6319 (tmm) cc_final: 0.5922 (tmm)
REVERT: A  280 ARG cc_start: 0.7263 (ttm-80) cc_final: 0.6993 (ttm-80)
REVERT: A  283 ARG cc_start: 0.7507 (ptt180) cc_final: 0.7282 (ptp-170)
REVERT: A  314 GLU cc_start: 0.7065 (mp0) cc_final: 0.6745 (mp0)
REVERT: A  346 LEU cc_start: 0.6681 (mm) cc_final: 0.6465 (mt)
REVERT: B   55 LEU cc_start: 0.8355 (mt) cc_final: 0.8128 (mp)
REVERT: B   78 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8085 (mtmm)
REVERT: B   79 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7498 (mt)
REVERT: B   84 SER cc_start: 0.7911 (m) cc_final: 0.7611 (p)
REVERT: B  111 TYR cc_start: 0.8376 (m-80) cc_final: 0.8109 (m-80)
REVERT: B  188 MET cc_start: 0.8008 (mmm) cc_final: 0.7740 (mmm)
REVERT: B  217 MET cc_start: 0.7403 (ppp) cc_final: 0.6443 (ppp)
REVERT: B  219 ARG cc_start: 0.7770 (mtp85) cc_final: 0.7118 (mtp85)
REVERT: B  262 MET cc_start: 0.7565 (pmm) cc_final: 0.6924 (pmm)
REVERT: B  275 SER cc_start: 0.8008 (t) cc_final: 0.7666 (t)
REVERT: B  289 TYR cc_start: 0.8326 (m-80) cc_final: 0.8059 (m-80)
REVERT: B  316 SER cc_start: 0.8111 (t) cc_final: 0.7801 (p)
REVERT: B  327 VAL cc_start: 0.8184 (t) cc_final: 0.7960 (p)
REVERT: N   13 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7608 (mp10)
REVERT: N   59 SER cc_start: 0.7643 (m) cc_final: 0.7188 (t)
REVERT: N  108 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7004 (m-80)
REVERT: R   36 GLU cc_start: 0.7053 (tp30) cc_final: 0.6840 (tp30)
REVERT: R  181 ARG cc_start: 0.7111 (mmm-85) cc_final: 0.6700 (mmm-85)
REVERT: R  342 VAL cc_start: 0.7539 (t) cc_final: 0.7221 (p)
REVERT: R  404 ARG cc_start: 0.7207 (mtt90) cc_final: 0.6920 (mtt90)
REVERT: R  431 GLU cc_start: 0.6931 (mp0) cc_final: 0.6648 (mp0)
  outliers start: 21
  outliers final: 11
  residues processed: 218
  average time/residue: 0.2757
  time to fit residues: 79.5281
Evaluate side-chains
  212 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 197
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  302 GLU
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  354 LEU
Chi-restraints excluded: chain R residue  420 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 57 optimal weight:    8.9990
   chunk 31 optimal weight:    0.0370
   chunk 85 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 28 optimal weight:    0.3980
   chunk 102 optimal weight:    0.5980
   chunk 111 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   overall best weight:    1.0062

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
B  54 HIS
N  31 ASN
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   9897  Z= 0.330
  Angle     :  0.802  32.478  13369  Z= 0.356
  Chirality :  0.070   1.687   1471
  Planarity :  0.004   0.040   1652
  Dihedral  : 12.323 177.566   1824
  Min Nonbonded Distance : 1.676

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 17.86 %
    Favored  : 78.84 %
  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:  0.87 (0.25), residues: 1147
  helix:  2.09 (0.25), residues: 453
  sheet:  0.69 (0.38), residues: 196
  loop : -0.93 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 211 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.029   0.002   PHE R 335 
 TYR   0.026   0.002   TYR R 191 
 ARG   0.006   0.001   ARG R 390 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 201
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6286 (tmm) cc_final: 0.5825 (tmm)
REVERT: A  280 ARG cc_start: 0.7272 (ttm-80) cc_final: 0.7054 (ttm-80)
REVERT: A  309 GLU cc_start: 0.7772 (mp0) cc_final: 0.7362 (mp0)
REVERT: A  314 GLU cc_start: 0.7123 (mp0) cc_final: 0.6695 (mp0)
REVERT: A  346 LEU cc_start: 0.6834 (mm) cc_final: 0.6490 (mt)
REVERT: A  381 ASP cc_start: 0.8184 (t0) cc_final: 0.7950 (t0)
REVERT: B   84 SER cc_start: 0.7997 (m) cc_final: 0.7752 (p)
REVERT: B  212 ASP cc_start: 0.7866 (t0) cc_final: 0.7648 (t70)
REVERT: B  217 MET cc_start: 0.7513 (ppp) cc_final: 0.6587 (ppp)
REVERT: B  219 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7106 (mtt-85)
REVERT: B  221 THR cc_start: 0.7974 (m) cc_final: 0.7529 (t)
REVERT: B  262 MET cc_start: 0.7711 (pmm) cc_final: 0.7396 (pmm)
REVERT: B  275 SER cc_start: 0.8051 (t) cc_final: 0.7718 (t)
REVERT: B  298 ASP cc_start: 0.7481 (t0) cc_final: 0.7264 (t0)
REVERT: B  316 SER cc_start: 0.8209 (t) cc_final: 0.7747 (p)
REVERT: N  108 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7311 (m-80)
REVERT: R   36 GLU cc_start: 0.7159 (tp30) cc_final: 0.6934 (tp30)
REVERT: R  181 ARG cc_start: 0.7076 (mmm-85) cc_final: 0.6657 (mmm-85)
REVERT: R  312 MET cc_start: 0.6695 (tmm) cc_final: 0.6476 (tmm)
REVERT: R  342 VAL cc_start: 0.7610 (t) cc_final: 0.7254 (p)
REVERT: R  360 LYS cc_start: 0.8220 (ptpp) cc_final: 0.7991 (pttm)
REVERT: R  408 LYS cc_start: 0.8058 (tmtt) cc_final: 0.7842 (tptp)
REVERT: R  429 TYR cc_start: 0.8456 (m-10) cc_final: 0.8172 (m-80)
  outliers start: 33
  outliers final: 19
  residues processed: 222
  average time/residue: 0.2909
  time to fit residues: 83.8992
Evaluate side-chains
  214 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 194
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain P residue   26 HIS
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  302 GLU
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  346 LEU
Chi-restraints excluded: chain R residue  354 LEU
Chi-restraints excluded: chain R residue  368 LEU
Chi-restraints excluded: chain R residue  419 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   chunk 109 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   9897  Z= 0.280
  Angle     :  0.778  32.276  13369  Z= 0.339
  Chirality :  0.070   1.706   1471
  Planarity :  0.004   0.037   1652
  Dihedral  : 12.204 176.714   1824
  Min Nonbonded Distance : 1.680

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 18.06 %
    Favored  : 78.44 %
  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:  0.84 (0.26), residues: 1147
  helix:  2.15 (0.25), residues: 451
  sheet:  0.55 (0.37), residues: 198
  loop : -0.97 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.012   0.001   HIS R 420 
 PHE   0.026   0.002   PHE R 335 
 TYR   0.022   0.002   TYR R 191 
 ARG   0.007   0.001   ARG A  31 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 192
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6216 (tmm) cc_final: 0.5770 (tmm)
REVERT: A   25 LYS cc_start: 0.7818 (ttmm) cc_final: 0.7462 (ttmm)
REVERT: A  280 ARG cc_start: 0.7262 (ttm-80) cc_final: 0.7044 (ttm-80)
REVERT: A  309 GLU cc_start: 0.7757 (mp0) cc_final: 0.7381 (mp0)
REVERT: A  314 GLU cc_start: 0.7171 (mp0) cc_final: 0.6673 (mp0)
REVERT: A  343 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7228 (m-30)
REVERT: A  344 GLU cc_start: 0.7760 (tp30) cc_final: 0.7106 (tp30)
REVERT: A  381 ASP cc_start: 0.8164 (t0) cc_final: 0.7945 (t0)
REVERT: B   84 SER cc_start: 0.7970 (m) cc_final: 0.7758 (p)
REVERT: B  212 ASP cc_start: 0.7843 (t0) cc_final: 0.7637 (t70)
REVERT: B  217 MET cc_start: 0.7499 (ppp) cc_final: 0.6633 (ppp)
REVERT: B  219 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7157 (mtt-85)
REVERT: B  262 MET cc_start: 0.7610 (pmm) cc_final: 0.7330 (pmm)
REVERT: B  275 SER cc_start: 0.8023 (t) cc_final: 0.7678 (t)
REVERT: B  289 TYR cc_start: 0.8613 (m-80) cc_final: 0.8329 (m-80)
REVERT: B  298 ASP cc_start: 0.7502 (t0) cc_final: 0.7030 (t0)
REVERT: B  316 SER cc_start: 0.8177 (t) cc_final: 0.7722 (p)
REVERT: N   13 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7667 (mp10)
REVERT: N  108 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7142 (m-80)
REVERT: R   35 GLU cc_start: 0.7393 (mp0) cc_final: 0.6636 (mp0)
REVERT: R   36 GLU cc_start: 0.7175 (tp30) cc_final: 0.6961 (tp30)
REVERT: R  181 ARG cc_start: 0.7078 (mmm-85) cc_final: 0.6651 (mmm-85)
REVERT: R  312 MET cc_start: 0.6802 (tmm) cc_final: 0.6575 (tmm)
REVERT: R  342 VAL cc_start: 0.7608 (t) cc_final: 0.7261 (p)
REVERT: R  360 LYS cc_start: 0.8224 (ptpp) cc_final: 0.8017 (pttm)
REVERT: R  368 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7380 (mp)
REVERT: R  408 LYS cc_start: 0.7927 (tmtt) cc_final: 0.7595 (tmtt)
  outliers start: 35
  outliers final: 21
  residues processed: 214
  average time/residue: 0.2922
  time to fit residues: 81.7173
Evaluate side-chains
  208 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 183
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  343 ASP
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain P residue   26 HIS
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  301 VAL
Chi-restraints excluded: chain R residue  302 GLU
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  368 LEU
Chi-restraints excluded: chain R residue  411 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 62 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0770
   chunk 45 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 98 optimal weight:    0.0570
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.5856

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

Flipped N/Q/H residues before XYZ refinement:
** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 364 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.3277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9897  Z= 0.213
  Angle     :  0.752  32.236  13369  Z= 0.325
  Chirality :  0.069   1.714   1471
  Planarity :  0.004   0.035   1652
  Dihedral  : 12.052 176.358   1824
  Min Nonbonded Distance : 1.671

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.36 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.26), residues: 1147
  helix:  2.45 (0.25), residues: 445
  sheet:  0.55 (0.37), residues: 197
  loop : -1.04 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 211 
 HIS   0.012   0.001   HIS R 420 
 PHE   0.023   0.001   PHE R 335 
 TYR   0.024   0.001   TYR R 191 
 ARG   0.005   0.000   ARG A  31 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 184
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6182 (tmm) cc_final: 0.5742 (tmm)
REVERT: A  280 ARG cc_start: 0.7248 (ttm-80) cc_final: 0.7019 (ttm-80)
REVERT: A  309 GLU cc_start: 0.7756 (mp0) cc_final: 0.7346 (mp0)
REVERT: A  314 GLU cc_start: 0.7136 (mp0) cc_final: 0.6687 (mp0)
REVERT: A  343 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7432 (m-30)
REVERT: A  344 GLU cc_start: 0.7723 (tp30) cc_final: 0.7091 (tp30)
REVERT: A  381 ASP cc_start: 0.8168 (t0) cc_final: 0.7931 (t0)
REVERT: B   78 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7889 (mtmm)
REVERT: B   84 SER cc_start: 0.7969 (m) cc_final: 0.7731 (p)
REVERT: B  219 ARG cc_start: 0.7855 (mtp85) cc_final: 0.7237 (mtt-85)
REVERT: B  262 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7284 (pmm)
REVERT: B  275 SER cc_start: 0.8075 (t) cc_final: 0.7729 (t)
REVERT: B  289 TYR cc_start: 0.8616 (m-80) cc_final: 0.8374 (m-80)
REVERT: B  298 ASP cc_start: 0.7463 (t0) cc_final: 0.7045 (t0)
REVERT: B  316 SER cc_start: 0.8128 (t) cc_final: 0.7709 (p)
REVERT: N   13 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7693 (mp10)
REVERT: N  108 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.7132 (m-80)
REVERT: R   36 GLU cc_start: 0.7167 (tp30) cc_final: 0.6965 (tp30)
REVERT: R  181 ARG cc_start: 0.7024 (mmm-85) cc_final: 0.6627 (mmm-85)
REVERT: R  226 LEU cc_start: 0.7524 (tp) cc_final: 0.7174 (tp)
REVERT: R  282 ARG cc_start: 0.7942 (mtt-85) cc_final: 0.7727 (mtt-85)
REVERT: R  312 MET cc_start: 0.6780 (tmm) cc_final: 0.6533 (tmm)
REVERT: R  342 VAL cc_start: 0.7639 (t) cc_final: 0.7287 (p)
REVERT: R  408 LYS cc_start: 0.7933 (tmtt) cc_final: 0.7544 (tmtt)
  outliers start: 40
  outliers final: 24
  residues processed: 208
  average time/residue: 0.2862
  time to fit residues: 77.7700
Evaluate side-chains
  212 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 183
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  343 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain P residue   26 HIS
Chi-restraints excluded: chain R residue   34 LYS
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  302 GLU
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  317 GLU
Chi-restraints excluded: chain R residue  423 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 109 optimal weight:    0.5980
   chunk 90 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 105 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9897  Z= 0.267
  Angle     :  0.766  32.123  13369  Z= 0.332
  Chirality :  0.070   1.724   1471
  Planarity :  0.004   0.033   1652
  Dihedral  : 12.009 176.135   1824
  Min Nonbonded Distance : 1.680

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 19.06 %
    Favored  : 76.65 %
  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:  0.91 (0.25), residues: 1147
  helix:  2.31 (0.25), residues: 451
  sheet:  0.52 (0.36), residues: 196
  loop : -1.01 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.012   0.001   HIS R 420 
 PHE   0.022   0.002   PHE R 335 
 TYR   0.024   0.001   TYR R 191 
 ARG   0.005   0.000   ARG A  31 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 186
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6232 (tmm) cc_final: 0.5844 (tmm)
REVERT: A  280 ARG cc_start: 0.7262 (ttm-80) cc_final: 0.7043 (ttm-80)
REVERT: A  309 GLU cc_start: 0.7752 (mp0) cc_final: 0.7344 (mp0)
REVERT: A  314 GLU cc_start: 0.7149 (mp0) cc_final: 0.6700 (mp0)
REVERT: A  343 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7475 (m-30)
REVERT: A  344 GLU cc_start: 0.7727 (tp30) cc_final: 0.7135 (tp30)
REVERT: B   78 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7877 (mtmm)
REVERT: B   84 SER cc_start: 0.7942 (m) cc_final: 0.7741 (p)
REVERT: B  217 MET cc_start: 0.7524 (ppp) cc_final: 0.6629 (ppp)
REVERT: B  219 ARG cc_start: 0.7877 (mtp85) cc_final: 0.7164 (mtt-85)
REVERT: B  221 THR cc_start: 0.7968 (m) cc_final: 0.7505 (t)
REVERT: B  262 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7351 (pmm)
REVERT: B  275 SER cc_start: 0.8090 (t) cc_final: 0.7718 (t)
REVERT: B  316 SER cc_start: 0.8165 (t) cc_final: 0.7708 (p)
REVERT: N   13 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7722 (mp10)
REVERT: N  108 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.7229 (m-80)
REVERT: R   35 GLU cc_start: 0.7370 (mp0) cc_final: 0.6697 (mp0)
REVERT: R   36 GLU cc_start: 0.7197 (tp30) cc_final: 0.6974 (tp30)
REVERT: R  181 ARG cc_start: 0.7040 (mmm-85) cc_final: 0.6630 (mmm-85)
REVERT: R  312 MET cc_start: 0.6793 (tmm) cc_final: 0.6515 (tmm)
REVERT: R  342 VAL cc_start: 0.7666 (t) cc_final: 0.7323 (p)
REVERT: R  408 LYS cc_start: 0.7879 (tmtt) cc_final: 0.7422 (tmtt)
  outliers start: 43
  outliers final: 25
  residues processed: 212
  average time/residue: 0.2868
  time to fit residues: 79.3031
Evaluate side-chains
  215 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 185
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  343 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain P residue   22 PHE
Chi-restraints excluded: chain P residue   26 HIS
Chi-restraints excluded: chain R residue   34 LYS
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  302 GLU
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  317 GLU
Chi-restraints excluded: chain R residue  423 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 62 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0670
   chunk 92 optimal weight:    0.7980
   chunk 108 optimal weight:    0.1980
   chunk 68 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9897  Z= 0.191
  Angle     :  0.743  32.103  13369  Z= 0.320
  Chirality :  0.069   1.721   1471
  Planarity :  0.004   0.041   1652
  Dihedral  : 11.893 176.538   1824
  Min Nonbonded Distance : 1.673

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 20.36 %
    Favored  : 76.35 %
  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:  1.03 (0.26), residues: 1147
  helix:  2.46 (0.25), residues: 454
  sheet:  0.54 (0.36), residues: 197
  loop : -1.00 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 234 
 HIS   0.011   0.001   HIS R 420 
 PHE   0.020   0.001   PHE R 335 
 TYR   0.024   0.001   TYR R 191 
 ARG   0.008   0.000   ARG A  31 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 204
  time to evaluate  : 1.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6142 (tmm) cc_final: 0.5764 (tmm)
REVERT: A   25 LYS cc_start: 0.7770 (ttmm) cc_final: 0.7558 (ttmm)
REVERT: A  248 VAL cc_start: 0.8582 (t) cc_final: 0.8276 (p)
REVERT: A  280 ARG cc_start: 0.7241 (ttm-80) cc_final: 0.6995 (ttm-80)
REVERT: A  309 GLU cc_start: 0.7741 (mp0) cc_final: 0.7329 (mp0)
REVERT: A  314 GLU cc_start: 0.7161 (mp0) cc_final: 0.6720 (mp0)
REVERT: A  344 GLU cc_start: 0.7685 (tp30) cc_final: 0.7120 (tp30)
REVERT: B   78 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7838 (mtmm)
REVERT: B   84 SER cc_start: 0.7960 (m) cc_final: 0.7735 (p)
REVERT: B  219 ARG cc_start: 0.7865 (mtp85) cc_final: 0.7232 (mtt-85)
REVERT: B  221 THR cc_start: 0.7928 (m) cc_final: 0.7470 (t)
REVERT: B  262 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7277 (pmm)
REVERT: B  275 SER cc_start: 0.8085 (t) cc_final: 0.7718 (t)
REVERT: B  316 SER cc_start: 0.8097 (t) cc_final: 0.7739 (p)
REVERT: B  327 VAL cc_start: 0.8249 (t) cc_final: 0.7940 (p)
REVERT: N   13 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7719 (mp10)
REVERT: N  108 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.7093 (m-80)
REVERT: R   35 GLU cc_start: 0.7404 (mp0) cc_final: 0.6697 (mp0)
REVERT: R   36 GLU cc_start: 0.7188 (tp30) cc_final: 0.6955 (tp30)
REVERT: R  181 ARG cc_start: 0.6969 (mmm-85) cc_final: 0.6605 (mmm-85)
REVERT: R  226 LEU cc_start: 0.7523 (tp) cc_final: 0.7191 (tp)
REVERT: R  282 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7700 (mtt-85)
REVERT: R  312 MET cc_start: 0.6774 (tmm) cc_final: 0.6489 (tmm)
REVERT: R  342 VAL cc_start: 0.7652 (t) cc_final: 0.7301 (p)
REVERT: R  408 LYS cc_start: 0.7919 (tmtt) cc_final: 0.7410 (tmtt)
REVERT: R  429 TYR cc_start: 0.8525 (m-10) cc_final: 0.8109 (m-80)
REVERT: R  444 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7092 (mm-30)
  outliers start: 33
  outliers final: 23
  residues processed: 223
  average time/residue: 0.2879
  time to fit residues: 83.9642
Evaluate side-chains
  224 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 197
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain P residue   22 PHE
Chi-restraints excluded: chain P residue   26 HIS
Chi-restraints excluded: chain R residue   34 LYS
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  302 GLU
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  317 GLU
Chi-restraints excluded: chain R residue  346 LEU
Chi-restraints excluded: chain R residue  423 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 85 optimal weight:    6.9990
   chunk 99 optimal weight:    1.9990
   chunk 104 optimal weight:    0.7980
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9897  Z= 0.285
  Angle     :  0.773  32.070  13369  Z= 0.336
  Chirality :  0.070   1.725   1471
  Planarity :  0.004   0.043   1652
  Dihedral  : 11.887 176.569   1824
  Min Nonbonded Distance : 1.684

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 20.66 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.25), residues: 1147
  helix:  2.35 (0.25), residues: 451
  sheet:  0.53 (0.36), residues: 201
  loop : -1.00 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.012   0.001   HIS R 420 
 PHE   0.025   0.002   PHE R 335 
 TYR   0.022   0.002   TYR R 191 
 ARG   0.010   0.000   ARG A  31 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 194
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6232 (tmm) cc_final: 0.5842 (tmm)
REVERT: A   25 LYS cc_start: 0.7773 (ttmm) cc_final: 0.7564 (ttmm)
REVERT: A  280 ARG cc_start: 0.7271 (ttm-80) cc_final: 0.7042 (ttm-80)
REVERT: A  309 GLU cc_start: 0.7762 (mp0) cc_final: 0.7356 (mp0)
REVERT: A  314 GLU cc_start: 0.7164 (mp0) cc_final: 0.6738 (mp0)
REVERT: A  344 GLU cc_start: 0.7741 (tp30) cc_final: 0.7172 (tp30)
REVERT: B   84 SER cc_start: 0.8002 (m) cc_final: 0.7772 (p)
REVERT: B  217 MET cc_start: 0.7480 (ppp) cc_final: 0.6636 (ppp)
REVERT: B  219 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7178 (mtt-85)
REVERT: B  221 THR cc_start: 0.7946 (m) cc_final: 0.7474 (t)
REVERT: B  262 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7374 (pmm)
REVERT: B  275 SER cc_start: 0.8078 (t) cc_final: 0.7719 (t)
REVERT: N   13 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7731 (mp10)
REVERT: N  108 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.7216 (m-80)
REVERT: R   35 GLU cc_start: 0.7389 (mp0) cc_final: 0.6760 (mp0)
REVERT: R   36 GLU cc_start: 0.7240 (tp30) cc_final: 0.7010 (tp30)
REVERT: R  181 ARG cc_start: 0.7023 (mmm-85) cc_final: 0.6605 (mmm-85)
REVERT: R  195 TYR cc_start: 0.7948 (m-80) cc_final: 0.7514 (m-80)
REVERT: R  312 MET cc_start: 0.6787 (tmm) cc_final: 0.6515 (tmm)
REVERT: R  342 VAL cc_start: 0.7691 (t) cc_final: 0.7332 (p)
REVERT: R  408 LYS cc_start: 0.7867 (tmtt) cc_final: 0.7340 (tmtt)
REVERT: R  444 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7072 (mm-30)
  outliers start: 36
  outliers final: 28
  residues processed: 217
  average time/residue: 0.2961
  time to fit residues: 83.7366
Evaluate side-chains
  218 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 187
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  343 ASP
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain P residue   22 PHE
Chi-restraints excluded: chain P residue   26 HIS
Chi-restraints excluded: chain R residue   34 LYS
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  237 ILE
Chi-restraints excluded: chain R residue  302 GLU
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  317 GLU
Chi-restraints excluded: chain R residue  346 LEU
Chi-restraints excluded: chain R residue  423 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    0.0770
   chunk 104 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 95 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0000
   chunk 107 optimal weight:    0.3980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.3542

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.3639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9897  Z= 0.167
  Angle     :  0.741  32.011  13369  Z= 0.318
  Chirality :  0.069   1.732   1471
  Planarity :  0.003   0.043   1652
  Dihedral  : 11.753 177.062   1824
  Min Nonbonded Distance : 1.670

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 21.06 %
    Favored  : 75.65 %
  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:  1.15 (0.26), residues: 1147
  helix:  2.69 (0.25), residues: 446
  sheet:  0.58 (0.35), residues: 208
  loop : -1.04 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.013   0.001   HIS R 420 
 PHE   0.021   0.001   PHE R 335 
 TYR   0.022   0.001   TYR R 191 
 ARG   0.010   0.000   ARG A  31 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 201
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6118 (tmm) cc_final: 0.5742 (tmm)
REVERT: A  248 VAL cc_start: 0.8573 (t) cc_final: 0.8305 (p)
REVERT: A  280 ARG cc_start: 0.7264 (ttm-80) cc_final: 0.7010 (ttm-80)
REVERT: A  309 GLU cc_start: 0.7755 (mp0) cc_final: 0.7346 (mp0)
REVERT: A  314 GLU cc_start: 0.7180 (mp0) cc_final: 0.6741 (mp0)
REVERT: A  344 GLU cc_start: 0.7649 (tp30) cc_final: 0.7079 (tp30)
REVERT: B   61 MET cc_start: 0.7892 (ppp) cc_final: 0.7482 (ppp)
REVERT: B   78 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7817 (mtmm)
REVERT: B   84 SER cc_start: 0.7979 (m) cc_final: 0.7726 (p)
REVERT: B  221 THR cc_start: 0.7893 (m) cc_final: 0.7400 (t)
REVERT: B  262 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7253 (pmm)
REVERT: B  275 SER cc_start: 0.8094 (t) cc_final: 0.7749 (t)
REVERT: N   13 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7736 (mp10)
REVERT: N  108 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.7050 (m-80)
REVERT: P   13 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7899 (ttpp)
REVERT: R   35 GLU cc_start: 0.7429 (mp0) cc_final: 0.6681 (mp0)
REVERT: R   36 GLU cc_start: 0.7193 (tp30) cc_final: 0.6958 (tp30)
REVERT: R  181 ARG cc_start: 0.6920 (mmm-85) cc_final: 0.6575 (mmm-85)
REVERT: R  195 TYR cc_start: 0.7910 (m-80) cc_final: 0.7532 (m-80)
REVERT: R  226 LEU cc_start: 0.7519 (tp) cc_final: 0.7183 (tp)
REVERT: R  297 TYR cc_start: 0.7903 (m-80) cc_final: 0.7411 (m-80)
REVERT: R  312 MET cc_start: 0.6737 (tmm) cc_final: 0.6459 (tmm)
REVERT: R  342 VAL cc_start: 0.7636 (t) cc_final: 0.7285 (p)
REVERT: R  408 LYS cc_start: 0.7901 (tmtt) cc_final: 0.7338 (tmtt)
REVERT: R  444 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7120 (mm-30)
  outliers start: 33
  outliers final: 22
  residues processed: 222
  average time/residue: 0.2890
  time to fit residues: 83.4040
Evaluate side-chains
  225 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 198
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain P residue   13 LYS
Chi-restraints excluded: chain P residue   22 PHE
Chi-restraints excluded: chain P residue   26 HIS
Chi-restraints excluded: chain R residue   34 LYS
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  302 GLU
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  317 GLU
Chi-restraints excluded: chain R residue  423 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 112 optimal weight:    0.8980
   chunk 103 optimal weight:    0.5980
   chunk 89 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 95 optimal weight:    0.4980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 358 ASN
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.3753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9897  Z= 0.246
  Angle     :  0.765  31.981  13369  Z= 0.331
  Chirality :  0.070   1.731   1471
  Planarity :  0.004   0.043   1652
  Dihedral  : 11.754 177.285   1824
  Min Nonbonded Distance : 1.675

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 21.76 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.26), residues: 1147
  helix:  2.47 (0.25), residues: 453
  sheet:  0.52 (0.35), residues: 210
  loop : -1.05 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.012   0.001   HIS R 420 
 PHE   0.026   0.002   PHE R 335 
 TYR   0.022   0.001   TYR R 191 
 ARG   0.010   0.001   ARG A  31 

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

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

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2294 Ramachandran restraints generated.
    1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 192
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6144 (tmm) cc_final: 0.5759 (tmm)
REVERT: A  295 ASP cc_start: 0.8041 (p0) cc_final: 0.7814 (p0)
REVERT: A  309 GLU cc_start: 0.7761 (mp0) cc_final: 0.7346 (mp0)
REVERT: A  314 GLU cc_start: 0.7195 (mp0) cc_final: 0.6742 (mp0)
REVERT: A  344 GLU cc_start: 0.7698 (tp30) cc_final: 0.7139 (tp30)
REVERT: B   61 MET cc_start: 0.7953 (ppp) cc_final: 0.7495 (ppp)
REVERT: B   78 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7812 (mtmm)
REVERT: B   84 SER cc_start: 0.7982 (m) cc_final: 0.7727 (p)
REVERT: B  217 MET cc_start: 0.7485 (ppp) cc_final: 0.6692 (ppp)
REVERT: B  221 THR cc_start: 0.7940 (m) cc_final: 0.7445 (t)
REVERT: B  262 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7291 (pmm)
REVERT: B  275 SER cc_start: 0.8129 (t) cc_final: 0.7783 (t)
REVERT: N   13 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7741 (mp10)
REVERT: N  108 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7158 (m-80)
REVERT: P   13 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7754 (ttmm)
REVERT: R   35 GLU cc_start: 0.7405 (mp0) cc_final: 0.6740 (mp0)
REVERT: R   36 GLU cc_start: 0.7220 (tp30) cc_final: 0.6991 (tp30)
REVERT: R  181 ARG cc_start: 0.6980 (mmm-85) cc_final: 0.6580 (mmm-85)
REVERT: R  195 TYR cc_start: 0.7909 (m-80) cc_final: 0.7443 (m-80)
REVERT: R  226 LEU cc_start: 0.7549 (tp) cc_final: 0.7192 (tp)
REVERT: R  312 MET cc_start: 0.6751 (tmm) cc_final: 0.6469 (tmm)
REVERT: R  342 VAL cc_start: 0.7672 (t) cc_final: 0.7319 (p)
REVERT: R  408 LYS cc_start: 0.7903 (tmtt) cc_final: 0.7343 (tmtt)
REVERT: R  414 MET cc_start: 0.7207 (mtp) cc_final: 0.6996 (ttm)
  outliers start: 29
  outliers final: 20
  residues processed: 211
  average time/residue: 0.2996
  time to fit residues: 81.7516
Evaluate side-chains
  215 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 190
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain P residue   13 LYS
Chi-restraints excluded: chain P residue   22 PHE
Chi-restraints excluded: chain P residue   26 HIS
Chi-restraints excluded: chain R residue   34 LYS
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  302 GLU
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  317 GLU
Chi-restraints excluded: chain R residue  423 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 92 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
R 358 ASN
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.138394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.113105 restraints weight = 13049.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.81
r_work: 0.3258 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9897  Z= 0.256
  Angle     :  0.774  31.948  13369  Z= 0.337
  Chirality :  0.070   1.733   1471
  Planarity :  0.004   0.042   1652
  Dihedral  : 11.728 177.383   1824
  Min Nonbonded Distance : 1.673

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.46 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.25), residues: 1147
  helix:  2.44 (0.25), residues: 450
  sheet:  0.47 (0.35), residues: 209
  loop : -1.05 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.012   0.001   HIS R 420 
 PHE   0.029   0.002   PHE R 335 
 TYR   0.023   0.001   TYR R 191 
 ARG   0.010   0.000   ARG A  31 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2673.67 seconds
wall clock time: 48 minutes 59.98 seconds (2939.98 seconds total)