Starting phenix.real_space_refine (version: dev)
on Mon Apr  4 22:58:37 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwo_10633/04_2022/6xwo_10633.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwo_10633/04_2022/6xwo_10633.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwo_10633/04_2022/6xwo_10633.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwo_10633/04_2022/6xwo_10633.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwo_10633/04_2022/6xwo_10633.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwo_10633/04_2022/6xwo_10633.pdb"
  }
  resolution = 3.39
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.020
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "A ARG    8": "NH1" <-> "NH2"
    Residue "A ARG   79": "NH1" <-> "NH2"
    Residue "A TYR   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  107": "NH1" <-> "NH2"
    Residue "A ARG  173": "NH1" <-> "NH2"
    Residue "A ARG  187": "NH1" <-> "NH2"
    Residue "A GLU  221": "OE1" <-> "OE2"
    Residue "A ARG  265": "NH1" <-> "NH2"
    Residue "A GLU  293": "OE1" <-> "OE2"
    Residue "A GLU  294": "OE1" <-> "OE2"
    Residue "A ASP  298": "OD1" <-> "OD2"
    Residue "A ASP  315": "OD1" <-> "OD2"
    Residue "A GLU  422": "OE1" <-> "OE2"
    Residue "B ASP   11": "OD1" <-> "OD2"
    Residue "B TYR   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  221": "OE1" <-> "OE2"
    Residue "B ARG  265": "NH1" <-> "NH2"
    Residue "B GLU  294": "OE1" <-> "OE2"
    Residue "B ASP  298": "OD1" <-> "OD2"
    Residue "B ASP  315": "OD1" <-> "OD2"
    Residue "C ARG    8": "NH1" <-> "NH2"
    Residue "C ASP   50": "OD1" <-> "OD2"
    Residue "C GLU  126": "OE1" <-> "OE2"
    Residue "C ASP  259": "OD1" <-> "OD2"
    Residue "C ASP  269": "OD1" <-> "OD2"
    Residue "C ARG  278": "NH1" <-> "NH2"
    Residue "C ASP  298": "OD1" <-> "OD2"
    Residue "C PHE  302": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  409": "OD1" <-> "OD2"
    Residue "C GLU  420": "OE1" <-> "OE2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib"
  Total number of atoms: 9555
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3184
          Classifications: {'peptide': 427}
          Link IDs: {'PTRANS': 18, 'TRANS': 408}
    Chain: "B"
      Number of atoms: 3184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3184
          Classifications: {'peptide': 427}
          Link IDs: {'PTRANS': 18, 'TRANS': 408}
    Chain: "C"
      Number of atoms: 3187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3187
          Classifications: {'peptide': 427}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 408}
          Chain breaks: 1
  Time building chain proxies: 5.72, per 1000 atoms: 0.60
  Number of scatterers: 9555
  At special positions: 0
  Unit cell: (79.948, 109.296, 120.428, 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      48     16.00
     O    1661      8.00
     N    1545      7.00
     C    6301      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.96
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2292

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 0 sheets defined
      77.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 10
    Processing helix  chain 'A' and resid 13 through 36
    Processing helix  chain 'A' and resid 37 through 45
      removed outlier: 3.698A  pdb=" N   TYR A  44 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 58
      removed outlier: 3.736A  pdb=" N   GLY A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 75
    Processing helix  chain 'A' and resid 81 through 110
      removed outlier: 3.996A  pdb=" N   VAL A  85 " --> pdb=" O   GLY A  81 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LYS A  86 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   TYR A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 138
    Processing helix  chain 'A' and resid 143 through 150
    Processing helix  chain 'A' and resid 153 through 171
    Processing helix  chain 'A' and resid 176 through 222
      Proline residue:  A 208  - end of helix
      removed outlier: 3.816A  pdb=" N   VAL A 218 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLN A 222 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 256
      removed outlier: 4.846A  pdb=" N   PHE A 250 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 278
      removed outlier: 5.604A  pdb=" N   ASP A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   ALA A 270 " --> pdb=" O   LYS A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 298 through 303
    Processing helix  chain 'A' and resid 305 through 310
    Processing helix  chain 'A' and resid 314 through 332
      removed outlier: 3.763A  pdb=" N   VAL A 325 " --> pdb=" O   GLN A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 350
    Processing helix  chain 'A' and resid 351 through 353
      No H-bonds generated for 'chain 'A' and resid 351 through 353'
    Processing helix  chain 'A' and resid 362 through 374
    Processing helix  chain 'A' and resid 381 through 420
      removed outlier: 3.729A  pdb=" N   LEU A 385 " --> pdb=" O   SER A 381 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   ALA A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   ILE A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU A 397 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   MET A 399 " --> pdb=" O   ALA A 395 " (cutoff:3.500A)
      removed outlier: 5.107A  pdb=" N   GLY A 400 " --> pdb=" O   ILE A 396 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASP A 409 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A 410 " --> pdb=" O   VAL A 406 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   VAL A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ILE A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 428
    Processing helix  chain 'B' and resid 6 through 12
    Processing helix  chain 'B' and resid 17 through 32
    Processing helix  chain 'B' and resid 37 through 45
    Processing helix  chain 'B' and resid 45 through 58
      removed outlier: 3.884A  pdb=" N   GLY B  49 " --> pdb=" O   ILE B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 76
    Processing helix  chain 'B' and resid 81 through 109
      removed outlier: 3.740A  pdb=" N   VAL B  85 " --> pdb=" O   GLY B  81 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   TYR B  90 " --> pdb=" O   LYS B  86 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER B  95 " --> pdb=" O   TYR B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 139
    Processing helix  chain 'B' and resid 143 through 150
    Processing helix  chain 'B' and resid 152 through 172
      removed outlier: 3.575A  pdb=" N   VAL B 156 " --> pdb=" O   GLU B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 223
      Proline residue:  B 208  - end of helix
    Processing helix  chain 'B' and resid 227 through 255
      removed outlier: 4.570A  pdb=" N   GLY B 235 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
      removed outlier: 6.084A  pdb=" N   TYR B 238 " --> pdb=" O   VAL B 234 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   PHE B 250 " --> pdb=" O   VAL B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 278
      removed outlier: 5.706A  pdb=" N   ASP B 269 " --> pdb=" O   ARG B 265 " (cutoff:3.500A)
      removed outlier: 5.632A  pdb=" N   ALA B 270 " --> pdb=" O   LYS B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 293
    Processing helix  chain 'B' and resid 298 through 313
      removed outlier: 3.551A  pdb=" N   PHE B 302 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   PHE B 304 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU B 306 " --> pdb=" O   PHE B 302 " (cutoff:3.500A)
      Proline residue:  B 307  - end of helix
      removed outlier: 4.478A  pdb=" N   THR B 311 " --> pdb=" O   PRO B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 332
      removed outlier: 3.911A  pdb=" N   LEU B 326 " --> pdb=" O   GLY B 322 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL B 328 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 352
    Processing helix  chain 'B' and resid 360 through 374
      removed outlier: 3.707A  pdb=" N   ILE B 364 " --> pdb=" O   GLY B 360 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   MET B 365 " --> pdb=" O   ALA B 361 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU B 366 " --> pdb=" O   GLY B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 393
      removed outlier: 3.567A  pdb=" N   LEU B 385 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ILE B 393 " --> pdb=" O   MET B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 411
      removed outlier: 4.513A  pdb=" N   MET B 403 " --> pdb=" O   MET B 399 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL B 404 " --> pdb=" O   GLY B 400 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ASN B 405 " --> pdb=" O   ARG B 401 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   VAL B 406 " --> pdb=" O   THR B 402 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   ASP B 409 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU B 410 " --> pdb=" O   VAL B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 419
    Processing helix  chain 'C' and resid 14 through 34
      removed outlier: 4.264A  pdb=" N   TRP C  20 " --> pdb=" O   TRP C  16 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY C  21 " --> pdb=" O   LYS C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 59
      removed outlier: 3.559A  pdb=" N   GLY C  49 " --> pdb=" O   ILE C  45 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 73
      removed outlier: 3.885A  pdb=" N   SER C  67 " --> pdb=" O   ILE C  63 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU C  68 " --> pdb=" O   VAL C  64 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLY C  71 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 109
      removed outlier: 3.872A  pdb=" N   ARG C  82 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   PHE C 100 " --> pdb=" O   ALA C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 138
    Processing helix  chain 'C' and resid 143 through 149
    Processing helix  chain 'C' and resid 152 through 171
      removed outlier: 3.881A  pdb=" N   VAL C 156 " --> pdb=" O   GLU C 152 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA C 166 " --> pdb=" O   ILE C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 222
      removed outlier: 3.910A  pdb=" N   GLN C 205 " --> pdb=" O   GLY C 201 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   TYR C 206 " --> pdb=" O   GLY C 202 " (cutoff:3.500A)
      Proline residue:  C 208  - end of helix
      removed outlier: 3.615A  pdb=" N   VAL C 218 " --> pdb=" O   LEU C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 247
      removed outlier: 3.621A  pdb=" N   TYR C 238 " --> pdb=" O   VAL C 234 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   THR C 239 " --> pdb=" O   GLY C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 256
    Processing helix  chain 'C' and resid 259 through 275
      removed outlier: 5.608A  pdb=" N   ASP C 269 " --> pdb=" O   ARG C 265 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   ALA C 270 " --> pdb=" O   LYS C 266 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 292
      removed outlier: 3.514A  pdb=" N   VAL C 290 " --> pdb=" O   VAL C 286 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 313
      removed outlier: 4.304A  pdb=" N   PHE C 304 " --> pdb=" O   GLY C 300 " (cutoff:3.500A)
      Proline residue:  C 307  - end of helix
      removed outlier: 4.574A  pdb=" N   THR C 311 " --> pdb=" O   PRO C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 331
      removed outlier: 3.747A  pdb=" N   VAL C 323 " --> pdb=" O   LEU C 319 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   VAL C 325 " --> pdb=" O   GLN C 321 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 348
      removed outlier: 3.733A  pdb=" N   VAL C 344 " --> pdb=" O   GLN C 340 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL C 345 " --> pdb=" O   GLN C 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 350 through 355
      removed outlier: 4.131A  pdb=" N   GLY C 354 " --> pdb=" O   LEU C 350 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   THR C 355 " --> pdb=" O   ALA C 351 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 350 through 355'
    Processing helix  chain 'C' and resid 361 through 371
      removed outlier: 3.629A  pdb=" N   MET C 365 " --> pdb=" O   ALA C 361 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA C 367 " --> pdb=" O   ALA C 363 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   MET C 368 " --> pdb=" O   ILE C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 387 through 392
      removed outlier: 3.599A  pdb=" N   GLY C 392 " --> pdb=" O   ALA C 388 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 393 through 401
      removed outlier: 3.624A  pdb=" N   LEU C 397 " --> pdb=" O   ILE C 393 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   MET C 399 " --> pdb=" O   ALA C 395 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   GLY C 400 " --> pdb=" O   ILE C 396 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 403 through 420
      removed outlier: 3.789A  pdb=" N   ASP C 409 " --> pdb=" O   ASN C 405 " (cutoff:3.500A)

    650 hydrogen bonds defined for protein.
    1944 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: 2.71

  Time building geometry restraints manager: 4.32 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2967
        1.34 -     1.46: 1444
        1.46 -     1.57: 5224
        1.57 -     1.69: 0
        1.69 -     1.81: 96
  Bond restraints: 9731
  Sorted by residual:
  bond pdb=" C   THR C 378 "
       pdb=" N   PRO C 379 "
    ideal  model  delta    sigma   weight residual
    1.330  1.356 -0.026 1.23e-02 6.61e+03 4.30e+00
  bond pdb=" CB  THR B 168 "
       pdb=" CG2 THR B 168 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 3.30e-02 9.18e+02 2.59e+00
  bond pdb=" CB  VAL B 115 "
       pdb=" CG2 VAL B 115 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.40e+00
  bond pdb=" CB  VAL A 233 "
       pdb=" CG2 VAL A 233 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.40e+00
  bond pdb=" CB  VAL B 404 "
       pdb=" CG2 VAL B 404 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.39e+00
  ... (remaining 9726 not shown)

  Histogram of bond angle deviations from ideal:
       98.93 -   105.95: 245
      105.95 -   112.97: 5494
      112.97 -   120.00: 3493
      120.00 -   127.02: 3934
      127.02 -   134.04: 78
  Bond angle restraints: 13244
  Sorted by residual:
  angle pdb=" N   TYR C 387 "
        pdb=" CA  TYR C 387 "
        pdb=" C   TYR C 387 "
      ideal   model   delta    sigma   weight residual
     114.56  109.64    4.92 1.27e+00 6.20e-01 1.50e+01
  angle pdb=" N   LEU C 385 "
        pdb=" CA  LEU C 385 "
        pdb=" C   LEU C 385 "
      ideal   model   delta    sigma   weight residual
     112.68  108.44    4.24 1.33e+00 5.65e-01 1.01e+01
  angle pdb=" N   ALA A 207 "
        pdb=" CA  ALA A 207 "
        pdb=" C   ALA A 207 "
      ideal   model   delta    sigma   weight residual
     109.81  116.37   -6.56 2.21e+00 2.05e-01 8.80e+00
  angle pdb=" N   ALA C 386 "
        pdb=" CA  ALA C 386 "
        pdb=" C   ALA C 386 "
      ideal   model   delta    sigma   weight residual
     112.93  110.04    2.89 1.12e+00 7.97e-01 6.66e+00
  angle pdb=" N   ASP A 394 "
        pdb=" CA  ASP A 394 "
        pdb=" C   ASP A 394 "
      ideal   model   delta    sigma   weight residual
     110.80  116.23   -5.43 2.13e+00 2.20e-01 6.51e+00
  ... (remaining 13239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 5204
       17.74 -    35.49: 455
       35.49 -    53.23: 65
       53.23 -    70.97: 9
       70.97 -    88.72: 4
  Dihedral angle restraints: 5737
    sinusoidal: 2126
      harmonic: 3611
  Sorted by residual:
  dihedral pdb=" CA  TRP C  16 "
           pdb=" C   TRP C  16 "
           pdb=" N   LYS C  17 "
           pdb=" CA  LYS C  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.04   25.96     0      5.00e+00 4.00e-02 2.70e+01
  dihedral pdb=" CA  PRO C 129 "
           pdb=" C   PRO C 129 "
           pdb=" N   PRO C 130 "
           pdb=" CA  PRO C 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.74  -24.26     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  TRP B  16 "
           pdb=" C   TRP B  16 "
           pdb=" N   LYS B  17 "
           pdb=" CA  LYS B  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.94   20.06     0      5.00e+00 4.00e-02 1.61e+01
  ... (remaining 5734 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 900
       0.032 -    0.063: 522
       0.063 -    0.095: 153
       0.095 -    0.126: 68
       0.126 -    0.158: 7
  Chirality restraints: 1650
  Sorted by residual:
  chirality pdb=" CG  LEU C 241 "
            pdb=" CB  LEU C 241 "
            pdb=" CD1 LEU C 241 "
            pdb=" CD2 LEU C 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.24e-01
  chirality pdb=" CA  ILE C  75 "
            pdb=" N   ILE C  75 "
            pdb=" C   ILE C  75 "
            pdb=" CB  ILE C  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.86e-01
  chirality pdb=" CA  TRP C  16 "
            pdb=" N   TRP C  16 "
            pdb=" C   TRP C  16 "
            pdb=" CB  TRP C  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.58e-01
  ... (remaining 1647 not shown)

  Planarity restraints: 1627
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 245 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   ILE B 245 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ILE B 245 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL B 246 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 235 "    0.010 2.00e-02 2.50e+03   2.04e-02 4.15e+00
        pdb=" C   GLY B 235 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLY B 235 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA B 236 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 207 "    0.033 5.00e-02 4.00e+02   4.96e-02 3.94e+00
        pdb=" N   PRO C 208 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO C 208 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 208 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1624 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 403
        2.71 -     3.26: 10374
        3.26 -     3.81: 15713
        3.81 -     4.35: 19709
        4.35 -     4.90: 33672
  Nonbonded interactions: 79871
  Sorted by model distance:
  nonbonded pdb=" O   THR B 378 "
            pdb=" OG  SER B 381 "
     model   vdw
     2.167 2.440
  nonbonded pdb=" O   ASP C 269 "
            pdb=" OG1 THR C 273 "
     model   vdw
     2.234 2.440
  nonbonded pdb=" OH  TYR B 238 "
            pdb=" O   ILE B 396 "
     model   vdw
     2.238 2.440
  nonbonded pdb=" OG1 THR B 305 "
            pdb=" OG1 THR B 413 "
     model   vdw
     2.243 2.440
  nonbonded pdb=" O   TYR B   9 "
            pdb=" NZ  LYS B  17 "
     model   vdw
     2.247 2.520
  ... (remaining 79866 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 5 through 430)
  selection = (chain 'B' and resid 5 through 430)
  selection = (chain 'C' and resid 5 through 430)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6301      2.51       5
     N    1545      2.21       5
     O    1661      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
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:             0.720
  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:          4.320
  Check model and map are aligned:         0.150
  Convert atoms to be neutral:             0.080
  Process input model:                     29.040
  Find NCS groups from input model:        0.660
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Set scattering table:                    0.020
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
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      :  0.006   0.053   9731  Z= 0.415
  Angle     :  0.692   8.766  13244  Z= 0.372
  Chirality :  0.044   0.158   1650
  Planarity :  0.005   0.050   1627
  Dihedral  : 13.226  88.717   3445
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.53 (0.20), residues: 1274
  helix: -2.02 (0.14), residues: 979
  sheet:  None (None), residues: 0
  loop : -2.77 (0.33), residues: 295

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.100 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.2111
  time to fit residues: 35.0580
Evaluate side-chains
  91 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.137 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3758
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 98 optimal weight:    0.0370
   chunk 38 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 114 optimal weight:    0.9990
   overall best weight:    0.7260

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

Flipped N/Q/H residues before XYZ refinement:
A 371 GLN
B 321 GLN
B 330 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9731  Z= 0.177
  Angle     :  0.565   8.837  13244  Z= 0.286
  Chirality :  0.039   0.131   1650
  Planarity :  0.005   0.054   1627
  Dihedral  :  4.612  46.760   1365
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer Outliers :  1.39 %
  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: -1.47 (0.23), residues: 1274
  helix: -0.48 (0.16), residues: 971
  sheet:  None (None), residues: 0
  loop : -2.21 (0.34), residues: 303

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 1.190 
Fit side-chains
  outliers start: 14
  outliers final: 6
  residues processed: 114
  average time/residue: 0.1849
  time to fit residues: 31.5576
Evaluate side-chains
  93 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 1.201 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0933
  time to fit residues: 2.5273
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0980
   chunk 95 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 114 optimal weight:    0.6980
   chunk 123 optimal weight:    5.9990
   chunk 102 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
A 371 GLN
** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 321 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9731  Z= 0.159
  Angle     :  0.544   7.891  13244  Z= 0.273
  Chirality :  0.039   0.177   1650
  Planarity :  0.005   0.055   1627
  Dihedral  :  4.281  33.630   1365
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer Outliers :  1.09 %
  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: -0.65 (0.24), residues: 1274
  helix:  0.11 (0.17), residues: 971
  sheet:  None (None), residues: 0
  loop : -1.94 (0.35), residues: 303

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 1.216 
Fit side-chains
  outliers start: 11
  outliers final: 5
  residues processed: 114
  average time/residue: 0.1803
  time to fit residues: 31.1935
Evaluate side-chains
  94 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 1.070 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0809
  time to fit residues: 2.0814
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 113 optimal weight:    0.6980
   chunk 86 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 54 optimal weight:    0.2980
   chunk 76 optimal weight:    0.9990
   chunk 115 optimal weight:    1.9990
   chunk 121 optimal weight:    0.0870
   chunk 60 optimal weight:    0.8980
   chunk 109 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
B 321 GLN
** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.047   9731  Z= 0.154
  Angle     :  0.543   8.331  13244  Z= 0.270
  Chirality :  0.039   0.176   1650
  Planarity :  0.004   0.053   1627
  Dihedral  :  4.137  27.619   1365
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer Outliers :  1.09 %
  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: -0.17 (0.24), residues: 1274
  helix:  0.45 (0.17), residues: 967
  sheet:  None (None), residues: 0
  loop : -1.68 (0.35), residues: 307

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 1.193 
Fit side-chains
  outliers start: 11
  outliers final: 3
  residues processed: 119
  average time/residue: 0.1813
  time to fit residues: 32.4960
Evaluate side-chains
  96 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 1.190 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0893
  time to fit residues: 1.9438
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 69 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
B 321 GLN
** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9731  Z= 0.200
  Angle     :  0.560   9.733  13244  Z= 0.278
  Chirality :  0.040   0.199   1650
  Planarity :  0.004   0.053   1627
  Dihedral  :  4.097  29.156   1365
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer Outliers :  1.09 %
  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:  0.16 (0.24), residues: 1274
  helix:  0.65 (0.17), residues: 970
  sheet:  None (None), residues: 0
  loop : -1.47 (0.36), residues: 304

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 1.096 
Fit side-chains
  outliers start: 11
  outliers final: 5
  residues processed: 103
  average time/residue: 0.1849
  time to fit residues: 28.8226
Evaluate side-chains
  94 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 1.165 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0998
  time to fit residues: 2.3532
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 109 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 121 optimal weight:    7.9990
   chunk 101 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0770
   chunk 10 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 117 optimal weight:    9.9990
   overall best weight:    3.0146

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

Flipped N/Q/H residues before XYZ refinement:
B 321 GLN
** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.051   9731  Z= 0.386
  Angle     :  0.666   9.657  13244  Z= 0.332
  Chirality :  0.043   0.197   1650
  Planarity :  0.004   0.054   1627
  Dihedral  :  4.314  29.797   1365
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer Outliers :  1.69 %
  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: -0.01 (0.24), residues: 1274
  helix:  0.53 (0.17), residues: 993
  sheet:  None (None), residues: 0
  loop : -1.72 (0.37), residues: 281

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 1.171 
Fit side-chains
  outliers start: 17
  outliers final: 7
  residues processed: 99
  average time/residue: 0.1793
  time to fit residues: 27.3741
Evaluate side-chains
  92 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 1.185 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0944
  time to fit residues: 2.6637
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 69 optimal weight:    7.9990
   chunk 89 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 102 optimal weight:    0.8980
   chunk 121 optimal weight:    8.9990
   chunk 76 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 321 GLN
** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9731  Z= 0.176
  Angle     :  0.567  10.538  13244  Z= 0.280
  Chirality :  0.039   0.204   1650
  Planarity :  0.004   0.054   1627
  Dihedral  :  4.168  25.224   1365
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer Outliers :  1.49 %
  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:  0.41 (0.25), residues: 1274
  helix:  0.83 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop : -1.50 (0.38), residues: 289

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 1.197 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 6
  residues processed: 106
  average time/residue: 0.1739
  time to fit residues: 28.3746
Evaluate side-chains
  94 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 1.105 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0858
  time to fit residues: 2.4384
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 77 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 95 optimal weight:    1.9990
   chunk 110 optimal weight:    5.9990
   chunk 116 optimal weight:    7.9990
   chunk 106 optimal weight:    0.0170
   overall best weight:    0.9820

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

Flipped N/Q/H residues before XYZ refinement:
B 128 GLN
** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9731  Z= 0.191
  Angle     :  0.587  10.390  13244  Z= 0.287
  Chirality :  0.040   0.200   1650
  Planarity :  0.004   0.054   1627
  Dihedral  :  4.117  25.877   1365
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer Outliers :  0.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.25), residues: 1274
  helix:  0.96 (0.17), residues: 984
  sheet:  None (None), residues: 0
  loop : -1.39 (0.38), residues: 290

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 98
  average time/residue: 0.1760
  time to fit residues: 26.6795
Evaluate side-chains
  99 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 1.033 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0853
  time to fit residues: 1.8671
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 107 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 119 optimal weight:    5.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
B 128 GLN
B 321 GLN
** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9731  Z= 0.256
  Angle     :  0.615   9.811  13244  Z= 0.301
  Chirality :  0.041   0.197   1650
  Planarity :  0.004   0.054   1627
  Dihedral  :  4.153  27.082   1365
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer Outliers :  0.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.25), residues: 1274
  helix:  0.99 (0.17), residues: 986
  sheet:  None (None), residues: 0
  loop : -1.39 (0.38), residues: 288

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 1.176 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 93
  average time/residue: 0.1807
  time to fit residues: 26.3901
Evaluate side-chains
  92 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 1.059 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1024
  time to fit residues: 2.0023
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 83 optimal weight:    0.2980
   chunk 125 optimal weight:    0.9990
   chunk 115 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 77 optimal weight:    0.0000
   chunk 61 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
B 128 GLN
B 321 GLN
** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9731  Z= 0.162
  Angle     :  0.577  10.085  13244  Z= 0.282
  Chirality :  0.039   0.200   1650
  Planarity :  0.004   0.054   1627
  Dihedral  :  4.028  26.019   1365
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer Outliers :  0.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.25), residues: 1274
  helix:  1.08 (0.17), residues: 988
  sheet:  None (None), residues: 0
  loop : -1.18 (0.37), residues: 286

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 101
  average time/residue: 0.1801
  time to fit residues: 27.6973
Evaluate side-chains
  92 residues out of total 1005 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 1.117 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1291
  time to fit residues: 1.7280
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 100 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0670
   chunk 102 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0020
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.4132

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

Flipped N/Q/H residues before XYZ refinement:
B 321 GLN
** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.073579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.060707 restraints weight = 28107.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 3.09
r_work: 0.2953 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work: 0.2935 rms_B_bonded: 2.88 restraints_weight: 0.1250
r_work: 0.2925 rms_B_bonded: 2.93 restraints_weight: 0.0625
r_work: 0.2916 rms_B_bonded: 3.00 restraints_weight: 0.0312
r_work: 0.2905 rms_B_bonded: 3.10 restraints_weight: 0.0156
r_work: 0.2895 rms_B_bonded: 3.22 restraints_weight: 0.0078
r_work: 0.2884 rms_B_bonded: 3.36 restraints_weight: 0.0039
r_work: 0.2873 rms_B_bonded: 3.53 restraints_weight: 0.0020
r_work: 0.2861 rms_B_bonded: 3.71 restraints_weight: 0.0010
r_work: 0.2849 rms_B_bonded: 3.91 restraints_weight: 0.0005
r_work: 0.2837 rms_B_bonded: 4.13 restraints_weight: 0.0002
r_work: 0.2823 rms_B_bonded: 4.38 restraints_weight: 0.0001
r_work: 0.2810 rms_B_bonded: 4.66 restraints_weight: 0.0001
r_work: 0.2795 rms_B_bonded: 4.96 restraints_weight: 0.0000
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9731  Z= 0.230
  Angle     :  0.605  11.204  13244  Z= 0.294
  Chirality :  0.040   0.196   1650
  Planarity :  0.004   0.054   1627
  Dihedral  :  4.053  28.634   1365
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer Outliers :  0.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.24), residues: 1274
  helix:  1.10 (0.17), residues: 987
  sheet:  None (None), residues: 0
  loop : -1.08 (0.37), residues: 287

===============================================================================
Job complete
usr+sys time: 1697.62 seconds
wall clock time: 31 minutes 43.15 seconds (1903.15 seconds total)