Starting phenix.real_space_refine
on Tue Mar  3 20:56:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zds_14668/03_2026/7zds_14668_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zds_14668/03_2026/7zds_14668.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zds_14668/03_2026/7zds_14668_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zds_14668/03_2026/7zds_14668_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zds_14668/03_2026/7zds_14668.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zds_14668/03_2026/7zds_14668.map"
  }
  resolution = 3.26
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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      29      5.16       5
     C    5600      2.51       5
     N    1538      2.21       5
     O    1569      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 79 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8736
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 4319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 564, 4319
          Classifications: {'peptide': 564}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 18, 'TRANS': 545}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "D"
      Number of atoms: 4417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4417
          Classifications: {'peptide': 565}
          Link IDs: {'PTRANS': 26, 'TRANS': 538}
  Time building chain proxies: 2.10, per 1000 atoms: 0.24
  Number of scatterers: 8736
  At special positions: 0
  Unit cell: (122.202, 86.211, 105.462, 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      29     16.00
     O    1569      8.00
     N    1538      7.00
     C    5600      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 357.9 milliseconds
  

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2090

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 4 sheets defined
      64.0% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'C' and resid 4 through 12
      removed outlier: 3.629A  pdb=" N   ALA C   9 " --> pdb=" O   LEU C   5 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   LEU C  10 " --> pdb=" O   PRO C   6 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 15 through 50
      removed outlier: 3.630A  pdb=" N   ALA C  25 " --> pdb=" O   GLY C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 104
      removed outlier: 3.506A  pdb=" N   ARG C  67 " --> pdb=" O   ALA C  63 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   HIS C  94 " --> pdb=" O   ARG C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 113
      removed outlier: 3.746A  pdb=" N   ARG C 113 " --> pdb=" O   GLY C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 131
      removed outlier: 3.767A  pdb=" N   ASN C 121 " --> pdb=" O   GLY C 117 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL C 124 " --> pdb=" O   LEU C 120 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   THR C 129 " --> pdb=" O   ALA C 125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 137
    Processing helix  chain 'C' and resid 137 through 156
    Processing helix  chain 'C' and resid 159 through 175
      removed outlier: 3.845A  pdb=" N   THR C 165 " --> pdb=" O   THR C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 185
    Processing helix  chain 'C' and resid 185 through 208
      removed outlier: 3.538A  pdb=" N   GLY C 189 " --> pdb=" O   GLY C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 215
      removed outlier: 3.868A  pdb=" N   ILE C 215 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 269
      removed outlier: 3.707A  pdb=" N   GLN C 225 " --> pdb=" O   ARG C 221 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU C 226 " --> pdb=" O   TYR C 222 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLN C 240 " --> pdb=" O   ALA C 236 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU C 243 " --> pdb=" O   ARG C 239 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   THR C 244 " --> pdb=" O   GLN C 240 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL C 259 " --> pdb=" O   GLY C 255 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER C 267 " --> pdb=" O   LEU C 263 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLY C 269 " --> pdb=" O   MET C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 290
      removed outlier: 3.658A  pdb=" N   LEU C 282 " --> pdb=" O   ALA C 278 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   PHE C 283 " --> pdb=" O   LEU C 279 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 296 through 316
      removed outlier: 3.900A  pdb=" N   GLN C 302 " --> pdb=" O   THR C 298 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   HIS C 303 " --> pdb=" O   GLY C 299 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY C 305 " --> pdb=" O   PHE C 301 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ILE C 314 " --> pdb=" O   SER C 310 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 378 through 387
      removed outlier: 3.786A  pdb=" N   LEU C 382 " --> pdb=" O   GLY C 378 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU C 383 " --> pdb=" O   LYS C 379 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 408 through 415
      removed outlier: 4.020A  pdb=" N   GLN C 414 " --> pdb=" O   ALA C 410 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 435
    Processing helix  chain 'C' and resid 442 through 454
      removed outlier: 3.525A  pdb=" N   SER C 447 " --> pdb=" O   ASP C 443 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY C 454 " --> pdb=" O   LEU C 450 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 480 through 492
    Processing helix  chain 'C' and resid 506 through 521
      removed outlier: 3.590A  pdb=" N   MET C 520 " --> pdb=" O   LEU C 516 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 534 through 539
      removed outlier: 4.556A  pdb=" N   SER C 537 " --> pdb=" O   ARG C 534 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG C 538 " --> pdb=" O   GLY C 535 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 5 through 17
    Processing helix  chain 'D' and resid 22 through 54
      removed outlier: 3.509A  pdb=" N   SER D  27 " --> pdb=" O   TRP D  23 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ARG D  28 " --> pdb=" O   LEU D  24 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE D  39 " --> pdb=" O   GLY D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 59 through 61
      No H-bonds generated for 'chain 'D' and resid 59 through 61'
    Processing helix  chain 'D' and resid 62 through 115
      removed outlier: 3.612A  pdb=" N   LEU D  71 " --> pdb=" O   THR D  67 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLU D  84 " --> pdb=" O   VAL D  80 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ARG D  85 " --> pdb=" O   TRP D  81 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ILE D  94 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      Proline residue:  D 111  - end of helix
    Processing helix  chain 'D' and resid 118 through 127
      removed outlier: 3.849A  pdb=" N   LEU D 125 " --> pdb=" O   SER D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 127 through 132
    Processing helix  chain 'D' and resid 133 through 138
      removed outlier: 3.728A  pdb=" N   TYR D 137 " --> pdb=" O   MET D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 159
      removed outlier: 4.159A  pdb=" N   VAL D 148 " --> pdb=" O   MET D 144 " (cutoff:3.500A)
      Proline residue:  D 151  - end of helix
    Processing helix  chain 'D' and resid 164 through 194
      removed outlier: 3.784A  pdb=" N   LEU D 169 " --> pdb=" O   ALA D 165 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   THR D 172 " --> pdb=" O   ILE D 168 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ALA D 173 " --> pdb=" O   LEU D 169 " (cutoff:3.500A)
      Proline residue:  D 174  - end of helix
      Proline residue:  D 177  - end of helix
      removed outlier: 3.971A  pdb=" N   GLY D 186 " --> pdb=" O   LEU D 182 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG D 192 " --> pdb=" O   ALA D 188 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 203
      removed outlier: 4.098A  pdb=" N   GLY D 203 " --> pdb=" O   ALA D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 203 through 210
    Processing helix  chain 'D' and resid 211 through 218
      removed outlier: 3.607A  pdb=" N   LEU D 215 " --> pdb=" O   GLY D 211 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ILE D 217 " --> pdb=" O   GLU D 213 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE D 218 " --> pdb=" O   THR D 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 223 through 274
      removed outlier: 3.786A  pdb=" N   SER D 227 " --> pdb=" O   ALA D 223 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ARG D 244 " --> pdb=" O   MET D 240 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   LEU D 245 " --> pdb=" O   GLU D 241 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU D 248 " --> pdb=" O   ARG D 244 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER D 250 " --> pdb=" O   ALA D 246 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   LEU D 253 " --> pdb=" O   SER D 249 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLU D 254 " --> pdb=" O   SER D 250 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER D 258 " --> pdb=" O   GLU D 254 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE D 261 " --> pdb=" O   THR D 257 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU D 273 " --> pdb=" O   GLY D 269 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 311
      removed outlier: 3.816A  pdb=" N   ALA D 293 " --> pdb=" O   ALA D 289 " (cutoff:3.500A)
      Proline residue:  D 298  - end of helix
      removed outlier: 3.880A  pdb=" N   PHE D 301 " --> pdb=" O   ALA D 297 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
    Processing helix  chain 'D' and resid 311 through 330
      removed outlier: 3.728A  pdb=" N   ALA D 315 " --> pdb=" O   TYR D 311 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER D 323 " --> pdb=" O   GLY D 319 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 390 through 398
    Processing helix  chain 'D' and resid 417 through 422
    Processing helix  chain 'D' and resid 438 through 444
      removed outlier: 3.697A  pdb=" N   VAL D 443 " --> pdb=" O   LEU D 439 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU D 444 " --> pdb=" O   ARG D 440 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 451 through 462
      removed outlier: 3.617A  pdb=" N   ASN D 461 " --> pdb=" O   ALA D 457 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA D 462 " --> pdb=" O   ALA D 458 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 473 through 477
      removed outlier: 4.071A  pdb=" N   ASP D 476 " --> pdb=" O   GLN D 473 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 487 through 501
      removed outlier: 3.702A  pdb=" N   ARG D 493 " --> pdb=" O   GLY D 489 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA D 495 " --> pdb=" O   ALA D 491 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 517 through 529
      removed outlier: 3.748A  pdb=" N   ARG D 523 " --> pdb=" O   HIS D 519 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 359 through 362
      removed outlier: 6.219A  pdb=" N   ILE C 359 " --> pdb=" O   ASP C 343 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ASP C 343 " --> pdb=" O   ILE C 359 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   GLU C 396 " --> pdb=" O   ARG C 342 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419
      removed outlier: 6.741A  pdb=" N   VAL C 496 " --> pdb=" O   LEU C 527 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   VAL C 529 " --> pdb=" O   VAL C 496 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   LEU C 498 " --> pdb=" O   VAL C 529 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ILE C 369 " --> pdb=" O   MET C 528 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   THR C 530 " --> pdb=" O   ILE C 369 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   ILE C 371 " --> pdb=" O   THR C 530 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   GLN C 541 " --> pdb=" O   HIS C 368 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ASP C 546 " --> pdb=" O   ILE C 550 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   ILE C 550 " --> pdb=" O   ASP C 546 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 364 through 373
      removed outlier: 6.523A  pdb=" N   LEU D 365 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   THR D 358 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   GLY D 367 " --> pdb=" O   PHE D 356 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   PHE D 356 " --> pdb=" O   GLY D 367 " (cutoff:3.500A)
      removed outlier: 5.623A  pdb=" N   LEU D 369 " --> pdb=" O   GLU D 354 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLU D 354 " --> pdb=" O   LEU D 369 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   ALA D 352 " --> pdb=" O   ARG D 407 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   ARG D 407 " --> pdb=" O   ALA D 352 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   GLU D 354 " --> pdb=" O   SER D 405 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   SER D 405 " --> pdb=" O   GLU D 354 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER D 401 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 425 through 428
      removed outlier: 6.329A  pdb=" N   SER D 426 " --> pdb=" O   LEU D 508 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   ASP D 510 " --> pdb=" O   SER D 426 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL D 428 " --> pdb=" O   ASP D 510 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   LEU D 507 " --> pdb=" O   LEU D 538 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   VAL D 540 " --> pdb=" O   LEU D 507 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU D 509 " --> pdb=" O   VAL D 540 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   VAL D 380 " --> pdb=" O   TRP D 554 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   MET D 556 " --> pdb=" O   VAL D 380 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   VAL D 382 " --> pdb=" O   MET D 556 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLU D 563 " --> pdb=" O   VAL D 555 " (cutoff:3.500A)

    491 hydrogen bonds defined for protein.
    1455 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: 1.52

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1836
        1.33 -     1.45: 1933
        1.45 -     1.57: 5083
        1.57 -     1.69: 1
        1.69 -     1.81: 55
  Bond restraints: 8908
  Sorted by residual:
  bond pdb=" N   VAL C 344 "
       pdb=" CA  VAL C 344 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.99e+00
  bond pdb=" N   GLU C 460 "
       pdb=" CA  GLU C 460 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.033 1.19e-02 7.06e+03 7.88e+00
  bond pdb=" N   SER C 466 "
       pdb=" CA  SER C 466 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.034 1.25e-02 6.40e+03 7.21e+00
  bond pdb=" C   PRO C 178 "
       pdb=" O   PRO C 178 "
    ideal  model  delta    sigma   weight residual
    1.240  1.210  0.030 1.12e-02 7.97e+03 7.20e+00
  bond pdb=" N   ARG C 332 "
       pdb=" CA  ARG C 332 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.21e-02 6.83e+03 6.86e+00
  ... (remaining 8903 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 11507
        1.54 -     3.09: 496
        3.09 -     4.63: 83
        4.63 -     6.18: 17
        6.18 -     7.72: 4
  Bond angle restraints: 12107
  Sorted by residual:
  angle pdb=" CA  PRO D 432 "
        pdb=" N   PRO D 432 "
        pdb=" CD  PRO D 432 "
      ideal   model   delta    sigma   weight residual
     112.00  104.84    7.16 1.40e+00 5.10e-01 2.62e+01
  angle pdb=" N   VAL C 312 "
        pdb=" CA  VAL C 312 "
        pdb=" C   VAL C 312 "
      ideal   model   delta    sigma   weight residual
     112.96  109.00    3.96 1.00e+00 1.00e+00 1.57e+01
  angle pdb=" C   GLU C 460 "
        pdb=" CA  GLU C 460 "
        pdb=" CB  GLU C 460 "
      ideal   model   delta    sigma   weight residual
     110.88  116.68   -5.80 1.57e+00 4.06e-01 1.36e+01
  angle pdb=" CA  GLN C 354 "
        pdb=" C   GLN C 354 "
        pdb=" O   GLN C 354 "
      ideal   model   delta    sigma   weight residual
     122.14  117.63    4.51 1.24e+00 6.50e-01 1.32e+01
  angle pdb=" CA  ALA C 355 "
        pdb=" C   ALA C 355 "
        pdb=" O   ALA C 355 "
      ideal   model   delta    sigma   weight residual
     120.63  116.77    3.86 1.08e+00 8.57e-01 1.27e+01
  ... (remaining 12102 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 4790
       17.54 -    35.08: 432
       35.08 -    52.62: 69
       52.62 -    70.16: 17
       70.16 -    87.69: 11
  Dihedral angle restraints: 5319
    sinusoidal: 2080
      harmonic: 3239
  Sorted by residual:
  dihedral pdb=" CA  GLU D  84 "
           pdb=" C   GLU D  84 "
           pdb=" N   ARG D  85 "
           pdb=" CA  ARG D  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.24   23.76     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" C   GLU C 460 "
           pdb=" N   GLU C 460 "
           pdb=" CA  GLU C 460 "
           pdb=" CB  GLU C 460 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.30    9.70     0      2.50e+00 1.60e-01 1.51e+01
  dihedral pdb=" CA  PHE C 291 "
           pdb=" C   PHE C 291 "
           pdb=" N   GLU C 292 "
           pdb=" CA  GLU C 292 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.24   18.76     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 5316 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1135
       0.051 -    0.103: 239
       0.103 -    0.154: 37
       0.154 -    0.206: 2
       0.206 -    0.257: 2
  Chirality restraints: 1415
  Sorted by residual:
  chirality pdb=" CA  LEU C 425 "
            pdb=" N   LEU C 425 "
            pdb=" C   LEU C 425 "
            pdb=" CB  LEU C 425 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  GLU C 460 "
            pdb=" N   GLU C 460 "
            pdb=" C   GLU C 460 "
            pdb=" CB  GLU C 460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CA  PHE C 426 "
            pdb=" N   PHE C 426 "
            pdb=" C   PHE C 426 "
            pdb=" CB  PHE C 426 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1412 not shown)

  Planarity restraints: 1550
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D 431 "   -0.073 5.00e-02 4.00e+02   1.06e-01 1.79e+01
        pdb=" N   PRO D 432 "    0.183 5.00e-02 4.00e+02
        pdb=" CA  PRO D 432 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO D 432 "   -0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 295 "    0.038 5.00e-02 4.00e+02   5.76e-02 5.30e+00
        pdb=" N   PRO C 296 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO C 296 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 296 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 341 "    0.010 2.00e-02 2.50e+03   2.03e-02 4.10e+00
        pdb=" C   LEU C 341 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   LEU C 341 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ARG C 342 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1547 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 56
        2.59 -     3.17: 7352
        3.17 -     3.75: 13456
        3.75 -     4.32: 18944
        4.32 -     4.90: 31727
  Nonbonded interactions: 71535
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 427 "
            pdb=" OD2 ASP D 207 "
     model   vdw
     2.017 3.040
  nonbonded pdb=" OG  SER C 438 "
            pdb=" OG  SER C 441 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" OG  SER D 417 "
            pdb=" OG  SER D 420 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" O   SER C 427 "
            pdb=" OG  SER C 427 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   PHE C 426 "
            pdb=" OD2 ASP D 207 "
     model   vdw
     2.230 3.040
  ... (remaining 71530 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:             1.600
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.460
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.126   8908  Z= 0.278
  Angle     :  0.737   7.720  12107  Z= 0.458
  Chirality :  0.044   0.257   1415
  Planarity :  0.005   0.106   1550
  Dihedral  : 14.062  87.694   3229
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.62 (0.23), residues: 1125
  helix: -1.95 (0.18), residues: 654
  sheet: -1.10 (0.69), residues: 57
  loop : -1.11 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 560 
 TYR   0.012   0.001   TYR C   7 
 PHE   0.011   0.001   PHE C 426 
 TRP   0.013   0.001   TRP D 463 
 HIS   0.004   0.001   HIS C 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 8908)
  covalent geometry    : angle       0.73676 (12107)
  hydrogen bonds       : bond        0.27354 (  491)
  hydrogen bonds       : angle      10.18882 ( 1455)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.340 
Fit side-chains
REVERT: C  517 LEU cc_start: 0.8199 (tt) cc_final: 0.7661 (mp)
REVERT: C  521 MET cc_start: 0.8904 (mtm) cc_final: 0.8495 (mtt)
REVERT: D   54 MET cc_start: 0.8788 (mmm) cc_final: 0.8582 (mmp)
REVERT: D  377 GLN cc_start: 0.7846 (mt0) cc_final: 0.7527 (tt0)
REVERT: D  558 ASP cc_start: 0.6614 (t70) cc_final: 0.6349 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1176
  time to fit residues: 17.1256
Evaluate side-chains
  91 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.0670
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
C  93 GLN
C 121 ASN
C 512 GLN
D  16 GLN
D  89 HIS
D 191 ASN
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.137345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.101349 restraints weight = 10201.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 1.37
r_work: 0.2891 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.1365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8908  Z= 0.148
  Angle     :  0.619   8.490  12107  Z= 0.315
  Chirality :  0.042   0.169   1415
  Planarity :  0.005   0.043   1550
  Dihedral  :  4.491  21.953   1228
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  7.04 %
    Favored  : 91.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.24), residues: 1125
  helix: -0.09 (0.20), residues: 654
  sheet: -0.76 (0.66), residues: 65
  loop : -0.99 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 139 
 TYR   0.015   0.002   TYR D  88 
 PHE   0.016   0.001   PHE C 164 
 TRP   0.010   0.001   TRP C  41 
 HIS   0.006   0.001   HIS C 556 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8908)
  covalent geometry    : angle       0.61929 (12107)
  hydrogen bonds       : bond        0.05238 (  491)
  hydrogen bonds       : angle       5.09974 ( 1455)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.329 
Fit side-chains
REVERT: C  517 LEU cc_start: 0.8150 (tt) cc_final: 0.7781 (mp)
REVERT: C  521 MET cc_start: 0.9057 (mtm) cc_final: 0.8598 (mtt)
REVERT: D   94 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9002 (mp)
REVERT: D  234 ASP cc_start: 0.8459 (t0) cc_final: 0.7908 (m-30)
REVERT: D  377 GLN cc_start: 0.8034 (mt0) cc_final: 0.7639 (tt0)
REVERT: D  566 ARG cc_start: 0.5833 (ttp80) cc_final: 0.5380 (mtp180)
  outliers start: 10
  outliers final: 5
  residues processed: 113
  average time/residue: 0.0931
  time to fit residues: 14.5727
Evaluate side-chains
  100 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  399 LEU
Chi-restraints excluded: chain C residue  427 SER
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 56 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 69 optimal weight:    0.1980
   chunk 53 optimal weight:    8.9990
   chunk 13 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 121 ASN
C 210 GLN
D  89 HIS
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.138074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.103317 restraints weight = 9963.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.28
r_work: 0.2911 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2783 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8908  Z= 0.131
  Angle     :  0.553   7.838  12107  Z= 0.277
  Chirality :  0.040   0.138   1415
  Planarity :  0.004   0.037   1550
  Dihedral  :  4.203  16.787   1228
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.12 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.25), residues: 1125
  helix:  0.70 (0.20), residues: 658
  sheet: -0.73 (0.65), residues: 65
  loop : -0.93 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 139 
 TYR   0.015   0.001   TYR D  88 
 PHE   0.012   0.001   PHE C 426 
 TRP   0.010   0.001   TRP D 463 
 HIS   0.004   0.001   HIS D 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8908)
  covalent geometry    : angle       0.55261 (12107)
  hydrogen bonds       : bond        0.04415 (  491)
  hydrogen bonds       : angle       4.52619 ( 1455)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.363 
Fit side-chains
REVERT: C  323 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7200 (mm-30)
REVERT: C  362 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7603 (tm-30)
REVERT: C  399 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7915 (mp)
REVERT: C  490 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8401 (mm)
REVERT: C  517 LEU cc_start: 0.8097 (tt) cc_final: 0.7783 (mp)
REVERT: D   94 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9008 (mp)
REVERT: D  234 ASP cc_start: 0.8346 (t0) cc_final: 0.7880 (m-30)
REVERT: D  377 GLN cc_start: 0.7922 (mt0) cc_final: 0.7541 (tt0)
REVERT: D  566 ARG cc_start: 0.5724 (ttp80) cc_final: 0.5421 (mtp180)
  outliers start: 11
  outliers final: 7
  residues processed: 117
  average time/residue: 0.1101
  time to fit residues: 17.3687
Evaluate side-chains
  109 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  339 LEU
Chi-restraints excluded: chain C residue  399 LEU
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  459 LEU
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 54 optimal weight:    8.9990
   chunk 91 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 11 optimal weight:    0.1980
   chunk 69 optimal weight:    0.5980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C 121 ASN
** D 442 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 = 0.3509 r_free = 0.3509 target = 0.139071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.103117 restraints weight = 10174.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 1.31
r_work: 0.2909 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8908  Z= 0.125
  Angle     :  0.544   8.646  12107  Z= 0.268
  Chirality :  0.040   0.136   1415
  Planarity :  0.004   0.036   1550
  Dihedral  :  4.081  15.792   1228
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 11.88 %
    Favored  : 85.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.25), residues: 1125
  helix:  1.12 (0.21), residues: 658
  sheet: -0.60 (0.66), residues: 65
  loop : -0.94 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 139 
 TYR   0.014   0.001   TYR D  88 
 PHE   0.010   0.001   PHE C 426 
 TRP   0.008   0.001   TRP D 463 
 HIS   0.004   0.001   HIS D 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8908)
  covalent geometry    : angle       0.54447 (12107)
  hydrogen bonds       : bond        0.04051 (  491)
  hydrogen bonds       : angle       4.29519 ( 1455)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.295 
Fit side-chains
REVERT: C   11 TYR cc_start: 0.8750 (m-80) cc_final: 0.8490 (m-80)
REVERT: C  362 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7661 (tm-30)
REVERT: C  490 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8251 (mm)
REVERT: C  517 LEU cc_start: 0.8071 (tt) cc_final: 0.7800 (mp)
REVERT: D   94 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8979 (mp)
REVERT: D  234 ASP cc_start: 0.8340 (t0) cc_final: 0.7860 (m-30)
REVERT: D  377 GLN cc_start: 0.7849 (mt0) cc_final: 0.7438 (tt0)
REVERT: D  459 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7870 (mp)
REVERT: D  463 TRP cc_start: 0.7708 (m-10) cc_final: 0.7346 (m-10)
  outliers start: 21
  outliers final: 14
  residues processed: 121
  average time/residue: 0.1051
  time to fit residues: 17.2489
Evaluate side-chains
  111 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  225 GLN
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  441 SER
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  370 ASN
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  382 VAL
Chi-restraints excluded: chain D residue  459 LEU
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 106 optimal weight:    0.9990
   chunk 89 optimal weight:    5.9990
   chunk 101 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0670
   chunk 33 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0770
   chunk 18 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6282

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.139155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.104998 restraints weight = 10210.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 1.31
r_work: 0.2922 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8908  Z= 0.125
  Angle     :  0.537   8.402  12107  Z= 0.263
  Chirality :  0.040   0.136   1415
  Planarity :  0.004   0.038   1550
  Dihedral  :  3.996  15.442   1228
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 13.53 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.25), residues: 1125
  helix:  1.29 (0.21), residues: 657
  sheet: -0.48 (0.66), residues: 65
  loop : -0.89 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 452 
 TYR   0.014   0.001   TYR D  88 
 PHE   0.009   0.001   PHE C 181 
 TRP   0.008   0.001   TRP C  41 
 HIS   0.004   0.001   HIS D 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8908)
  covalent geometry    : angle       0.53651 (12107)
  hydrogen bonds       : bond        0.03966 (  491)
  hydrogen bonds       : angle       4.17999 ( 1455)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.286 
Fit side-chains
REVERT: C   11 TYR cc_start: 0.8736 (m-80) cc_final: 0.8492 (m-80)
REVERT: C  362 GLN cc_start: 0.8413 (tm-30) cc_final: 0.7639 (tm-30)
REVERT: C  490 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8221 (mm)
REVERT: C  517 LEU cc_start: 0.8067 (tt) cc_final: 0.7804 (mp)
REVERT: D   94 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8981 (mp)
REVERT: D  234 ASP cc_start: 0.8317 (t0) cc_final: 0.7813 (m-30)
REVERT: D  370 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7808 (t0)
REVERT: D  377 GLN cc_start: 0.7803 (mt0) cc_final: 0.7425 (tt0)
REVERT: D  463 TRP cc_start: 0.7743 (m-10) cc_final: 0.7359 (m-10)
REVERT: D  525 MET cc_start: 0.7740 (mmm) cc_final: 0.7467 (mmm)
  outliers start: 22
  outliers final: 16
  residues processed: 111
  average time/residue: 0.0955
  time to fit residues: 14.7731
Evaluate side-chains
  108 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  225 GLN
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  339 LEU
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  370 ASN
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  459 LEU
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 81 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   chunk 108 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 37 optimal weight:    0.5980
   chunk 63 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.139332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.104896 restraints weight = 10051.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.40
r_work: 0.2927 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8908  Z= 0.125
  Angle     :  0.540   8.984  12107  Z= 0.262
  Chirality :  0.040   0.146   1415
  Planarity :  0.004   0.043   1550
  Dihedral  :  3.932  15.542   1228
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 14.30 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.25), residues: 1125
  helix:  1.43 (0.21), residues: 656
  sheet: -0.44 (0.66), residues: 65
  loop : -0.87 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 451 
 TYR   0.014   0.001   TYR D  88 
 PHE   0.010   0.001   PHE C 181 
 TRP   0.009   0.001   TRP D 463 
 HIS   0.004   0.001   HIS D  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8908)
  covalent geometry    : angle       0.54020 (12107)
  hydrogen bonds       : bond        0.03911 (  491)
  hydrogen bonds       : angle       4.12632 ( 1455)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.353 
Fit side-chains
REVERT: C   11 TYR cc_start: 0.8720 (m-80) cc_final: 0.8452 (m-80)
REVERT: C  362 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7624 (tm-30)
REVERT: C  490 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8196 (mm)
REVERT: C  517 LEU cc_start: 0.8043 (tt) cc_final: 0.7798 (mp)
REVERT: D   94 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8957 (mp)
REVERT: D  234 ASP cc_start: 0.8324 (t0) cc_final: 0.7808 (m-30)
REVERT: D  370 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7836 (t0)
REVERT: D  377 GLN cc_start: 0.7747 (mt0) cc_final: 0.7386 (tt0)
REVERT: D  459 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7913 (mp)
REVERT: D  463 TRP cc_start: 0.7787 (m-10) cc_final: 0.7374 (m-10)
  outliers start: 21
  outliers final: 16
  residues processed: 113
  average time/residue: 0.0992
  time to fit residues: 15.3565
Evaluate side-chains
  113 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  225 GLN
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  370 ASN
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  459 LEU
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 80 optimal weight:    0.5980
   chunk 88 optimal weight:    0.0070
   chunk 75 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.0602

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.162274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.127815 restraints weight = 9653.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.33
r_work: 0.3262 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8908  Z= 0.160
  Angle     :  0.570   8.975  12107  Z= 0.274
  Chirality :  0.042   0.278   1415
  Planarity :  0.004   0.041   1550
  Dihedral  :  3.989  15.700   1228
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 14.85 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.25), residues: 1125
  helix:  1.40 (0.21), residues: 653
  sheet: -0.46 (0.65), residues: 65
  loop : -0.87 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 452 
 TYR   0.016   0.001   TYR D  88 
 PHE   0.010   0.001   PHE C 181 
 TRP   0.009   0.001   TRP D 463 
 HIS   0.004   0.001   HIS D  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 8908)
  covalent geometry    : angle       0.57006 (12107)
  hydrogen bonds       : bond        0.04082 (  491)
  hydrogen bonds       : angle       4.20574 ( 1455)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.298 
Fit side-chains
REVERT: C   11 TYR cc_start: 0.8800 (m-80) cc_final: 0.8546 (m-80)
REVERT: C  362 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7654 (tm-30)
REVERT: C  490 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8303 (mm)
REVERT: C  517 LEU cc_start: 0.8115 (tt) cc_final: 0.7887 (mp)
REVERT: D   94 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9038 (mp)
REVERT: D  234 ASP cc_start: 0.8424 (t0) cc_final: 0.7879 (m-30)
REVERT: D  370 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.7885 (t0)
REVERT: D  377 GLN cc_start: 0.7906 (mt0) cc_final: 0.7528 (tt0)
REVERT: D  459 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7966 (mp)
  outliers start: 23
  outliers final: 16
  residues processed: 115
  average time/residue: 0.1100
  time to fit residues: 16.9390
Evaluate side-chains
  116 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  225 GLN
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  370 ASN
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  459 LEU
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 109 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 105 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 10 optimal weight:    0.3980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.162543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.129048 restraints weight = 9568.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.32
r_work: 0.3240 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8908  Z= 0.157
  Angle     :  0.576   9.695  12107  Z= 0.277
  Chirality :  0.042   0.253   1415
  Planarity :  0.004   0.040   1550
  Dihedral  :  4.010  15.934   1228
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 14.96 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.25), residues: 1125
  helix:  1.41 (0.21), residues: 653
  sheet: -0.46 (0.65), residues: 65
  loop : -0.87 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 452 
 TYR   0.016   0.001   TYR D  88 
 PHE   0.010   0.001   PHE C 181 
 TRP   0.012   0.001   TRP D 463 
 HIS   0.004   0.001   HIS D  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8908)
  covalent geometry    : angle       0.57644 (12107)
  hydrogen bonds       : bond        0.04079 (  491)
  hydrogen bonds       : angle       4.22709 ( 1455)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.328 
Fit side-chains
REVERT: C   11 TYR cc_start: 0.8806 (m-80) cc_final: 0.8597 (m-80)
REVERT: C  362 GLN cc_start: 0.8489 (tm-30) cc_final: 0.7695 (tm-30)
REVERT: C  490 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8318 (mm)
REVERT: C  517 LEU cc_start: 0.8123 (tt) cc_final: 0.7895 (mp)
REVERT: D   94 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.9051 (mp)
REVERT: D  234 ASP cc_start: 0.8470 (t0) cc_final: 0.7912 (m-30)
REVERT: D  244 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7850 (mtt90)
REVERT: D  370 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.7922 (t0)
REVERT: D  377 GLN cc_start: 0.7925 (mt0) cc_final: 0.7554 (tt0)
REVERT: D  459 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7985 (mp)
  outliers start: 23
  outliers final: 18
  residues processed: 114
  average time/residue: 0.0951
  time to fit residues: 14.7808
Evaluate side-chains
  116 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  225 GLN
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  346 ASP
Chi-restraints excluded: chain D residue  370 ASN
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  459 LEU
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 109 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 89 optimal weight:    0.6980
   chunk 111 optimal weight:    5.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.160683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.127612 restraints weight = 9618.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.32
r_work: 0.3265 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8908  Z= 0.154
  Angle     :  0.570   9.568  12107  Z= 0.275
  Chirality :  0.041   0.231   1415
  Planarity :  0.004   0.039   1550
  Dihedral  :  4.011  15.803   1228
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.07 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.25), residues: 1125
  helix:  1.43 (0.20), residues: 653
  sheet: -0.47 (0.65), residues: 65
  loop : -0.88 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 452 
 TYR   0.016   0.001   TYR D  88 
 PHE   0.010   0.001   PHE C 181 
 TRP   0.013   0.001   TRP D 463 
 HIS   0.004   0.001   HIS D  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 8908)
  covalent geometry    : angle       0.56973 (12107)
  hydrogen bonds       : bond        0.04063 (  491)
  hydrogen bonds       : angle       4.23026 ( 1455)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.283 
Fit side-chains
REVERT: C  490 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8282 (mm)
REVERT: C  517 LEU cc_start: 0.8136 (tt) cc_final: 0.7920 (mp)
REVERT: D   94 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9044 (mp)
REVERT: D  234 ASP cc_start: 0.8399 (t0) cc_final: 0.7871 (m-30)
REVERT: D  244 ARG cc_start: 0.8140 (mtt90) cc_final: 0.7837 (mtt90)
REVERT: D  370 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.7910 (t0)
REVERT: D  377 GLN cc_start: 0.7913 (mt0) cc_final: 0.7550 (tt0)
REVERT: D  459 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8008 (mp)
  outliers start: 24
  outliers final: 18
  residues processed: 115
  average time/residue: 0.1079
  time to fit residues: 16.9111
Evaluate side-chains
  115 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  225 GLN
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  346 ASP
Chi-restraints excluded: chain D residue  370 ASN
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  459 LEU
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 73 optimal weight:    0.4980
   chunk 42 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.167768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 115)---------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.134186 restraints weight = 9816.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.37
r_work: 0.3292 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8585
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8908  Z= 0.122
  Angle     :  0.561  11.419  12107  Z= 0.266
  Chirality :  0.041   0.334   1415
  Planarity :  0.004   0.039   1550
  Dihedral  :  3.918  15.363   1228
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.29 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.25), residues: 1125
  helix:  1.60 (0.21), residues: 653
  sheet: -0.39 (0.65), residues: 65
  loop : -0.86 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 452 
 TYR   0.015   0.001   TYR D  88 
 PHE   0.009   0.001   PHE C 181 
 TRP   0.013   0.001   TRP D 463 
 HIS   0.004   0.001   HIS D  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8908)
  covalent geometry    : angle       0.56085 (12107)
  hydrogen bonds       : bond        0.03846 (  491)
  hydrogen bonds       : angle       4.14255 ( 1455)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.315 
Fit side-chains
REVERT: C  490 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8271 (mm)
REVERT: C  517 LEU cc_start: 0.8107 (tt) cc_final: 0.7899 (mp)
REVERT: D   94 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.9018 (mp)
REVERT: D  234 ASP cc_start: 0.8332 (t0) cc_final: 0.7807 (m-30)
REVERT: D  244 ARG cc_start: 0.8104 (mtt90) cc_final: 0.7812 (mtt90)
REVERT: D  370 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.7907 (t0)
REVERT: D  377 GLN cc_start: 0.7827 (mt0) cc_final: 0.7492 (tt0)
REVERT: D  459 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7942 (mp)
  outliers start: 23
  outliers final: 18
  residues processed: 112
  average time/residue: 0.1053
  time to fit residues: 15.9201
Evaluate side-chains
  114 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  225 GLN
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  346 ASP
Chi-restraints excluded: chain D residue  370 ASN
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  459 LEU
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 109 optimal weight:    0.0170
   chunk 73 optimal weight:    0.0000
   chunk 90 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.4022

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.165115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.130767 restraints weight = 9534.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.32
r_work: 0.3298 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8908  Z= 0.107
  Angle     :  0.545  10.446  12107  Z= 0.258
  Chirality :  0.040   0.312   1415
  Planarity :  0.004   0.039   1550
  Dihedral  :  3.789  13.152   1228
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.51 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.25), residues: 1125
  helix:  1.78 (0.21), residues: 658
  sheet: -0.30 (0.66), residues: 65
  loop : -0.82 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 452 
 TYR   0.014   0.001   TYR D  88 
 PHE   0.009   0.001   PHE C 181 
 TRP   0.011   0.001   TRP D 463 
 HIS   0.004   0.001   HIS C 556 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 8908)
  covalent geometry    : angle       0.54460 (12107)
  hydrogen bonds       : bond        0.03658 (  491)
  hydrogen bonds       : angle       4.03117 ( 1455)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2228.73 seconds
wall clock time: 38 minutes 38.45 seconds (2318.45 seconds total)