Starting phenix.real_space_refine
on Wed Mar  4 02:25:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ran_4781/03_2026/6ran_4781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ran_4781/03_2026/6ran_4781.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ran_4781/03_2026/6ran_4781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ran_4781/03_2026/6ran_4781.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ran_4781/03_2026/6ran_4781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ran_4781/03_2026/6ran_4781.cif"
  }
  resolution = 4.2
  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=   0.002
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      25      5.16       5
     C    6579      2.51       5
     N    1795      2.21       5
     O    1774      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 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: 10173
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 4741
          Classifications: {'peptide': 592}
          Link IDs: {'PTRANS': 24, 'TRANS': 567}
    Chain: "B"
      Number of atoms: 4535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 574, 4535
          Classifications: {'peptide': 574}
          Link IDs: {'PTRANS': 18, 'TRANS': 555}
    Chain: "C"
      Number of atoms: 897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 897
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 6, 'TRANS': 114}
  Time building chain proxies: 2.21, per 1000 atoms: 0.22
  Number of scatterers: 10173
  At special positions: 0
  Unit cell: (104.469, 91.545, 159.396, 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      25     16.00
     O    1774      8.00
     N    1795      7.00
     C    6579      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  50 " - pdb=" SG  CYS C 108 " distance=2.06

  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: 0.63
  Conformation dependent library (CDL) restraints added in 441.5 milliseconds
  

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2356

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 6 sheets defined
      66.7% alpha, 10.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 20
      removed outlier: 3.587A  pdb=" N   ARG A  17 " --> pdb=" O   ALA A  13 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ILE A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 24
      Proline residue:  A  24  - end of helix
      No H-bonds generated for 'chain 'A' and resid 21 through 24'
    Processing helix  chain 'A' and resid 25 through 45
      removed outlier: 3.603A  pdb=" N   PHE A  35 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 56
    Processing helix  chain 'A' and resid 64 through 71
    Processing helix  chain 'A' and resid 72 through 120
    Processing helix  chain 'A' and resid 121 through 128
      removed outlier: 4.313A  pdb=" N   TYR A 125 " --> pdb=" O   HIS A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 138
      removed outlier: 3.519A  pdb=" N   LEU A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 150
      removed outlier: 3.592A  pdb=" N   ILE A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 173
      removed outlier: 3.848A  pdb=" N   VAL A 155 " --> pdb=" O   GLY A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 182
      removed outlier: 4.337A  pdb=" N   VAL A 179 " --> pdb=" O   LYS A 175 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL A 180 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 222
    Processing helix  chain 'A' and resid 222 through 230
    Processing helix  chain 'A' and resid 231 through 285
      removed outlier: 3.897A  pdb=" N   ARG A 241 " --> pdb=" O   GLU A 237 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   LEU A 242 " --> pdb=" O   LYS A 238 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   LEU A 259 " --> pdb=" O   ARG A 255 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   PHE A 260 " --> pdb=" O   TRP A 256 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   PHE A 261 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      Proline residue:  A 262  - end of helix
      removed outlier: 3.654A  pdb=" N   VAL A 284 " --> pdb=" O   GLY A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 314
      removed outlier: 3.739A  pdb=" N   PHE A 304 " --> pdb=" O   THR A 300 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   GLN A 305 " --> pdb=" O   ARG A 301 " (cutoff:3.500A)
      Proline residue:  A 306  - end of helix
      removed outlier: 3.865A  pdb=" N   ASP A 309 " --> pdb=" O   GLN A 305 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   SER A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ASP A 312 " --> pdb=" O   GLN A 308 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE A 314 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 332
      removed outlier: 4.092A  pdb=" N   GLY A 319 " --> pdb=" O   ASN A 315 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ARG A 326 " --> pdb=" O   ALA A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 407
      removed outlier: 3.995A  pdb=" N   VAL A 403 " --> pdb=" O   LYS A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 427
      No H-bonds generated for 'chain 'A' and resid 425 through 427'
    Processing helix  chain 'A' and resid 428 through 433
    Processing helix  chain 'A' and resid 449 through 455
    Processing helix  chain 'A' and resid 462 through 473
      removed outlier: 3.797A  pdb=" N   VAL A 466 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU A 467 " --> pdb=" O   PRO A 463 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLU A 468 " --> pdb=" O   GLU A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 482
    Processing helix  chain 'A' and resid 484 through 488
      removed outlier: 3.829A  pdb=" N   THR A 488 " --> pdb=" O   GLY A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 514
    Processing helix  chain 'A' and resid 529 through 544
    Processing helix  chain 'A' and resid 555 through 560
    Processing helix  chain 'A' and resid 578 through 586
      removed outlier: 3.822A  pdb=" N   GLY A 586 " --> pdb=" O   LEU A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 602
      removed outlier: 3.685A  pdb=" N   ALA A 590 " --> pdb=" O   GLY A 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 19
      removed outlier: 3.993A  pdb=" N   LEU B   9 " --> pdb=" O   SER B   5 " (cutoff:3.500A)
      Proline residue:  B  15  - end of helix
    Processing helix  chain 'B' and resid 20 through 54
      removed outlier: 3.896A  pdb=" N   TYR B  24 " --> pdb=" O   TYR B  20 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE B  35 " --> pdb=" O   GLY B  31 " (cutoff:3.500A)
      Proline residue:  B  42  - end of helix
    Processing helix  chain 'B' and resid 57 through 103
      removed outlier: 4.521A  pdb=" N   TYR B  61 " --> pdb=" O   GLY B  57 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL B  85 " --> pdb=" O   ARG B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 113
      removed outlier: 4.155A  pdb=" N   TYR B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LYS B 112 " --> pdb=" O   ASP B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 133
      removed outlier: 3.643A  pdb=" N   ASN B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 158
      removed outlier: 4.050A  pdb=" N   LEU B 148 " --> pdb=" O   SER B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 207
      removed outlier: 3.814A  pdb=" N   ALA B 162 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ILE B 168 " --> pdb=" O   TYR B 164 " (cutoff:3.500A)
      Proline residue:  B 170  - end of helix
      removed outlier: 3.665A  pdb=" N   LEU B 174 " --> pdb=" O   PRO B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 212
    Processing helix  chain 'B' and resid 216 through 243
      removed outlier: 4.091A  pdb=" N   VAL B 241 " --> pdb=" O   ALA B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 271
      removed outlier: 3.849A  pdb=" N   PHE B 255 " --> pdb=" O   PHE B 251 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA B 256 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 287
    Processing helix  chain 'B' and resid 288 through 318
      removed outlier: 4.204A  pdb=" N   ILE B 292 " --> pdb=" O   LEU B 288 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   LEU B 293 " --> pdb=" O   THR B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 335
      removed outlier: 3.540A  pdb=" N   LEU B 335 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 384
      removed outlier: 3.708A  pdb=" N   ALA B 381 " --> pdb=" O   LYS B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 405
      No H-bonds generated for 'chain 'B' and resid 403 through 405'
    Processing helix  chain 'B' and resid 406 through 413
    Processing helix  chain 'B' and resid 427 through 433
    Processing helix  chain 'B' and resid 440 through 451
      removed outlier: 3.751A  pdb=" N   VAL B 444 " --> pdb=" O   ASP B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 460
      removed outlier: 3.802A  pdb=" N   PHE B 460 " --> pdb=" O   GLU B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 466
      removed outlier: 3.719A  pdb=" N   THR B 466 " --> pdb=" O   GLY B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 491
      removed outlier: 3.727A  pdb=" N   LYS B 491 " --> pdb=" O   ARG B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 521
    Processing helix  chain 'B' and resid 532 through 538
      removed outlier: 4.212A  pdb=" N   HIS B 538 " --> pdb=" O   ALA B 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 563
    Processing helix  chain 'B' and resid 564 through 574
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.924A  pdb=" N   THR C  91 " --> pdb=" O   PRO C  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 383
      removed outlier: 5.563A  pdb=" N   LYS A 377 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   LEU A 360 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   PHE A 381 " --> pdb=" O   ARG A 356 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   ARG A 356 " --> pdb=" O   PHE A 381 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   VAL A 383 " --> pdb=" O   GLU A 354 " (cutoff:3.500A)
      removed outlier: 5.150A  pdb=" N   GLU A 354 " --> pdb=" O   VAL A 383 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   VAL A 358 " --> pdb=" O   ARG A 414 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ARG A 414 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439
      removed outlier: 6.483A  pdb=" N   LEU A 519 " --> pdb=" O   LEU A 550 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   ILE A 552 " --> pdb=" O   LEU A 519 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   LEU A 521 " --> pdb=" O   ILE A 552 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   LYS A 388 " --> pdb=" O   ARG A 564 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   LEU A 566 " --> pdb=" O   LYS A 388 " (cutoff:3.500A)
      removed outlier: 5.785A  pdb=" N   ALA A 390 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   PHE A 568 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   VAL A 392 " --> pdb=" O   PHE A 568 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   ILE A 565 " --> pdb=" O   GLU A 576 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   GLU A 576 " --> pdb=" O   ILE A 565 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL A 567 " --> pdb=" O   VAL A 574 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 351 through 361
      removed outlier: 6.999A  pdb=" N   LEU B 353 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   LYS B 347 " --> pdb=" O   LEU B 353 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ARG B 355 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   GLY B 345 " --> pdb=" O   ARG B 355 " (cutoff:3.500A)
      removed outlier: 4.973A  pdb=" N   LEU B 357 " --> pdb=" O   GLY B 343 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   VAL B 344 " --> pdb=" O   GLU B 392 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   GLU B 392 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 414 through 417
      removed outlier: 6.172A  pdb=" N   GLY B 415 " --> pdb=" O   ILE B 497 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   ASP B 499 " --> pdb=" O   GLY B 415 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ALA B 417 " --> pdb=" O   ASP B 499 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LEU B 367 " --> pdb=" O   LEU B 528 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   THR B 366 " --> pdb=" O   TRP B 541 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   ILE B 543 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   GLY B 368 " --> pdb=" O   ILE B 543 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   LEU B 545 " --> pdb=" O   GLY B 368 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   THR B 370 " --> pdb=" O   LEU B 545 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ALA C 101 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7
      removed outlier: 3.659A  pdb=" N   THR C  78 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.529A  pdb=" N   ALA C  92 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   ARG C  38 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   GLY C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)

    653 hydrogen bonds defined for protein.
    1917 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: 1.76

  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:
        1.18 -     1.31: 1620
        1.31 -     1.44: 3197
        1.44 -     1.57: 5520
        1.57 -     1.70: 2
        1.70 -     1.83: 45
  Bond restraints: 10384
  Sorted by residual:
  bond pdb=" N   PRO A 340 "
       pdb=" CD  PRO A 340 "
    ideal  model  delta    sigma   weight residual
    1.473  1.572 -0.099 1.40e-02 5.10e+03 4.96e+01
  bond pdb=" N   PRO B 291 "
       pdb=" CD  PRO B 291 "
    ideal  model  delta    sigma   weight residual
    1.473  1.539 -0.066 1.40e-02 5.10e+03 2.21e+01
  bond pdb=" CA  GLY B 345 "
       pdb=" C   GLY B 345 "
    ideal  model  delta    sigma   weight residual
    1.516  1.481  0.035 8.20e-03 1.49e+04 1.87e+01
  bond pdb=" CA  GLY B 415 "
       pdb=" C   GLY B 415 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 7.30e-03 1.88e+04 1.79e+01
  bond pdb=" N   ILE C  51 "
       pdb=" CA  ILE C  51 "
    ideal  model  delta    sigma   weight residual
    1.456  1.504 -0.048 1.15e-02 7.56e+03 1.76e+01
  ... (remaining 10379 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 11178
        2.41 -     4.83: 2335
        4.83 -     7.24: 466
        7.24 -     9.66: 82
        9.66 -    12.07: 13
  Bond angle restraints: 14074
  Sorted by residual:
  angle pdb=" N   VAL B 210 "
        pdb=" CA  VAL B 210 "
        pdb=" C   VAL B 210 "
      ideal   model   delta    sigma   weight residual
     111.81  103.51    8.30 8.60e-01 1.35e+00 9.31e+01
  angle pdb=" N   GLU B 442 "
        pdb=" CA  GLU B 442 "
        pdb=" C   GLU B 442 "
      ideal   model   delta    sigma   weight residual
     111.07  120.93   -9.86 1.07e+00 8.73e-01 8.49e+01
  angle pdb=" N   VAL A 186 "
        pdb=" CA  VAL A 186 "
        pdb=" C   VAL A 186 "
      ideal   model   delta    sigma   weight residual
     110.42  119.00   -8.58 9.60e-01 1.09e+00 7.98e+01
  angle pdb=" N   VAL B 444 "
        pdb=" CA  VAL B 444 "
        pdb=" CB  VAL B 444 "
      ideal   model   delta    sigma   weight residual
     110.55  120.47   -9.92 1.17e+00 7.31e-01 7.19e+01
  angle pdb=" N   VAL B 576 "
        pdb=" CA  VAL B 576 "
        pdb=" C   VAL B 576 "
      ideal   model   delta    sigma   weight residual
     107.80  119.82  -12.02 1.45e+00 4.76e-01 6.88e+01
  ... (remaining 14069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 5849
       17.38 -    34.75: 218
       34.75 -    52.13: 52
       52.13 -    69.50: 42
       69.50 -    86.88: 14
  Dihedral angle restraints: 6175
    sinusoidal: 2495
      harmonic: 3680
  Sorted by residual:
  dihedral pdb=" N   THR A 135 "
           pdb=" C   THR A 135 "
           pdb=" CA  THR A 135 "
           pdb=" CB  THR A 135 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  135.75  -12.35     0      2.50e+00 1.60e-01 2.44e+01
  dihedral pdb=" N   VAL B  90 "
           pdb=" C   VAL B  90 "
           pdb=" CA  VAL B  90 "
           pdb=" CB  VAL B  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  135.67  -12.27     0      2.50e+00 1.60e-01 2.41e+01
  dihedral pdb=" C   VAL B 483 "
           pdb=" N   VAL B 483 "
           pdb=" CA  VAL B 483 "
           pdb=" CB  VAL B 483 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.14   12.14     0      2.50e+00 1.60e-01 2.36e+01
  ... (remaining 6172 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 1010
       0.106 -    0.211: 397
       0.211 -    0.316: 137
       0.316 -    0.421: 39
       0.421 -    0.527: 24
  Chirality restraints: 1607
  Sorted by residual:
  chirality pdb=" CA  LEU A  33 "
            pdb=" N   LEU A  33 "
            pdb=" C   LEU A  33 "
            pdb=" CB  LEU A  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 6.93e+00
  chirality pdb=" CA  GLU B 442 "
            pdb=" N   GLU B 442 "
            pdb=" C   GLU B 442 "
            pdb=" CB  GLU B 442 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.35e+00
  chirality pdb=" CA  VAL B  90 "
            pdb=" N   VAL B  90 "
            pdb=" C   VAL B  90 "
            pdb=" CB  VAL B  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.94    0.50 2.00e-01 2.50e+01 6.30e+00
  ... (remaining 1604 not shown)

  Planarity restraints: 1790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 172 "    0.030 2.00e-02 2.50e+03   6.07e-02 3.68e+01
        pdb=" C   LEU A 172 "   -0.105 2.00e-02 2.50e+03
        pdb=" O   LEU A 172 "    0.040 2.00e-02 2.50e+03
        pdb=" N   SER A 173 "    0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  75 "   -0.059 2.00e-02 2.50e+03   2.86e-02 2.04e+01
        pdb=" CG  TRP A  75 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  75 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  75 "    0.021 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  75 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  75 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  75 "    0.041 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  75 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  75 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  75 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  22 "   -0.060 2.00e-02 2.50e+03   2.78e-02 1.94e+01
        pdb=" CG  TRP B  22 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  22 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  22 "    0.024 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  22 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  22 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  22 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  22 "   -0.028 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  22 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  22 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 1787 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 3616
        2.92 -     3.41: 10205
        3.41 -     3.91: 16524
        3.91 -     4.40: 18254
        4.40 -     4.90: 30613
  Nonbonded interactions: 79212
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG C  19 "
            pdb=" OE1 GLN C  82 "
     model   vdw
     2.421 3.120
  nonbonded pdb=" O   SER C  85 "
            pdb=" OG  SER C  85 "
     model   vdw
     2.450 3.040
  nonbonded pdb=" O   PRO A  47 "
            pdb=" N   PHE A  50 "
     model   vdw
     2.451 3.120
  nonbonded pdb=" N   LEU B 468 "
            pdb=" O   LEU B 468 "
     model   vdw
     2.481 2.496
  nonbonded pdb=" N   LEU B 388 "
            pdb=" O   LEU B 388 "
     model   vdw
     2.485 2.496
  ... (remaining 79207 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.200
  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:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.910
  Find NCS groups from input model:        0.050
  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: 0.7088
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      :  0.017   0.099  10386  Z= 1.141
  Angle     :  2.079  12.069  14078  Z= 1.488
  Chirality :  0.140   0.527   1607
  Planarity :  0.012   0.092   1790
  Dihedral  : 12.459  86.879   3813
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.67 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.47 %
    Favored  : 97.44 %
  Cbeta Deviations :  1.61 %
  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:  0.16 (0.22), residues: 1281
  helix:  1.09 (0.18), residues: 784
  sheet:  0.14 (0.44), residues: 131
  loop : -2.07 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  23 
 TYR   0.058   0.006   TYR B 284 
 PHE   0.049   0.009   PHE A 270 
 TRP   0.060   0.009   TRP B  22 
 HIS   0.007   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.01673 (10384)
  covalent geometry    : angle       2.07935 (14074)
  SS BOND              : bond        0.02205 (    2)
  SS BOND              : angle       2.01641 (    4)
  hydrogen bonds       : bond        0.24159 (  653)
  hydrogen bonds       : angle       8.01061 ( 1917)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 333
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.7813 (m-80) cc_final: 0.7139 (m-80)
REVERT: A   40 THR cc_start: 0.8383 (p) cc_final: 0.8132 (t)
REVERT: A  205 MET cc_start: 0.8764 (tmm) cc_final: 0.8348 (tmm)
REVERT: A  359 TRP cc_start: 0.7247 (m100) cc_final: 0.6992 (m100)
REVERT: A  365 LYS cc_start: 0.6656 (mmtm) cc_final: 0.5317 (tptt)
REVERT: B   32 LEU cc_start: 0.9263 (mt) cc_final: 0.8880 (mt)
REVERT: B  102 LEU cc_start: 0.9222 (mt) cc_final: 0.8926 (mt)
REVERT: B  130 ARG cc_start: 0.8858 (ttp80) cc_final: 0.8393 (tmm160)
REVERT: B  132 MET cc_start: 0.8393 (ttp) cc_final: 0.7766 (tmm)
REVERT: B  145 PHE cc_start: 0.8508 (t80) cc_final: 0.8158 (t80)
REVERT: B  161 LEU cc_start: 0.8271 (tp) cc_final: 0.8052 (tp)
REVERT: B  173 PHE cc_start: 0.6584 (t80) cc_final: 0.6320 (t80)
REVERT: B  255 PHE cc_start: 0.6999 (m-10) cc_final: 0.6579 (m-10)
REVERT: B  258 LEU cc_start: 0.8111 (tt) cc_final: 0.7525 (tp)
REVERT: B  289 THR cc_start: 0.6625 (p) cc_final: 0.6383 (p)
REVERT: B  365 MET cc_start: 0.9128 (ppp) cc_final: 0.8806 (ppp)
REVERT: C    6 GLU cc_start: 0.5873 (mp0) cc_final: 0.5658 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 334
  average time/residue: 0.1229
  time to fit residues: 54.1178
Evaluate side-chains
  189 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
B 515 GLN
C  39 GLN
** C 116 GLN ** 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 = 0.4016 r_free = 0.4016 target = 0.124216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.102624 restraints weight = 27961.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.105195 restraints weight = 16150.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.106987 restraints weight = 10758.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.108184 restraints weight = 8024.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.108914 restraints weight = 6519.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.3652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10386  Z= 0.165
  Angle     :  0.672   7.619  14078  Z= 0.362
  Chirality :  0.043   0.203   1607
  Planarity :  0.006   0.080   1790
  Dihedral  :  5.025  27.084   1442
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.28 %
    Favored  : 97.53 %
  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:  1.24 (0.23), residues: 1281
  helix:  1.93 (0.18), residues: 785
  sheet:  0.14 (0.40), residues: 137
  loop : -1.44 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 426 
 TYR   0.024   0.002   TYR A 299 
 PHE   0.021   0.002   PHE A 472 
 TRP   0.024   0.002   TRP B 262 
 HIS   0.005   0.001   HIS B 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (10384)
  covalent geometry    : angle       0.67161 (14074)
  SS BOND              : bond        0.00496 (    2)
  SS BOND              : angle       0.18535 (    4)
  hydrogen bonds       : bond        0.05687 (  653)
  hydrogen bonds       : angle       4.90438 ( 1917)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 230
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 MET cc_start: 0.8712 (tmm) cc_final: 0.8398 (tmm)
REVERT: B   32 LEU cc_start: 0.9016 (mt) cc_final: 0.8770 (mt)
REVERT: B   76 SER cc_start: 0.9357 (t) cc_final: 0.9065 (p)
REVERT: B  109 PHE cc_start: 0.7919 (t80) cc_final: 0.7714 (t80)
REVERT: B  132 MET cc_start: 0.8697 (ttp) cc_final: 0.7712 (tmm)
REVERT: B  161 LEU cc_start: 0.8412 (tp) cc_final: 0.8208 (tp)
REVERT: B  365 MET cc_start: 0.9158 (ppp) cc_final: 0.8819 (ppp)
REVERT: B  434 PHE cc_start: 0.8907 (t80) cc_final: 0.8684 (t80)
REVERT: C   20 LEU cc_start: 0.5801 (mt) cc_final: 0.5498 (tp)
REVERT: C   31 TYR cc_start: 0.8042 (p90) cc_final: 0.7784 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 231
  average time/residue: 0.0957
  time to fit residues: 31.6186
Evaluate side-chains
  159 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 125 optimal weight:    8.9990
   chunk 86 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 122 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A  71 HIS
A 243 ASN
A 308 GLN
A 503 GLN
B 419 GLN
C  39 GLN
C  57 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.118343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.097147 restraints weight = 28754.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.099502 restraints weight = 16851.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.101117 restraints weight = 11419.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.102127 restraints weight = 8618.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.103007 restraints weight = 7117.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.4497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10386  Z= 0.187
  Angle     :  0.669   7.087  14078  Z= 0.350
  Chirality :  0.042   0.168   1607
  Planarity :  0.006   0.073   1790
  Dihedral  :  4.916  28.414   1442
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.46 %
    Favored  : 95.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.00 (0.22), residues: 1281
  helix:  1.60 (0.17), residues: 789
  sheet:  0.17 (0.42), residues: 130
  loop : -1.22 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 107 
 TYR   0.023   0.002   TYR B  92 
 PHE   0.017   0.002   PHE A 171 
 TRP   0.023   0.002   TRP B 262 
 HIS   0.007   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (10384)
  covalent geometry    : angle       0.66853 (14074)
  SS BOND              : bond        0.00323 (    2)
  SS BOND              : angle       0.64352 (    4)
  hydrogen bonds       : bond        0.05342 (  653)
  hydrogen bonds       : angle       4.69972 ( 1917)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 204
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.7673 (m-80) cc_final: 0.7401 (m-80)
REVERT: A  147 PHE cc_start: 0.6298 (t80) cc_final: 0.5996 (t80)
REVERT: A  205 MET cc_start: 0.8854 (tmm) cc_final: 0.8601 (tmm)
REVERT: A  519 LEU cc_start: 0.8875 (tp) cc_final: 0.8203 (tp)
REVERT: B   32 LEU cc_start: 0.9009 (mt) cc_final: 0.8502 (mt)
REVERT: B   43 TYR cc_start: 0.7922 (t80) cc_final: 0.7658 (t80)
REVERT: B   60 VAL cc_start: 0.8658 (m) cc_final: 0.8439 (p)
REVERT: B  111 HIS cc_start: 0.7463 (m-70) cc_final: 0.7258 (m-70)
REVERT: B  132 MET cc_start: 0.8766 (ttp) cc_final: 0.7640 (tmm)
REVERT: B  145 PHE cc_start: 0.8274 (t80) cc_final: 0.8064 (t80)
REVERT: C   31 TYR cc_start: 0.8085 (p90) cc_final: 0.7575 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 205
  average time/residue: 0.0960
  time to fit residues: 28.2406
Evaluate side-chains
  155 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 122 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 60 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 110 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   chunk 84 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 39 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
B 400 HIS
B 419 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.118924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.097971 restraints weight = 28505.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.100329 restraints weight = 16542.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.101957 restraints weight = 11233.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.102983 restraints weight = 8455.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.103743 restraints weight = 6972.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.4939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10386  Z= 0.149
  Angle     :  0.604   8.758  14078  Z= 0.312
  Chirality :  0.041   0.209   1607
  Planarity :  0.004   0.050   1790
  Dihedral  :  4.702  26.276   1442
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.17 (0.23), residues: 1281
  helix:  1.71 (0.18), residues: 792
  sheet:  0.08 (0.43), residues: 130
  loop : -1.04 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  19 
 TYR   0.019   0.001   TYR B  92 
 PHE   0.017   0.002   PHE A 472 
 TRP   0.020   0.002   TRP B 262 
 HIS   0.005   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (10384)
  covalent geometry    : angle       0.60369 (14074)
  SS BOND              : bond        0.00339 (    2)
  SS BOND              : angle       0.38995 (    4)
  hydrogen bonds       : bond        0.04798 (  653)
  hydrogen bonds       : angle       4.46816 ( 1917)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.7458 (m-80) cc_final: 0.7224 (m-80)
REVERT: A   34 LEU cc_start: 0.8265 (mt) cc_final: 0.7801 (tt)
REVERT: A  147 PHE cc_start: 0.6149 (t80) cc_final: 0.5886 (t80)
REVERT: A  205 MET cc_start: 0.8719 (tmm) cc_final: 0.8347 (tmm)
REVERT: A  328 PHE cc_start: 0.8049 (m-10) cc_final: 0.7300 (m-10)
REVERT: A  593 TYR cc_start: 0.6292 (t80) cc_final: 0.5761 (t80)
REVERT: B   32 LEU cc_start: 0.8747 (mt) cc_final: 0.8538 (mt)
REVERT: B   43 TYR cc_start: 0.7912 (t80) cc_final: 0.7580 (t80)
REVERT: B   91 GLU cc_start: 0.8455 (tt0) cc_final: 0.8180 (tm-30)
REVERT: B  132 MET cc_start: 0.8630 (ttp) cc_final: 0.7476 (tmm)
REVERT: B  203 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6908 (mm-30)
REVERT: B  255 PHE cc_start: 0.7567 (m-10) cc_final: 0.7220 (m-80)
REVERT: B  365 MET cc_start: 0.8998 (ppp) cc_final: 0.8795 (ppp)
REVERT: B  499 ASP cc_start: 0.7306 (t70) cc_final: 0.6261 (p0)
REVERT: C   18 LEU cc_start: 0.7678 (tt) cc_final: 0.7401 (mt)
REVERT: C   31 TYR cc_start: 0.8140 (p90) cc_final: 0.7704 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 198
  average time/residue: 0.0891
  time to fit residues: 26.1336
Evaluate side-chains
  151 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 60 optimal weight:    0.4980
   chunk 71 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 102 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0870
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.6760

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

Flipped N/Q/H residues before XYZ refinement:
B 419 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.120284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.098900 restraints weight = 28362.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.101301 restraints weight = 16577.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.102947 restraints weight = 11250.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.104142 restraints weight = 8493.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.104893 restraints weight = 6918.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.5257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10386  Z= 0.120
  Angle     :  0.560   6.896  14078  Z= 0.286
  Chirality :  0.040   0.208   1607
  Planarity :  0.004   0.048   1790
  Dihedral  :  4.469  24.470   1442
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  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:  1.41 (0.23), residues: 1281
  helix:  1.89 (0.18), residues: 794
  sheet:  0.14 (0.43), residues: 130
  loop : -0.92 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  19 
 TYR   0.010   0.001   TYR B  61 
 PHE   0.027   0.001   PHE A 472 
 TRP   0.041   0.002   TRP B 223 
 HIS   0.003   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10384)
  covalent geometry    : angle       0.55998 (14074)
  SS BOND              : bond        0.00334 (    2)
  SS BOND              : angle       0.37415 (    4)
  hydrogen bonds       : bond        0.04474 (  653)
  hydrogen bonds       : angle       4.19944 ( 1917)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.7321 (m-80) cc_final: 0.7111 (m-80)
REVERT: A  195 ARG cc_start: 0.8797 (mmm-85) cc_final: 0.8316 (mmt90)
REVERT: A  205 MET cc_start: 0.8786 (tmm) cc_final: 0.8399 (tmm)
REVERT: A  328 PHE cc_start: 0.8091 (m-10) cc_final: 0.7378 (m-10)
REVERT: A  544 MET cc_start: 0.8214 (mmp) cc_final: 0.7309 (ptt)
REVERT: A  593 TYR cc_start: 0.6252 (t80) cc_final: 0.5727 (t80)
REVERT: B   32 LEU cc_start: 0.8681 (mt) cc_final: 0.8435 (mt)
REVERT: B   38 PHE cc_start: 0.8565 (t80) cc_final: 0.8285 (t80)
REVERT: B   40 LEU cc_start: 0.8903 (tp) cc_final: 0.8178 (tt)
REVERT: B   91 GLU cc_start: 0.8438 (tt0) cc_final: 0.8169 (tm-30)
REVERT: B  111 HIS cc_start: 0.7244 (m-70) cc_final: 0.6948 (m-70)
REVERT: B  132 MET cc_start: 0.8658 (ttp) cc_final: 0.7391 (tmm)
REVERT: B  138 LEU cc_start: 0.8138 (tt) cc_final: 0.7306 (tt)
REVERT: B  365 MET cc_start: 0.8979 (ppp) cc_final: 0.8770 (ppp)
REVERT: B  465 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8004 (mp0)
REVERT: B  499 ASP cc_start: 0.7212 (t70) cc_final: 0.6147 (p0)
REVERT: C   18 LEU cc_start: 0.7686 (tt) cc_final: 0.7373 (mt)
REVERT: C   31 TYR cc_start: 0.8144 (p90) cc_final: 0.7744 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 198
  average time/residue: 0.0862
  time to fit residues: 25.3610
Evaluate side-chains
  155 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 30 optimal weight:    6.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
B 419 GLN
B 538 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.113929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.093178 restraints weight = 28366.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.095317 restraints weight = 16843.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.096653 restraints weight = 11519.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.097729 restraints weight = 8901.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.098340 restraints weight = 7331.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.5611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10386  Z= 0.196
  Angle     :  0.665   8.202  14078  Z= 0.341
  Chirality :  0.043   0.197   1607
  Planarity :  0.005   0.050   1790
  Dihedral  :  4.751  24.667   1442
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.04 %
    Favored  : 96.77 %
  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:  0.92 (0.23), residues: 1281
  helix:  1.41 (0.18), residues: 792
  sheet:  0.04 (0.44), residues: 131
  loop : -0.89 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 208 
 TYR   0.027   0.002   TYR B 155 
 PHE   0.023   0.002   PHE B 151 
 TRP   0.059   0.002   TRP B 223 
 HIS   0.006   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (10384)
  covalent geometry    : angle       0.66468 (14074)
  SS BOND              : bond        0.00402 (    2)
  SS BOND              : angle       0.84649 (    4)
  hydrogen bonds       : bond        0.04934 (  653)
  hydrogen bonds       : angle       4.56134 ( 1917)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 178
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 ARG cc_start: 0.8777 (mmm-85) cc_final: 0.8237 (mmt90)
REVERT: A  205 MET cc_start: 0.8535 (tmm) cc_final: 0.8273 (tmm)
REVERT: A  593 TYR cc_start: 0.6327 (t80) cc_final: 0.5793 (t80)
REVERT: B   32 LEU cc_start: 0.8750 (mt) cc_final: 0.8328 (mt)
REVERT: B   91 GLU cc_start: 0.8495 (tt0) cc_final: 0.8208 (tm-30)
REVERT: B  132 MET cc_start: 0.8689 (ttp) cc_final: 0.7409 (tmm)
REVERT: B  299 MET cc_start: 0.6005 (ttt) cc_final: 0.5794 (ttt)
REVERT: B  434 PHE cc_start: 0.8812 (t80) cc_final: 0.8593 (t80)
REVERT: C   18 LEU cc_start: 0.7847 (tt) cc_final: 0.7475 (mt)
REVERT: C   31 TYR cc_start: 0.8299 (p90) cc_final: 0.7977 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 179
  average time/residue: 0.0874
  time to fit residues: 23.2289
Evaluate side-chains
  136 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 109 optimal weight:    7.9990
   chunk 81 optimal weight:    4.9990
   chunk 108 optimal weight:    0.8980
   chunk 122 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
B 111 HIS
B 282 ASN
B 419 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.115443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.095006 restraints weight = 27560.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.097098 restraints weight = 16420.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.098373 restraints weight = 11220.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.099470 restraints weight = 8723.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.100144 restraints weight = 7182.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.5785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10386  Z= 0.149
  Angle     :  0.608   7.777  14078  Z= 0.309
  Chirality :  0.041   0.193   1607
  Planarity :  0.004   0.049   1790
  Dihedral  :  4.639  24.233   1442
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.90 %
    Favored  : 98.01 %
  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:  1.07 (0.23), residues: 1281
  helix:  1.55 (0.18), residues: 793
  sheet:  0.05 (0.43), residues: 131
  loop : -0.87 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  38 
 TYR   0.015   0.002   TYR C  31 
 PHE   0.030   0.002   PHE A 472 
 TRP   0.059   0.002   TRP B 223 
 HIS   0.005   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (10384)
  covalent geometry    : angle       0.60750 (14074)
  SS BOND              : bond        0.01183 (    2)
  SS BOND              : angle       1.12125 (    4)
  hydrogen bonds       : bond        0.04608 (  653)
  hydrogen bonds       : angle       4.37799 ( 1917)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8215 (mmt90)
REVERT: A  205 MET cc_start: 0.8645 (tmm) cc_final: 0.8110 (tmm)
REVERT: A  593 TYR cc_start: 0.6250 (t80) cc_final: 0.5735 (t80)
REVERT: B   91 GLU cc_start: 0.8486 (tt0) cc_final: 0.8202 (tm-30)
REVERT: B  132 MET cc_start: 0.8601 (ttp) cc_final: 0.7365 (tmm)
REVERT: B  203 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7062 (mm-30)
REVERT: B  299 MET cc_start: 0.6060 (ttt) cc_final: 0.5832 (ttt)
REVERT: B  434 PHE cc_start: 0.8766 (t80) cc_final: 0.8554 (t80)
REVERT: B  465 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7904 (mp0)
REVERT: B  499 ASP cc_start: 0.7837 (t0) cc_final: 0.6305 (p0)
REVERT: C    6 GLU cc_start: 0.5257 (mp0) cc_final: 0.4988 (mp0)
REVERT: C   18 LEU cc_start: 0.7781 (tt) cc_final: 0.7347 (mt)
REVERT: C   34 ILE cc_start: 0.7702 (mm) cc_final: 0.7352 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 183
  average time/residue: 0.0792
  time to fit residues: 22.0083
Evaluate side-chains
  142 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 83 optimal weight:    0.0370
   chunk 47 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 111 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.2064

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 HIS
B 400 HIS
B 419 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.115936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.095060 restraints weight = 28128.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.097184 restraints weight = 16810.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.098688 restraints weight = 11518.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.099728 restraints weight = 8778.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.100331 restraints weight = 7233.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.6026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10386  Z= 0.143
  Angle     :  0.606   9.416  14078  Z= 0.307
  Chirality :  0.041   0.195   1607
  Planarity :  0.004   0.048   1790
  Dihedral  :  4.566  23.608   1442
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  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:  1.14 (0.23), residues: 1281
  helix:  1.66 (0.18), residues: 792
  sheet: -0.13 (0.42), residues: 135
  loop : -0.90 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 107 
 TYR   0.021   0.002   TYR B 155 
 PHE   0.026   0.002   PHE B  38 
 TRP   0.044   0.002   TRP B 223 
 HIS   0.008   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10384)
  covalent geometry    : angle       0.60550 (14074)
  SS BOND              : bond        0.00271 (    2)
  SS BOND              : angle       1.10223 (    4)
  hydrogen bonds       : bond        0.04488 (  653)
  hydrogen bonds       : angle       4.30712 ( 1917)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 ARG cc_start: 0.8641 (mmm-85) cc_final: 0.8304 (mmt90)
REVERT: A  205 MET cc_start: 0.8613 (tmm) cc_final: 0.8170 (tmm)
REVERT: A  593 TYR cc_start: 0.6270 (t80) cc_final: 0.5767 (t80)
REVERT: B   40 LEU cc_start: 0.8952 (tp) cc_final: 0.8248 (tt)
REVERT: B   43 TYR cc_start: 0.7789 (t80) cc_final: 0.7450 (t80)
REVERT: B   91 GLU cc_start: 0.8472 (tt0) cc_final: 0.8195 (tm-30)
REVERT: B  132 MET cc_start: 0.8574 (ttp) cc_final: 0.7332 (tmm)
REVERT: B  282 ASN cc_start: 0.8630 (t0) cc_final: 0.8363 (t0)
REVERT: B  299 MET cc_start: 0.6079 (ttt) cc_final: 0.5843 (ttt)
REVERT: B  434 PHE cc_start: 0.8793 (t80) cc_final: 0.8556 (t80)
REVERT: B  465 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7984 (mp0)
REVERT: C    6 GLU cc_start: 0.5203 (mp0) cc_final: 0.4497 (mt-10)
REVERT: C   18 LEU cc_start: 0.8019 (tt) cc_final: 0.7524 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0785
  time to fit residues: 21.2075
Evaluate side-chains
  145 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 38 optimal weight:    8.9990
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 124 optimal weight:    0.9990
   chunk 83 optimal weight:    0.0040
   chunk 81 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 HIS
B 419 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.117790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.096487 restraints weight = 28252.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.098665 restraints weight = 16927.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.100149 restraints weight = 11628.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.101183 restraints weight = 8923.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.101786 restraints weight = 7389.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.6191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10386  Z= 0.119
  Angle     :  0.588   8.891  14078  Z= 0.293
  Chirality :  0.040   0.180   1607
  Planarity :  0.005   0.071   1790
  Dihedral  :  4.403  22.524   1442
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  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:  1.35 (0.23), residues: 1281
  helix:  1.84 (0.18), residues: 795
  sheet: -0.09 (0.42), residues: 135
  loop : -0.86 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 142 
 TYR   0.013   0.001   TYR A 299 
 PHE   0.024   0.002   PHE B  38 
 TRP   0.037   0.002   TRP B 223 
 HIS   0.004   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (10384)
  covalent geometry    : angle       0.58810 (14074)
  SS BOND              : bond        0.00277 (    2)
  SS BOND              : angle       0.90522 (    4)
  hydrogen bonds       : bond        0.04180 (  653)
  hydrogen bonds       : angle       4.12963 ( 1917)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 MET cc_start: 0.7976 (mtp) cc_final: 0.7058 (mtm)
REVERT: A  195 ARG cc_start: 0.8677 (mmm-85) cc_final: 0.8335 (mmt90)
REVERT: A  205 MET cc_start: 0.8806 (tmm) cc_final: 0.8324 (tmm)
REVERT: A  353 VAL cc_start: 0.7770 (t) cc_final: 0.7565 (p)
REVERT: A  544 MET cc_start: 0.8167 (mmp) cc_final: 0.7362 (ptt)
REVERT: A  593 TYR cc_start: 0.6294 (t80) cc_final: 0.5832 (t80)
REVERT: B   40 LEU cc_start: 0.8915 (tp) cc_final: 0.8280 (tt)
REVERT: B   43 TYR cc_start: 0.7754 (t80) cc_final: 0.7446 (t80)
REVERT: B  132 MET cc_start: 0.8626 (ttp) cc_final: 0.7315 (tmm)
REVERT: B  142 ARG cc_start: 0.7616 (ttp80) cc_final: 0.7182 (tmm-80)
REVERT: B  282 ASN cc_start: 0.8645 (t0) cc_final: 0.8364 (t0)
REVERT: B  299 MET cc_start: 0.5993 (ttt) cc_final: 0.5789 (ttt)
REVERT: B  434 PHE cc_start: 0.8782 (t80) cc_final: 0.8531 (t80)
REVERT: B  465 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7873 (mp0)
REVERT: C   36 TRP cc_start: 0.6459 (m100) cc_final: 0.5419 (m100)
REVERT: C   83 MET cc_start: 0.8107 (mmp) cc_final: 0.7864 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0896
  time to fit residues: 24.6333
Evaluate side-chains
  153 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 0 optimal weight:    9.9990
   chunk 116 optimal weight:    7.9990
   chunk 47 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 114 optimal weight:    6.9990
   chunk 125 optimal weight:    5.9990
   chunk 124 optimal weight:    5.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 HIS
B 419 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.117636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.096452 restraints weight = 28165.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.098667 restraints weight = 16761.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.100164 restraints weight = 11467.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.101241 restraints weight = 8752.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.101968 restraints weight = 7215.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.6332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10386  Z= 0.120
  Angle     :  0.587   8.950  14078  Z= 0.294
  Chirality :  0.040   0.186   1607
  Planarity :  0.005   0.063   1790
  Dihedral  :  4.327  21.948   1442
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.19 %
    Favored  : 99.72 %
  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:  1.46 (0.23), residues: 1281
  helix:  1.94 (0.18), residues: 794
  sheet: -0.06 (0.42), residues: 136
  loop : -0.85 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 403 
 TYR   0.026   0.001   TYR B 155 
 PHE   0.023   0.002   PHE B  38 
 TRP   0.034   0.002   TRP B 223 
 HIS   0.004   0.001   HIS B 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (10384)
  covalent geometry    : angle       0.58726 (14074)
  SS BOND              : bond        0.00254 (    2)
  SS BOND              : angle       0.87983 (    4)
  hydrogen bonds       : bond        0.04093 (  653)
  hydrogen bonds       : angle       4.12721 ( 1917)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 186
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8302 (mmt90)
REVERT: A  205 MET cc_start: 0.8799 (tmm) cc_final: 0.8323 (tmm)
REVERT: A  544 MET cc_start: 0.8184 (mmp) cc_final: 0.7350 (ptt)
REVERT: A  593 TYR cc_start: 0.6311 (t80) cc_final: 0.5856 (t80)
REVERT: B   40 LEU cc_start: 0.8906 (tp) cc_final: 0.8294 (tt)
REVERT: B   43 TYR cc_start: 0.7782 (t80) cc_final: 0.7485 (t80)
REVERT: B  132 MET cc_start: 0.8566 (ttp) cc_final: 0.7269 (tmm)
REVERT: B  142 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7060 (tmm-80)
REVERT: B  282 ASN cc_start: 0.8645 (t0) cc_final: 0.8435 (t0)
REVERT: B  299 MET cc_start: 0.6267 (ttt) cc_final: 0.5970 (ttt)
REVERT: B  465 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7818 (mp0)
REVERT: B  499 ASP cc_start: 0.7827 (t0) cc_final: 0.6186 (p0)
REVERT: B  529 ILE cc_start: 0.8119 (mt) cc_final: 0.7842 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0861
  time to fit residues: 23.8799
Evaluate side-chains
  147 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    0.1980
   chunk 47 optimal weight:    0.0770
   chunk 98 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0980
   chunk 0 optimal weight:    9.9990
   chunk 114 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.6740

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 HIS
B 419 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.118027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.096812 restraints weight = 28274.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.099037 restraints weight = 16807.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.100574 restraints weight = 11486.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.101580 restraints weight = 8752.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.102333 restraints weight = 7246.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.6490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10386  Z= 0.114
  Angle     :  0.578   8.851  14078  Z= 0.288
  Chirality :  0.040   0.181   1607
  Planarity :  0.005   0.066   1790
  Dihedral  :  4.222  21.470   1442
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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:  1.55 (0.23), residues: 1281
  helix:  2.03 (0.18), residues: 798
  sheet: -0.07 (0.42), residues: 136
  loop : -0.87 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 142 
 TYR   0.017   0.001   TYR B  92 
 PHE   0.023   0.001   PHE B  38 
 TRP   0.033   0.002   TRP B 262 
 HIS   0.005   0.001   HIS B 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (10384)
  covalent geometry    : angle       0.57821 (14074)
  SS BOND              : bond        0.00164 (    2)
  SS BOND              : angle       1.09006 (    4)
  hydrogen bonds       : bond        0.03989 (  653)
  hydrogen bonds       : angle       4.01049 ( 1917)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1671.01 seconds
wall clock time: 29 minutes 25.00 seconds (1765.00 seconds total)