Starting phenix.real_space_refine
on Fri Jul  3 14:08:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z8j_39848/07_2026/8z8j_39848.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z8j_39848/07_2026/8z8j_39848.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z8j_39848/07_2026/8z8j_39848.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z8j_39848/07_2026/8z8j_39848.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z8j_39848/07_2026/8z8j_39848.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z8j_39848/07_2026/8z8j_39848.cif"
  }
  resolution = 3.16
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1345 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      14      5.49       5
     S      80      5.16       5
     C    8698      2.51       5
     N    2387      2.21       5
     O    2587      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13766
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 621, 5021
          Classifications: {'peptide': 621}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 31, 'TRANS': 589}
    Chain: "B"
      Number of atoms: 5255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 656, 5255
          Classifications: {'peptide': 656}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 33, 'TRANS': 622}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 3170
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 388, 3158
          Classifications: {'peptide': 388}
          Link IDs: {'PTRANS': 27, 'TRANS': 360}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 388, 3158
          Classifications: {'peptide': 388}
          Link IDs: {'PTRANS': 27, 'TRANS': 360}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 3228
    Chain: "D"
      Number of atoms: 237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 237
          Classifications: {'RNA': 11}
          Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 6, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 3, 'rna3p': 7}
    Chain: "E"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 83
          Classifications: {'RNA': 4}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 1}
          Link IDs: {'rna2p': 2, 'rna3p': 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  ASER C 336 " occ=0.39
      ... (10 atoms not shown)
      pdb=" OG BSER C 336 " occ=0.61
    residue:
      pdb=" N  ASER C 384 " occ=0.01
      ... (10 atoms not shown)
      pdb=" OG BSER C 384 " occ=0.99
  Time building chain proxies: 3.92, per 1000 atoms: 0.28
  Number of scatterers: 13766
  At special positions: 0
  Unit cell: (89.8461, 101.526, 137.465, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      80     16.00
     P      14     15.00
     O    2587      8.00
     N    2387      7.00
     C    8698      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.15
  Conformation dependent library (CDL) restraints added in 797.9 milliseconds
  

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3182

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 16 sheets defined
      47.5% alpha, 10.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 18
      removed outlier: 4.547A  pdb=" N   THR A  18 " --> pdb=" O   GLU A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 46
    Processing helix  chain 'A' and resid 64 through 75
    Processing helix  chain 'A' and resid 126 through 133
    Processing helix  chain 'A' and resid 134 through 155
    Processing helix  chain 'A' and resid 157 through 167
    Processing helix  chain 'A' and resid 176 through 184
    Processing helix  chain 'A' and resid 185 through 187
      No H-bonds generated for 'chain 'A' and resid 185 through 187'
    Processing helix  chain 'A' and resid 233 through 237
      removed outlier: 3.548A  pdb=" N   ASP A 236 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 257
    Processing helix  chain 'A' and resid 270 through 272
      No H-bonds generated for 'chain 'A' and resid 270 through 272'
    Processing helix  chain 'A' and resid 273 through 287
      removed outlier: 3.631A  pdb=" N   LEU A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 298
      removed outlier: 3.734A  pdb=" N   ILE A 298 " --> pdb=" O   HIS A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 317
      removed outlier: 3.958A  pdb=" N   SER A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 345
      removed outlier: 4.165A  pdb=" N   GLU A 339 " --> pdb=" O   PRO A 335 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ARG A 345 " --> pdb=" O   MET A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 381
      removed outlier: 4.494A  pdb=" N   ARG A 381 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 401
      removed outlier: 3.531A  pdb=" N   SER A 386 " --> pdb=" O   THR A 382 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLN A 401 " --> pdb=" O   ARG A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 492
    Processing helix  chain 'A' and resid 493 through 497
    Processing helix  chain 'A' and resid 498 through 516
      removed outlier: 4.014A  pdb=" N   ASN A 516 " --> pdb=" O   ARG A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 557
    Processing helix  chain 'A' and resid 559 through 581
      removed outlier: 4.509A  pdb=" N   ARG A 571 " --> pdb=" O   ALA A 567 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   LEU A 572 " --> pdb=" O   ASN A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 599
      removed outlier: 3.758A  pdb=" N   LYS A 596 " --> pdb=" O   ARG A 592 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   VAL A 597 " --> pdb=" O   PRO A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 615
    Processing helix  chain 'B' and resid 15 through 20
    Processing helix  chain 'B' and resid 33 through 47
      removed outlier: 3.641A  pdb=" N   ARG B  43 " --> pdb=" O   GLU B  39 " (cutoff:3.500A)
      Proline residue:  B  44  - end of helix
    Processing helix  chain 'B' and resid 53 through 58
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 80 through 94
    Processing helix  chain 'B' and resid 96 through 108
      removed outlier: 3.792A  pdb=" N   LYS B 101 " --> pdb=" O   PRO B  97 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LEU B 102 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 120
    Processing helix  chain 'B' and resid 134 through 151
    Processing helix  chain 'B' and resid 157 through 169
      removed outlier: 3.615A  pdb=" N   MET B 169 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 224
    Processing helix  chain 'B' and resid 247 through 266
      removed outlier: 4.494A  pdb=" N   GLY B 252 " --> pdb=" O   MET B 248 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   PHE B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 277
    Processing helix  chain 'B' and resid 278 through 287
      removed outlier: 3.782A  pdb=" N   ALA B 282 " --> pdb=" O   GLU B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 308
      removed outlier: 3.538A  pdb=" N   GLU B 307 " --> pdb=" O   LYS B 304 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   CYS B 308 " --> pdb=" O   PHE B 305 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 304 through 308'
    Processing helix  chain 'B' and resid 310 through 325
      removed outlier: 3.937A  pdb=" N   MET B 314 " --> pdb=" O   ASP B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 335
    Processing helix  chain 'B' and resid 336 through 343
      removed outlier: 3.554A  pdb=" N   PHE B 342 " --> pdb=" O   PRO B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 406
      removed outlier: 3.604A  pdb=" N   THR B 401 " --> pdb=" O   ASN B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 409
      No H-bonds generated for 'chain 'B' and resid 407 through 409'
    Processing helix  chain 'B' and resid 432 through 449
      removed outlier: 3.600A  pdb=" N   LYS B 448 " --> pdb=" O   ARG B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 514
      removed outlier: 3.598A  pdb=" N   ALA B 502 " --> pdb=" O   MET B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 537
      removed outlier: 3.547A  pdb=" N   TYR B 537 " --> pdb=" O   TYR B 533 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 552
      removed outlier: 3.707A  pdb=" N   GLU B 551 " --> pdb=" O   ARG B 547 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASN B 552 " --> pdb=" O   PHE B 548 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 558 through 562
    Processing helix  chain 'B' and resid 575 through 583
    Processing helix  chain 'B' and resid 588 through 595
    Processing helix  chain 'B' and resid 646 through 666
      removed outlier: 4.103A  pdb=" N   ASN B 650 " --> pdb=" O   LYS B 646 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LYS B 651 " --> pdb=" O   ALA B 647 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 667 through 671
    Processing helix  chain 'B' and resid 679 through 694
    Processing helix  chain 'B' and resid 698 through 709
    Processing helix  chain 'C' and resid 11 through 27
    Processing helix  chain 'C' and resid 27 through 32
    Processing helix  chain 'C' and resid 34 through 36
      No H-bonds generated for 'chain 'C' and resid 34 through 36'
    Processing helix  chain 'C' and resid 37 through 42
    Processing helix  chain 'C' and resid 54 through 56
      No H-bonds generated for 'chain 'C' and resid 54 through 56'
    Processing helix  chain 'C' and resid 57 through 62
      removed outlier: 3.660A  pdb=" N   ARG C  62 " --> pdb=" O   VAL C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 107
    Processing helix  chain 'C' and resid 115 through 123
      removed outlier: 4.195A  pdb=" N   LEU C 123 " --> pdb=" O   VAL C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 124 through 134
    Processing helix  chain 'C' and resid 166 through 176
    Processing helix  chain 'C' and resid 181 through 187
    Processing helix  chain 'C' and resid 191 through 207
      Proline residue:  C 202  - end of helix
      removed outlier: 3.620A  pdb=" N   LYS C 205 " --> pdb=" O   GLU C 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 221
    Processing helix  chain 'C' and resid 234 through 240
      removed outlier: 3.575A  pdb=" N   GLU C 239 " --> pdb=" O   PRO C 235 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   MET C 240 " --> pdb=" O   ARG C 236 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 415
      removed outlier: 3.619A  pdb=" N   GLY C 414 " --> pdb=" O   ILE C 410 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 417 through 421
      removed outlier: 3.957A  pdb=" N   GLY C 420 " --> pdb=" O   ILE C 417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 431 through 446
      removed outlier: 3.607A  pdb=" N   PHE C 435 " --> pdb=" O   GLY C 431 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   SER C 444 " --> pdb=" O   PHE C 440 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 447 through 455
      removed outlier: 3.555A  pdb=" N   LEU C 451 " --> pdb=" O   HIS C 447 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51
    Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59
      removed outlier: 3.524A  pdb=" N   LYS A  97 " --> pdb=" O   HIS A 115 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   PHE A 119 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211
      removed outlier: 3.681A  pdb=" N   GLY B 300 " --> pdb=" O   PHE B 424 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 242
      removed outlier: 6.823A  pdb=" N   VAL A 464 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242
      removed outlier: 6.761A  pdb=" N   ILE A 414 " --> pdb=" O   TRP A 426 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   MET A 428 " --> pdb=" O   CYS A 412 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   CYS A 412 " --> pdb=" O   MET A 428 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   LEU A 430 " --> pdb=" O   THR A 410 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   THR A 410 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323
    Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 531
    Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 126
      removed outlier: 3.537A  pdb=" N   SER B 126 " --> pdb=" O   ARG B 131 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ARG B 131 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 175
    Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 245
      removed outlier: 3.796A  pdb=" N   ASN B 227 " --> pdb=" O   THR B 245 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   LEU B 226 " --> pdb=" O   ASP B 348 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 467 through 470
    Processing sheet with id=AB3, first strand: chain 'C' and resid 142 through 143
    Processing sheet with id=AB4, first strand: chain 'C' and resid 151 through 154
    Processing sheet with id=AB5, first strand: chain 'C' and resid 348 through 354
      removed outlier: 3.510A  pdb=" N   LYS C 349 " --> pdb=" O   ILE C 361 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU C 353 " --> pdb=" O   VAL C 357 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   VAL C 357 " --> pdb=" O   LEU C 353 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 370 through 376
      removed outlier: 4.319A  pdb=" N   GLU C 392 " --> pdb=" O  ASER C 384 " (cutoff:3.500A)
      removed outlier: 8.331A  pdb=" N   THR C 482 " --> pdb=" O   ASP C 391 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   ILE C 393 " --> pdb=" O   THR C 482 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 456 through 457
      removed outlier: 3.520A  pdb=" N   LYS C 477 " --> pdb=" O   ASP C 457 " (cutoff:3.500A)

    582 hydrogen bonds defined for protein.
    1612 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.46

  Time building geometry restraints manager: 1.54 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4411
        1.34 -     1.46: 2420
        1.46 -     1.58: 7123
        1.58 -     1.70: 27
        1.70 -     1.82: 129
  Bond restraints: 14110
  Sorted by residual:
  bond pdb=" CB  PRO C 343 "
       pdb=" CG  PRO C 343 "
    ideal  model  delta    sigma   weight residual
    1.492  1.567 -0.075 5.00e-02 4.00e+02 2.23e+00
  bond pdb=" CB  LYS C 458 "
       pdb=" CG  LYS C 458 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.95e-01
  bond pdb=" C   GLU C 418 "
       pdb=" N   PRO C 419 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 7.90e-01
  bond pdb=" CA  ASN A 156 "
       pdb=" CB  ASN A 156 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 7.77e-01
  bond pdb=" CB  ASN C  80 "
       pdb=" CG  ASN C  80 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.48e-01
  ... (remaining 14105 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 18907
        2.04 -     4.08: 228
        4.08 -     6.13: 27
        6.13 -     8.17: 6
        8.17 -    10.21: 2
  Bond angle restraints: 19170
  Sorted by residual:
  angle pdb=" N   VAL C 230 "
        pdb=" CA  VAL C 230 "
        pdb=" C   VAL C 230 "
      ideal   model   delta    sigma   weight residual
     112.96  107.93    5.03 1.00e+00 1.00e+00 2.53e+01
  angle pdb=" C   ASN A 155 "
        pdb=" N   ASN A 156 "
        pdb=" CA  ASN A 156 "
      ideal   model   delta    sigma   weight residual
     121.54  127.88   -6.34 1.91e+00 2.74e-01 1.10e+01
  angle pdb=" CA  PRO C 343 "
        pdb=" N   PRO C 343 "
        pdb=" CD  PRO C 343 "
      ideal   model   delta    sigma   weight residual
     112.00  107.49    4.51 1.40e+00 5.10e-01 1.04e+01
  angle pdb=" N   GLU B 653 "
        pdb=" CA  GLU B 653 "
        pdb=" CB  GLU B 653 "
      ideal   model   delta    sigma   weight residual
     110.28  115.26   -4.98 1.55e+00 4.16e-01 1.03e+01
  angle pdb=" CA  LEU A 402 "
        pdb=" CB  LEU A 402 "
        pdb=" CG  LEU A 402 "
      ideal   model   delta    sigma   weight residual
     116.30  126.51  -10.21 3.50e+00 8.16e-02 8.51e+00
  ... (remaining 19165 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 7820
       17.95 -    35.90: 641
       35.90 -    53.85: 103
       53.85 -    71.80: 30
       71.80 -    89.75: 11
  Dihedral angle restraints: 8605
    sinusoidal: 3706
      harmonic: 4899
  Sorted by residual:
  dihedral pdb=" CA  GLU C 418 "
           pdb=" C   GLU C 418 "
           pdb=" N   PRO C 419 "
           pdb=" CA  PRO C 419 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.13  -17.87     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CB  GLU B 372 "
           pdb=" CG  GLU B 372 "
           pdb=" CD  GLU B 372 "
           pdb=" OE1 GLU B 372 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.75  -89.75     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU B 550 "
           pdb=" CG  GLU B 550 "
           pdb=" CD  GLU B 550 "
           pdb=" OE1 GLU B 550 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.89   88.89     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 8602 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1387
       0.032 -    0.064: 511
       0.064 -    0.095: 165
       0.095 -    0.127: 64
       0.127 -    0.159: 8
  Chirality restraints: 2135
  Sorted by residual:
  chirality pdb=" CB  ILE B 620 "
            pdb=" CA  ILE B 620 "
            pdb=" CG1 ILE B 620 "
            pdb=" CG2 ILE B 620 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.31e-01
  chirality pdb=" CA  ASN A 156 "
            pdb=" N   ASN A 156 "
            pdb=" C   ASN A 156 "
            pdb=" CB  ASN A 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.24e-01
  chirality pdb=" CA  GLU C 405 "
            pdb=" N   GLU C 405 "
            pdb=" C   GLU C 405 "
            pdb=" CB  GLU C 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.23e-01
  ... (remaining 2132 not shown)

  Planarity restraints: 2401
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C 342 "    0.046 5.00e-02 4.00e+02   6.71e-02 7.20e+00
        pdb=" N   PRO C 343 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO C 343 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C 343 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 234 "   -0.040 5.00e-02 4.00e+02   6.06e-02 5.87e+00
        pdb=" N   PRO C 235 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO C 235 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C 235 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B  96 "   -0.037 5.00e-02 4.00e+02   5.64e-02 5.09e+00
        pdb=" N   PRO B  97 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B  97 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B  97 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 2398 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1765
        2.75 -     3.29: 13745
        3.29 -     3.83: 23114
        3.83 -     4.36: 27698
        4.36 -     4.90: 47543
  Nonbonded interactions: 113865
  Sorted by model distance:
  nonbonded pdb=" O   SER A 482 "
            pdb=" O2'   A D   3 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OG1 THR B 295 "
            pdb=" O   PRO B 464 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" ND2 ASN A 558 "
            pdb=" O   PRO B  25 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" O   ILE C 122 "
            pdb=" NE2 GLN C 207 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" OG1 THR B 245 "
            pdb=" NH2 ARG B 251 "
     model   vdw
     2.268 3.120
  ... (remaining 113860 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.01 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.780
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
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      :  0.002   0.075  14110  Z= 0.106
  Angle     :  0.549  10.211  19170  Z= 0.280
  Chirality :  0.040   0.159   2135
  Planarity :  0.005   0.067   2401
  Dihedral  : 13.582  89.746   5423
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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: -0.26 (0.21), residues: 1653
  helix:  1.02 (0.20), residues: 721
  sheet: -0.55 (0.40), residues: 172
  loop : -1.25 (0.21), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 704 
 TYR   0.023   0.001   TYR B 176 
 PHE   0.029   0.001   PHE B 290 
 TRP   0.011   0.001   TRP B 220 
 HIS   0.007   0.001   HIS C 442 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.11 (14110)
  covalent geometry    : angle       0.54920 /  0.28 (19170)
  hydrogen bonds       : bond        0.18599 / 12.84 (  578)
  hydrogen bonds       : angle       6.39146 /  4.30 ( 1612)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 ASN cc_start: 0.8160 (t0) cc_final: 0.6862 (t0)
REVERT: A   83 ASP cc_start: 0.7768 (m-30) cc_final: 0.7518 (m-30)
REVERT: A  163 GLU cc_start: 0.8831 (tp30) cc_final: 0.8510 (tp30)
REVERT: A  447 ILE cc_start: 0.9270 (mm) cc_final: 0.9052 (mm)
REVERT: B  393 MET cc_start: 0.7460 (tpt) cc_final: 0.6911 (tpt)
REVERT: B  422 ASP cc_start: 0.7992 (p0) cc_final: 0.7783 (p0)
REVERT: B  653 GLU cc_start: 0.8184 (mp0) cc_final: 0.7647 (mp0)
REVERT: C  378 GLN cc_start: 0.8881 (mm110) cc_final: 0.8523 (mm110)
REVERT: C  405 GLU cc_start: 0.7240 (pp20) cc_final: 0.6954 (pp20)
REVERT: C  410 ILE cc_start: 0.8818 (mt) cc_final: 0.8552 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1263
  time to fit residues: 40.8724
Evaluate side-chains
  188 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.3980
   chunk 10 optimal weight:    0.0980
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    7.9990
   chunk 149 optimal weight:    8.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 129 HIS
B 336 ASN
B 453 ASN
** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.126719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.095991 restraints weight = 48189.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 3.72
r_work: 0.3012 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8870
moved from start:          0.0861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14110  Z= 0.126
  Angle     :  0.569   8.433  19170  Z= 0.290
  Chirality :  0.041   0.158   2135
  Planarity :  0.005   0.060   2401
  Dihedral  :  8.480  74.763   2033
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  6.81 %
    Favored  : 92.59 %
  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: -0.15 (0.21), residues: 1653
  helix:  1.17 (0.20), residues: 729
  sheet: -0.81 (0.38), residues: 180
  loop : -1.20 (0.21), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  93 
 TYR   0.023   0.001   TYR C 382 
 PHE   0.018   0.001   PHE C  41 
 TRP   0.010   0.001   TRP A 336 
 HIS   0.005   0.001   HIS C 442 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.13 (14110)
  covalent geometry    : angle       0.56895 /  0.29 (19170)
  hydrogen bonds       : bond        0.04476 /  3.13 (  578)
  hydrogen bonds       : angle       5.02153 /  3.43 ( 1612)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 208
  time to evaluate  : 0.568 
Fit side-chains
REVERT: A   47 ASN cc_start: 0.8586 (t0) cc_final: 0.8173 (t0)
REVERT: A   48 MET cc_start: 0.7960 (ppp) cc_final: 0.7759 (ppp)
REVERT: A  163 GLU cc_start: 0.8932 (tp30) cc_final: 0.8532 (tp30)
REVERT: A  621 TYR cc_start: 0.8426 (m-80) cc_final: 0.8019 (m-80)
REVERT: B  283 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8344 (tppt)
REVERT: B  393 MET cc_start: 0.7966 (tpt) cc_final: 0.7321 (tpt)
REVERT: B  409 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7674 (mm-30)
REVERT: B  653 GLU cc_start: 0.8542 (mp0) cc_final: 0.7997 (mp0)
REVERT: C  371 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8539 (ttmm)
REVERT: C  377 ASP cc_start: 0.8675 (t0) cc_final: 0.8200 (t0)
REVERT: C  378 GLN cc_start: 0.8861 (mm110) cc_final: 0.8494 (mm110)
REVERT: C  405 GLU cc_start: 0.7344 (pp20) cc_final: 0.7050 (pp20)
REVERT: C  410 ILE cc_start: 0.8881 (mt) cc_final: 0.8646 (mt)
  outliers start: 9
  outliers final: 9
  residues processed: 216
  average time/residue: 0.1257
  time to fit residues: 39.5880
Evaluate side-chains
  188 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 179
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  295 THR
Chi-restraints excluded: chain B residue  327 CYS
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain B residue  626 VAL
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  391 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 152 optimal weight:    9.9990
   chunk 120 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 158 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 129 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 161 optimal weight:    6.9990
   chunk 142 optimal weight:    0.0470
   chunk 156 optimal weight:   10.0000
   overall best weight:    2.1682

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.123731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.091783 restraints weight = 53791.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 3.93
r_work: 0.2940 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8932
moved from start:          0.1246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14110  Z= 0.163
  Angle     :  0.566   7.223  19170  Z= 0.287
  Chirality :  0.042   0.195   2135
  Planarity :  0.005   0.059   2401
  Dihedral  :  8.506  74.566   2033
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  8.48 %
    Favored  : 90.45 %
  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: -0.07 (0.21), residues: 1653
  helix:  1.32 (0.20), residues: 727
  sheet: -1.06 (0.37), residues: 170
  loop : -1.16 (0.21), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 704 
 TYR   0.029   0.002   TYR C 363 
 PHE   0.018   0.001   PHE C 374 
 TRP   0.011   0.001   TRP A 336 
 HIS   0.004   0.001   HIS C 442 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00381 /  0.16 (14110)
  covalent geometry    : angle       0.56564 /  0.29 (19170)
  hydrogen bonds       : bond        0.04054 /  2.81 (  578)
  hydrogen bonds       : angle       4.72310 /  3.25 ( 1612)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 198
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASN cc_start: 0.8620 (t0) cc_final: 0.7994 (t0)
REVERT: A  163 GLU cc_start: 0.8945 (tp30) cc_final: 0.8548 (tp30)
REVERT: A  267 LYS cc_start: 0.8948 (mppt) cc_final: 0.8665 (tmtt)
REVERT: A  451 MET cc_start: 0.9286 (mtt) cc_final: 0.8978 (mtt)
REVERT: B  393 MET cc_start: 0.8030 (tpt) cc_final: 0.7517 (tpt)
REVERT: B  422 ASP cc_start: 0.8459 (p0) cc_final: 0.8184 (p0)
REVERT: C  210 GLU cc_start: 0.7947 (mp0) cc_final: 0.7625 (mp0)
REVERT: C  371 LYS cc_start: 0.8811 (mtpp) cc_final: 0.8562 (ttmm)
REVERT: C  377 ASP cc_start: 0.8649 (t0) cc_final: 0.8180 (t0)
REVERT: C  378 GLN cc_start: 0.8844 (mm110) cc_final: 0.8463 (mm110)
REVERT: C  410 ILE cc_start: 0.8906 (mt) cc_final: 0.8698 (mt)
  outliers start: 16
  outliers final: 10
  residues processed: 209
  average time/residue: 0.1279
  time to fit residues: 38.1630
Evaluate side-chains
  199 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 189
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  295 THR
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain B residue  626 VAL
Chi-restraints excluded: chain B residue  670 LEU
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  391 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 157 optimal weight:   20.0000
   chunk 97 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 87 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 115 optimal weight:    1.9990
   chunk 112 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    1.7386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 429 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.122481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.091058 restraints weight = 48028.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 3.69
r_work: 0.2953 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8930
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  14110  Z= 0.141
  Angle     :  0.558   9.249  19170  Z= 0.280
  Chirality :  0.041   0.160   2135
  Planarity :  0.004   0.058   2401
  Dihedral  :  8.487  74.757   2033
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  9.81 %
    Favored  : 88.92 %
  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: -0.02 (0.21), residues: 1653
  helix:  1.38 (0.20), residues: 728
  sheet: -1.12 (0.36), residues: 171
  loop : -1.14 (0.21), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 198 
 TYR   0.023   0.001   TYR C 363 
 PHE   0.018   0.001   PHE C 374 
 TRP   0.011   0.001   TRP A 336 
 HIS   0.005   0.001   HIS A  51 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.14 (14110)
  covalent geometry    : angle       0.55801 /  0.28 (19170)
  hydrogen bonds       : bond        0.03664 /  2.53 (  578)
  hydrogen bonds       : angle       4.54989 /  3.15 ( 1612)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 189
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.8186 (m-30) cc_final: 0.7983 (m-30)
REVERT: A  163 GLU cc_start: 0.8920 (tp30) cc_final: 0.8516 (tp30)
REVERT: A  451 MET cc_start: 0.9221 (mtt) cc_final: 0.8929 (mtt)
REVERT: B  393 MET cc_start: 0.8024 (tpt) cc_final: 0.7379 (tpt)
REVERT: B  422 ASP cc_start: 0.8473 (p0) cc_final: 0.8206 (p0)
REVERT: B  682 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8185 (tp30)
REVERT: C  410 ILE cc_start: 0.8894 (mt) cc_final: 0.8681 (mt)
REVERT: C  423 GLN cc_start: 0.7921 (tp40) cc_final: 0.7628 (tp-100)
  outliers start: 19
  outliers final: 10
  residues processed: 199
  average time/residue: 0.1177
  time to fit residues: 33.8216
Evaluate side-chains
  192 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 182
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  475 HIS
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain B residue  626 VAL
Chi-restraints excluded: chain B residue  653 GLU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  391 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 102 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 82 optimal weight:    6.9990
   chunk 139 optimal weight:    0.7980
   chunk 2 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   chunk 90 optimal weight:    3.9990
   chunk 111 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    2.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 132 ASN
B 433 HIS
** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.120271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.088963 restraints weight = 48473.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 3.82
r_work: 0.2906 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8973
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  14110  Z= 0.191
  Angle     :  0.584   7.717  19170  Z= 0.295
  Chirality :  0.043   0.282   2135
  Planarity :  0.004   0.057   2401
  Dihedral  :  8.544  74.653   2033
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.68 %
    Favored  : 88.12 %
  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: -0.04 (0.21), residues: 1653
  helix:  1.31 (0.20), residues: 735
  sheet: -1.19 (0.36), residues: 173
  loop : -1.10 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 704 
 TYR   0.021   0.001   TYR C 363 
 PHE   0.020   0.001   PHE C 374 
 TRP   0.012   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 582 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00452 /  0.19 (14110)
  covalent geometry    : angle       0.58399 /  0.29 (19170)
  hydrogen bonds       : bond        0.03818 /  2.63 (  578)
  hydrogen bonds       : angle       4.53418 /  3.16 ( 1612)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 187
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 ASN cc_start: 0.8664 (t0) cc_final: 0.8233 (t0)
REVERT: A   48 MET cc_start: 0.7838 (ppp) cc_final: 0.7443 (ppp)
REVERT: A  163 GLU cc_start: 0.8944 (tp30) cc_final: 0.8522 (tp30)
REVERT: A  451 MET cc_start: 0.9256 (mtt) cc_final: 0.9013 (mtt)
REVERT: B  283 LYS cc_start: 0.8621 (mtpt) cc_final: 0.8391 (tppt)
REVERT: B  393 MET cc_start: 0.8029 (tpt) cc_final: 0.7351 (tpt)
REVERT: B  422 ASP cc_start: 0.8581 (p0) cc_final: 0.8344 (p0)
REVERT: B  682 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8204 (tp30)
REVERT: C  210 GLU cc_start: 0.7932 (mp0) cc_final: 0.7500 (mp0)
REVERT: C  371 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8421 (ttmm)
REVERT: C  410 ILE cc_start: 0.8877 (mt) cc_final: 0.8670 (mt)
  outliers start: 18
  outliers final: 13
  residues processed: 196
  average time/residue: 0.1037
  time to fit residues: 29.4963
Evaluate side-chains
  193 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 180
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  295 THR
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  475 HIS
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain B residue  626 VAL
Chi-restraints excluded: chain B residue  653 GLU
Chi-restraints excluded: chain C residue   31 MET
Chi-restraints excluded: chain C residue  348 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 31 optimal weight:   20.0000
   chunk 65 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 158 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 103 optimal weight:    0.7980
   chunk 9 optimal weight:    7.9990
   chunk 100 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.1586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.122532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.092568 restraints weight = 50652.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 3.62
r_work: 0.2942 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2950
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2950 r_free = 0.2950    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2950 r_free = 0.2950    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2950
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8940
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14110  Z= 0.117
  Angle     :  0.537   7.220  19170  Z= 0.271
  Chirality :  0.040   0.158   2135
  Planarity :  0.004   0.058   2401
  Dihedral  :  8.466  75.018   2033
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.88 %
    Favored  : 87.58 %
  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:  0.05 (0.21), residues: 1653
  helix:  1.40 (0.20), residues: 735
  sheet: -1.03 (0.36), residues: 172
  loop : -1.10 (0.22), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 704 
 TYR   0.022   0.001   TYR C 382 
 PHE   0.018   0.001   PHE C  41 
 TRP   0.011   0.001   TRP A 336 
 HIS   0.006   0.001   HIS A 115 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.12 (14110)
  covalent geometry    : angle       0.53663 /  0.27 (19170)
  hydrogen bonds       : bond        0.03404 /  2.35 (  578)
  hydrogen bonds       : angle       4.37078 /  3.04 ( 1612)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 189
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 ASN cc_start: 0.8681 (t0) cc_final: 0.8296 (t0)
REVERT: A   48 MET cc_start: 0.7853 (ppp) cc_final: 0.7597 (ppp)
REVERT: A  163 GLU cc_start: 0.8917 (tp30) cc_final: 0.8490 (tp30)
REVERT: A  451 MET cc_start: 0.9212 (mtt) cc_final: 0.8953 (mtt)
REVERT: B  422 ASP cc_start: 0.8544 (p0) cc_final: 0.8322 (p0)
REVERT: B  499 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7698 (m)
REVERT: B  503 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8194 (mpp)
REVERT: B  682 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8164 (tp30)
REVERT: C  371 LYS cc_start: 0.8998 (ttmm) cc_final: 0.8463 (ttmm)
REVERT: C  410 ILE cc_start: 0.8899 (mt) cc_final: 0.8679 (mt)
REVERT: C  423 GLN cc_start: 0.7866 (tp40) cc_final: 0.7601 (tp-100)
  outliers start: 23
  outliers final: 17
  residues processed: 200
  average time/residue: 0.1117
  time to fit residues: 32.3974
Evaluate side-chains
  202 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 183
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  475 HIS
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  503 MET
Chi-restraints excluded: chain B residue  626 VAL
Chi-restraints excluded: chain B residue  653 GLU
Chi-restraints excluded: chain C residue   31 MET
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  391 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 125 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 127 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 138 optimal weight:    7.9990
   chunk 40 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 130 optimal weight:    0.1980
   chunk 101 optimal weight:    4.9990
   overall best weight:    2.8388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 358 ASN
** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.120457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.089356 restraints weight = 39629.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 3.34
r_work: 0.2914 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8973
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14110  Z= 0.198
  Angle     :  0.588  10.208  19170  Z= 0.295
  Chirality :  0.043   0.183   2135
  Planarity :  0.004   0.057   2401
  Dihedral  :  8.545  74.732   2033
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 11.01 %
    Favored  : 87.12 %
  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:  0.04 (0.21), residues: 1653
  helix:  1.38 (0.20), residues: 735
  sheet: -1.08 (0.36), residues: 173
  loop : -1.08 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 704 
 TYR   0.020   0.001   TYR C 382 
 PHE   0.018   0.001   PHE C  41 
 TRP   0.012   0.001   TRP A 336 
 HIS   0.005   0.001   HIS A 115 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00473 /  0.20 (14110)
  covalent geometry    : angle       0.58816 /  0.30 (19170)
  hydrogen bonds       : bond        0.03770 /  2.59 (  578)
  hydrogen bonds       : angle       4.45129 /  3.10 ( 1612)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 183
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 ASN cc_start: 0.8715 (t0) cc_final: 0.8238 (t0)
REVERT: A   48 MET cc_start: 0.7859 (ppp) cc_final: 0.7651 (ppp)
REVERT: A   82 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7196 (pmt-80)
REVERT: A  163 GLU cc_start: 0.8936 (tp30) cc_final: 0.8499 (tp30)
REVERT: B  140 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8162 (tm-30)
REVERT: B  283 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8405 (tppt)
REVERT: B  393 MET cc_start: 0.7878 (tpt) cc_final: 0.7636 (tpt)
REVERT: B  422 ASP cc_start: 0.8657 (p0) cc_final: 0.8447 (p0)
REVERT: B  499 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8110 (p)
REVERT: B  503 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8542 (mpp)
REVERT: B  682 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8153 (tp30)
REVERT: C  410 ILE cc_start: 0.8894 (mt) cc_final: 0.8681 (mt)
  outliers start: 28
  outliers final: 19
  residues processed: 199
  average time/residue: 0.1286
  time to fit residues: 36.9804
Evaluate side-chains
  202 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 180
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   82 ARG
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  472 SER
Chi-restraints excluded: chain B residue  475 HIS
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  503 MET
Chi-restraints excluded: chain B residue  531 HIS
Chi-restraints excluded: chain B residue  626 VAL
Chi-restraints excluded: chain B residue  653 GLU
Chi-restraints excluded: chain B residue  670 LEU
Chi-restraints excluded: chain C residue   31 MET
Chi-restraints excluded: chain C residue  391 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 114 optimal weight:    9.9990
   chunk 93 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 108 optimal weight:    9.9990
   chunk 154 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   chunk 141 optimal weight:    2.9990
   chunk 162 optimal weight:    6.9990
   overall best weight:    1.5188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 429 ASN
B 567 HIS
** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.121881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.090079 restraints weight = 53036.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 4.07
r_work: 0.2900 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2907
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2907
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8964
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14110  Z= 0.130
  Angle     :  0.550   9.787  19170  Z= 0.276
  Chirality :  0.041   0.161   2135
  Planarity :  0.004   0.058   2401
  Dihedral  :  8.479  74.991   2033
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.02 %
    Favored  : 86.58 %
  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:  0.08 (0.21), residues: 1653
  helix:  1.43 (0.20), residues: 735
  sheet: -1.04 (0.36), residues: 173
  loop : -1.07 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 704 
 TYR   0.019   0.001   TYR C 363 
 PHE   0.018   0.001   PHE C  41 
 TRP   0.012   0.001   TRP A 336 
 HIS   0.004   0.001   HIS A 115 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.13 (14110)
  covalent geometry    : angle       0.54999 /  0.28 (19170)
  hydrogen bonds       : bond        0.03449 /  2.38 (  578)
  hydrogen bonds       : angle       4.34772 /  3.02 ( 1612)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 184
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 ASN cc_start: 0.8758 (t0) cc_final: 0.8285 (t0)
REVERT: A   48 MET cc_start: 0.7932 (ppp) cc_final: 0.7721 (ppp)
REVERT: A  163 GLU cc_start: 0.9005 (tp30) cc_final: 0.8591 (tp30)
REVERT: A  451 MET cc_start: 0.9175 (mtt) cc_final: 0.8910 (mtt)
REVERT: B  140 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8209 (tm-30)
REVERT: B  393 MET cc_start: 0.7841 (tpt) cc_final: 0.7602 (tpt)
REVERT: B  422 ASP cc_start: 0.8720 (p0) cc_final: 0.8469 (p0)
REVERT: B  499 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.7850 (m)
REVERT: B  503 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8239 (mpp)
REVERT: B  682 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8154 (tp30)
REVERT: C  364 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.8153 (mtm-85)
REVERT: C  410 ILE cc_start: 0.8847 (mt) cc_final: 0.8635 (mt)
REVERT: C  423 GLN cc_start: 0.7861 (tp40) cc_final: 0.7647 (tp-100)
REVERT: C  472 GLU cc_start: 0.8579 (pt0) cc_final: 0.8353 (pp20)
  outliers start: 21
  outliers final: 18
  residues processed: 196
  average time/residue: 0.1102
  time to fit residues: 31.9424
Evaluate side-chains
  202 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 182
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  475 HIS
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  503 MET
Chi-restraints excluded: chain B residue  531 HIS
Chi-restraints excluded: chain B residue  626 VAL
Chi-restraints excluded: chain B residue  653 GLU
Chi-restraints excluded: chain C residue   31 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 118 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 35 optimal weight:   10.0000
   chunk 160 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0070
   chunk 78 optimal weight:    0.5980
   chunk 131 optimal weight:    1.9990
   chunk 146 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.8802

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 429 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.120825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.090149 restraints weight = 37999.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 3.29
r_work: 0.2947 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2949
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2949 r_free = 0.2949    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2949 r_free = 0.2949    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2949
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8923
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14110  Z= 0.110
  Angle     :  0.546   9.554  19170  Z= 0.272
  Chirality :  0.040   0.162   2135
  Planarity :  0.004   0.058   2401
  Dihedral  :  8.368  75.256   2033
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.55 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.21), residues: 1653
  helix:  1.48 (0.20), residues: 735
  sheet: -0.92 (0.36), residues: 172
  loop : -1.03 (0.22), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 704 
 TYR   0.017   0.001   TYR C 412 
 PHE   0.021   0.001   PHE B 290 
 TRP   0.012   0.001   TRP A 336 
 HIS   0.004   0.001   HIS A 115 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.11 (14110)
  covalent geometry    : angle       0.54582 /  0.27 (19170)
  hydrogen bonds       : bond        0.03252 /  2.27 (  578)
  hydrogen bonds       : angle       4.25649 /  2.96 ( 1612)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 184
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 ASN cc_start: 0.8713 (t0) cc_final: 0.8220 (t0)
REVERT: A   48 MET cc_start: 0.7930 (ppp) cc_final: 0.7677 (ppp)
REVERT: A  163 GLU cc_start: 0.8917 (tp30) cc_final: 0.8518 (tp30)
REVERT: A  451 MET cc_start: 0.9137 (mtt) cc_final: 0.8835 (mtt)
REVERT: B  140 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8125 (tm-30)
REVERT: B  283 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8365 (tppt)
REVERT: B  393 MET cc_start: 0.7809 (tpt) cc_final: 0.7608 (tpt)
REVERT: B  422 ASP cc_start: 0.8641 (p0) cc_final: 0.8360 (p0)
REVERT: B  503 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8468 (mpp)
REVERT: B  551 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8670 (pm20)
REVERT: B  682 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8104 (tp30)
REVERT: C  410 ILE cc_start: 0.8901 (mt) cc_final: 0.8690 (mt)
REVERT: C  423 GLN cc_start: 0.7818 (tp40) cc_final: 0.7606 (tp-100)
  outliers start: 19
  outliers final: 17
  residues processed: 197
  average time/residue: 0.1100
  time to fit residues: 32.1470
Evaluate side-chains
  195 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 176
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  475 HIS
Chi-restraints excluded: chain B residue  503 MET
Chi-restraints excluded: chain B residue  531 HIS
Chi-restraints excluded: chain B residue  551 GLU
Chi-restraints excluded: chain B residue  626 VAL
Chi-restraints excluded: chain B residue  653 GLU
Chi-restraints excluded: chain C residue   31 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0270
   chunk 142 optimal weight:    0.0070
   chunk 5 optimal weight:    0.6980
   chunk 51 optimal weight:   10.0000
   chunk 137 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 127 optimal weight:   10.0000
   overall best weight:    1.3460

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 173 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.120467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.088057 restraints weight = 61256.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 4.20
r_work: 0.2882 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2888
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8956
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14110  Z= 0.125
  Angle     :  0.554   9.475  19170  Z= 0.277
  Chirality :  0.041   0.167   2135
  Planarity :  0.004   0.058   2401
  Dihedral  :  8.354  75.255   2033
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 12.48 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.21), residues: 1653
  helix:  1.48 (0.20), residues: 736
  sheet: -0.92 (0.36), residues: 173
  loop : -1.04 (0.22), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 687 
 TYR   0.053   0.001   TYR C 179 
 PHE   0.018   0.001   PHE C  41 
 TRP   0.011   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 582 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.12 (14110)
  covalent geometry    : angle       0.55368 /  0.28 (19170)
  hydrogen bonds       : bond        0.03275 /  2.27 (  578)
  hydrogen bonds       : angle       4.25213 /  2.96 ( 1612)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 177
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 ASN cc_start: 0.8749 (t0) cc_final: 0.8238 (t0)
REVERT: A   48 MET cc_start: 0.7957 (ppp) cc_final: 0.7704 (ppp)
REVERT: A  163 GLU cc_start: 0.8976 (tp30) cc_final: 0.8574 (tp30)
REVERT: A  451 MET cc_start: 0.9124 (mtt) cc_final: 0.8831 (mtt)
REVERT: B  140 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8277 (tm-30)
REVERT: B  422 ASP cc_start: 0.8746 (p0) cc_final: 0.8469 (p0)
REVERT: B  499 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8091 (p)
REVERT: B  503 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8594 (mpp)
REVERT: B  551 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8660 (pm20)
REVERT: B  682 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8166 (tp30)
REVERT: C  410 ILE cc_start: 0.8909 (mt) cc_final: 0.8699 (mt)
REVERT: C  423 GLN cc_start: 0.7875 (tp40) cc_final: 0.7674 (tp-100)
REVERT: C  472 GLU cc_start: 0.8547 (pp20) cc_final: 0.8208 (pp20)
  outliers start: 20
  outliers final: 16
  residues processed: 191
  average time/residue: 0.1125
  time to fit residues: 32.0260
Evaluate side-chains
  196 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 177
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  475 HIS
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  503 MET
Chi-restraints excluded: chain B residue  531 HIS
Chi-restraints excluded: chain B residue  551 GLU
Chi-restraints excluded: chain B residue  626 VAL
Chi-restraints excluded: chain B residue  653 GLU
Chi-restraints excluded: chain C residue   31 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 161 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 45 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   overall best weight:    1.5584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.120248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.089251 restraints weight = 39866.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 3.39
r_work: 0.2921 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2931
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2931
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8936
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14110  Z= 0.132
  Angle     :  0.558   9.361  19170  Z= 0.279
  Chirality :  0.041   0.165   2135
  Planarity :  0.004   0.058   2401
  Dihedral  :  8.361  75.284   2033
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 13.02 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.15 (0.21), residues: 1653
  helix:  1.46 (0.20), residues: 736
  sheet: -0.91 (0.36), residues: 173
  loop : -1.04 (0.22), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 704 
 TYR   0.019   0.001   TYR C 412 
 PHE   0.018   0.001   PHE C  41 
 TRP   0.011   0.001   TRP A 336 
 HIS   0.004   0.001   HIS A 115 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.13 (14110)
  covalent geometry    : angle       0.55773 /  0.28 (19170)
  hydrogen bonds       : bond        0.03308 /  2.29 (  578)
  hydrogen bonds       : angle       4.25856 /  2.96 ( 1612)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2861.60 seconds
wall clock time: 50 minutes 11.20 seconds (3011.20 seconds total)