Starting phenix.real_space_refine
on Tue Mar  3 22:22:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dx4_30895/03_2026/7dx4_30895_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dx4_30895/03_2026/7dx4_30895.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dx4_30895/03_2026/7dx4_30895.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dx4_30895/03_2026/7dx4_30895.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dx4_30895/03_2026/7dx4_30895_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dx4_30895/03_2026/7dx4_30895_neut.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 805 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: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    5241      2.51       5
     N    1364      2.21       5
     O    1586      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8234
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4877
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
      Conformer: "B"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
          bond proxies already assigned to first conformer: 4998
    Chain: "E"
      Number of atoms: 1542
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
      Conformer: "B"
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
          bond proxies already assigned to first conformer: 1572
    Chain: "H"
      Number of atoms: 939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 939
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
    Chain: "L"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 806
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 7, 'TRANS': 104}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "E"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.92, per 1000 atoms: 0.35
  Number of scatterers: 8234
  At special positions: 0
  Unit cell: (144.56, 91.52, 78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      43     16.00
     O    1586      8.00
     N    1364      7.00
     C    5241      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H  97 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 546 "
      " NAG A 702 " - " ASN A  90 "
      " NAG A 703 " - " ASN A 322 "
      " NAG A 704 " - " ASN A  53 "
      " NAG E 601 " - " ASN E 343 "
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 384.4 milliseconds
  

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1902

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 12 sheets defined
      43.9% alpha, 12.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.988A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   SER A  47 " --> pdb=" O   SER A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.534A  pdb=" N   GLN A  60 " --> pdb=" O   GLU A  56 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LYS A  74 " --> pdb=" O   SER A  70 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   THR A  78 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.631A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
      removed outlier: 4.132A  pdb=" N   GLN A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.936A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.510A  pdb=" N   ARG A 115 " --> pdb=" O   ASP A 111 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   THR A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 157 through 171
      removed outlier: 3.613A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   TRP A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 193
      removed outlier: 3.572A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ARG A 177 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.627A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 204
    Processing helix  chain 'A' and resid 205 through 207
      No H-bonds generated for 'chain 'A' and resid 205 through 207'
    Processing helix  chain 'A' and resid 220 through 231
      removed outlier: 3.715A  pdb=" N   HIS A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   PHE A 230 " --> pdb=" O   VAL A 226 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLU A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 252
      removed outlier: 3.817A  pdb=" N   HIS A 239 " --> pdb=" O   PRO A 235 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ASN A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.558A  pdb=" N   PHE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.917A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ASN A 330 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 385
      removed outlier: 3.709A  pdb=" N   ALA A 372 " --> pdb=" O   ASP A 368 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   MET A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA A 384 " --> pdb=" O   GLN A 380 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 400 through 411
      removed outlier: 3.859A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 446
      removed outlier: 3.966A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS A 441 " --> pdb=" O   ASN A 437 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 465
      removed outlier: 4.392A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LYS A 465 " --> pdb=" O   TRP A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.664A  pdb=" N   TRP A 478 " --> pdb=" O   MET A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 515
    Processing helix  chain 'A' and resid 516 through 531
      removed outlier: 3.760A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.800A  pdb=" N   LEU A 554 " --> pdb=" O   ALA A 550 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.682A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
      removed outlier: 3.645A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS A 596 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ASP A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'E' and resid 338 through 343
    Processing helix  chain 'E' and resid 365 through 370
      removed outlier: 3.606A  pdb=" N   TYR E 369 " --> pdb=" O   TYR E 365 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASN E 370 " --> pdb=" O   SER E 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 365 through 370'
    Processing helix  chain 'E' and resid 385 through 390
      removed outlier: 3.554A  pdb=" N   ASN E 388 " --> pdb=" O   THR E 385 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU E 390 " --> pdb=" O   LEU E 387 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 404 through 408
      removed outlier: 3.788A  pdb=" N   ARG E 408 " --> pdb=" O   ASP E 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 438 through 443
    Processing helix  chain 'E' and resid 502 through 506
      removed outlier: 3.653A  pdb=" N   GLN E 506 " --> pdb=" O   VAL E 503 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 81 through 85
      removed outlier: 3.760A  pdb=" N   GLU L  85 " --> pdb=" O   ALA L  82 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.635A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358
      removed outlier: 3.817A  pdb=" N   ASN E 394 " --> pdb=" O   GLU E 516 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE E 402 " --> pdb=" O   TYR E 508 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   CYS E 432 " --> pdb=" O   LEU E 513 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 361 through 362
      removed outlier: 6.917A  pdb=" N   CYS E 361 " --> pdb=" O   CYS E 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474
    Processing sheet with id=AA8, first strand: chain 'H' and resid 6 through 7
      removed outlier: 4.157A  pdb=" N   VAL H  21 " --> pdb=" O   MET H  82 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR H  79 " --> pdb=" O   ASP H  74 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 13
      removed outlier: 3.568A  pdb=" N   VAL H  38 " --> pdb=" O   TYR H  96 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ILE H  35 " --> pdb=" O   GLY H  51 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   GLY H  51 " --> pdb=" O   ILE H  35 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   TRP H  37 " --> pdb=" O   MET H  49 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12
    Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12
      removed outlier: 3.794A  pdb=" N   GLY L  99 " --> pdb=" O   ASP L  94 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 17 through 21
      removed outlier: 3.612A  pdb=" N   SER L  74 " --> pdb=" O   SER L  67 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    866 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.24

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2374
        1.33 -     1.45: 1789
        1.45 -     1.58: 4226
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 8455
  Sorted by residual:
  bond pdb=" C   GLY A 319 "
       pdb=" N   LEU A 320 "
    ideal  model  delta    sigma   weight residual
    1.330  1.362 -0.032 1.37e-02 5.33e+03 5.36e+00
  bond pdb=" C1  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.64e+00
  bond pdb=" C1  NAG A 703 "
       pdb=" O5  NAG A 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.36e+00
  bond pdb=" CB  MET A 579 "
       pdb=" CG  MET A 579 "
    ideal  model  delta    sigma   weight residual
    1.520  1.467  0.053 3.00e-02 1.11e+03 3.13e+00
  bond pdb=" C1  NAG A 704 "
       pdb=" O5  NAG A 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.13e+00
  ... (remaining 8450 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 11077
        2.29 -     4.57: 355
        4.57 -     6.86: 40
        6.86 -     9.15: 15
        9.15 -    11.43: 4
  Bond angle restraints: 11491
  Sorted by residual:
  angle pdb=" N   ASP H 113 "
        pdb=" CA  ASP H 113 "
        pdb=" C   ASP H 113 "
      ideal   model   delta    sigma   weight residual
     114.16  102.73   11.43 1.48e+00 4.57e-01 5.97e+01
  angle pdb=" C   PHE H 112 "
        pdb=" N   ASP H 113 "
        pdb=" CA  ASP H 113 "
      ideal   model   delta    sigma   weight residual
     120.70  131.47  -10.77 1.63e+00 3.76e-01 4.36e+01
  angle pdb=" N   ASN E 440 "
        pdb=" CA  ASN E 440 "
        pdb=" CB  ASN E 440 "
      ideal   model   delta    sigma   weight residual
     110.13  102.65    7.48 1.48e+00 4.57e-01 2.56e+01
  angle pdb=" C   GLY L  52 "
        pdb=" N   ASN L  53 "
        pdb=" CA  ASN L  53 "
      ideal   model   delta    sigma   weight residual
     121.54  130.87   -9.33 1.91e+00 2.74e-01 2.39e+01
  angle pdb=" C   ILE L  50 "
        pdb=" N   TYR L  51 "
        pdb=" CA  TYR L  51 "
      ideal   model   delta    sigma   weight residual
     120.94  128.52   -7.58 1.57e+00 4.06e-01 2.33e+01
  ... (remaining 11486 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.43: 4892
       20.43 -    40.85: 119
       40.85 -    61.28: 23
       61.28 -    81.71: 4
       81.71 -   102.13: 8
  Dihedral angle restraints: 5046
    sinusoidal: 2058
      harmonic: 2988
  Sorted by residual:
  dihedral pdb=" CA  PHE H 112 "
           pdb=" C   PHE H 112 "
           pdb=" N   ASP H 113 "
           pdb=" CA  ASP H 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  127.40   52.60     0      5.00e+00 4.00e-02 1.11e+02
  dihedral pdb=" CA  LEU L  48 "
           pdb=" C   LEU L  48 "
           pdb=" N   LEU L  49 "
           pdb=" CA  LEU L  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.43   29.57     0      5.00e+00 4.00e-02 3.50e+01
  dihedral pdb=" CA  ALA H 108 "
           pdb=" C   ALA H 108 "
           pdb=" N   ALA H 109 "
           pdb=" CA  ALA H 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.19  -27.81     0      5.00e+00 4.00e-02 3.09e+01
  ... (remaining 5043 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1030
       0.073 -    0.145: 173
       0.145 -    0.218: 16
       0.218 -    0.291: 4
       0.291 -    0.363: 2
  Chirality restraints: 1225
  Sorted by residual:
  chirality pdb=" CG  LEU A 558 "
            pdb=" CB  LEU A 558 "
            pdb=" CD1 LEU A 558 "
            pdb=" CD2 LEU A 558 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.23   -0.36 2.00e-01 2.50e+01 3.30e+00
  chirality pdb=" CB  ILE H  35 "
            pdb=" CA  ILE H  35 "
            pdb=" CG1 ILE H  35 "
            pdb=" CG2 ILE H  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.41e+00
  chirality pdb=" CG  LEU A 333 "
            pdb=" CB  LEU A 333 "
            pdb=" CD1 LEU A 333 "
            pdb=" CD2 LEU A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.68e+00
  ... (remaining 1222 not shown)

  Planarity restraints: 1489
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN E 440 "    0.018 2.00e-02 2.50e+03   3.70e-02 1.37e+01
        pdb=" CG  ASN E 440 "   -0.064 2.00e-02 2.50e+03
        pdb=" OD1 ASN E 440 "    0.024 2.00e-02 2.50e+03
        pdb=" ND2 ASN E 440 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 497 "    0.019 2.00e-02 2.50e+03   2.14e-02 8.02e+00
        pdb=" CG  PHE E 497 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 497 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 497 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 497 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 497 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 497 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 582 "    0.046 5.00e-02 4.00e+02   6.88e-02 7.57e+00
        pdb=" N   PRO A 583 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 583 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 583 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1486 not shown)

  Histogram of nonbonded interaction distances:
        0.77 -     1.59: 5
        1.59 -     2.42: 43
        2.42 -     3.25: 8163
        3.25 -     4.07: 21544
        4.07 -     4.90: 39724
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 69479
  Sorted by model distance:
  nonbonded pdb=" C   LEU H   4 "
            pdb=" OG  SER H  26 "
     model   vdw
     0.766 3.270
  nonbonded pdb=" N   LEU H   5 "
            pdb=" OG  SER H  26 "
     model   vdw
     0.943 3.120
  nonbonded pdb=" CA  LEU H   5 "
            pdb=" CB  SER H  26 "
     model   vdw
     1.145 3.870
  nonbonded pdb=" O   LEU H   4 "
            pdb=" OG  SER H  26 "
     model   vdw
     1.387 3.040
  nonbonded pdb=" O   THR H  29 "
            pdb=" NH2 ARG H  99 "
     model   vdw
     1.521 3.120
  ... (remaining 69474 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.610
  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:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.740
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
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      :  0.007   0.062   8469  Z= 0.302
  Angle     :  1.008  11.433  11524  Z= 0.576
  Chirality :  0.057   0.363   1225
  Planarity :  0.007   0.069   1484
  Dihedral  : 11.251 102.133   3117
  Min Nonbonded Distance : 0.766

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.99 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.25 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -4.20 (0.21), residues: 1021
  helix: -3.94 (0.14), residues: 368
  sheet: -2.19 (0.43), residues: 137
  loop : -1.95 (0.24), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.002   ARG A 169 
 TYR   0.037   0.004   TYR E 495 
 PHE   0.049   0.004   PHE E 497 
 TRP   0.034   0.004   TRP A 302 
 HIS   0.014   0.002   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00673 ( 8455)
  covalent geometry    : angle       1.00210 (11491)
  SS BOND              : bond        0.00430 (    9)
  SS BOND              : angle       1.18801 (   18)
  hydrogen bonds       : bond        0.28797 (  316)
  hydrogen bonds       : angle      10.43201 (  866)
  link_NAG-ASN         : bond        0.00538 (    5)
  link_NAG-ASN         : angle       2.99324 (   15)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 TYR cc_start: 0.7745 (m-80) cc_final: 0.7152 (m-10)
REVERT: E  385 THR cc_start: 0.8294 (p) cc_final: 0.8025 (t)
REVERT: E  444 LYS cc_start: 0.8917 (pttt) cc_final: 0.8090 (mttm)
REVERT: E  470 THR cc_start: 0.8507 (p) cc_final: 0.8271 (p)
REVERT: H   48 TRP cc_start: 0.8687 (t60) cc_final: 0.8090 (t60)
REVERT: L  108 LEU cc_start: 0.8540 (tt) cc_final: 0.7894 (tp)
REVERT: L  109 THR cc_start: 0.8894 (p) cc_final: 0.8677 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.0951
  time to fit residues: 28.9738
Evaluate side-chains
  129 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 194 ASN
A 239 HIS
A 305 GLN
A 540 HIS
A 599 ASN
E 501 ASN
H  40 GLN
** L  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.120183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.097412 restraints weight = 38552.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.103367 restraints weight = 15072.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.107018 restraints weight = 6600.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.107688 restraints weight = 4366.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.108762 restraints weight = 3563.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3811
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3811 r_free = 0.3811    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3809 r_free = 0.3809    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3809
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8469  Z= 0.165
  Angle     :  0.720   8.827  11524  Z= 0.378
  Chirality :  0.046   0.189   1225
  Planarity :  0.006   0.060   1484
  Dihedral  :  8.292  62.648   1226
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  7.83 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.24), residues: 1021
  helix: -2.12 (0.21), residues: 392
  sheet: -1.57 (0.42), residues: 142
  loop : -1.18 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  99 
 TYR   0.024   0.002   TYR E 495 
 PHE   0.031   0.002   PHE E 497 
 TRP   0.032   0.002   TRP A 302 
 HIS   0.003   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 8455)
  covalent geometry    : angle       0.71421 (11491)
  SS BOND              : bond        0.00894 (    9)
  SS BOND              : angle       1.63812 (   18)
  hydrogen bonds       : bond        0.04557 (  316)
  hydrogen bonds       : angle       5.84659 (  866)
  link_NAG-ASN         : bond        0.00189 (    5)
  link_NAG-ASN         : angle       2.00735 (   15)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 TYR cc_start: 0.7647 (m-80) cc_final: 0.7040 (m-10)
REVERT: A  366 MET cc_start: 0.8148 (tpp) cc_final: 0.7769 (tpp)
REVERT: A  375 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7957 (mm-30)
REVERT: A  484 ILE cc_start: 0.8027 (mm) cc_final: 0.7697 (mm)
REVERT: E  385 THR cc_start: 0.8436 (p) cc_final: 0.8154 (t)
REVERT: E  444 LYS cc_start: 0.9145 (pttt) cc_final: 0.8082 (mttm)
REVERT: E  506 GLN cc_start: 0.7699 (mt0) cc_final: 0.7327 (mt0)
REVERT: H   48 TRP cc_start: 0.8687 (t60) cc_final: 0.7954 (t60)
REVERT: L   34 ASP cc_start: 0.7508 (m-30) cc_final: 0.7131 (m-30)
  outliers start: 16
  outliers final: 12
  residues processed: 170
  average time/residue: 0.0730
  time to fit residues: 17.9466
Evaluate side-chains
  127 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   41 LEU
Chi-restraints excluded: chain L residue   48 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 55 optimal weight:    0.1980
   chunk 49 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0050
   chunk 44 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   chunk 39 optimal weight:    0.4980
   chunk 59 optimal weight:    0.2980
   chunk 86 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.2594

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 540 HIS
A 572 ASN
A 599 ASN
** L  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.119999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.097447 restraints weight = 24651.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.102868 restraints weight = 10592.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.104652 restraints weight = 5043.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.105494 restraints weight = 3930.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.105750 restraints weight = 3507.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3798
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3798 r_free = 0.3798    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3798 r_free = 0.3798    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3798
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8469  Z= 0.127
  Angle     :  0.696  17.104  11524  Z= 0.345
  Chirality :  0.046   0.458   1225
  Planarity :  0.005   0.046   1484
  Dihedral  :  6.305  50.544   1226
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  8.85 %
    Favored  : 89.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.65 (0.25), residues: 1021
  helix: -0.96 (0.24), residues: 391
  sheet: -1.27 (0.39), residues: 155
  loop : -0.99 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H 101 
 TYR   0.018   0.002   TYR E 495 
 PHE   0.035   0.002   PHE H 112 
 TRP   0.021   0.001   TRP A 302 
 HIS   0.003   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8455)
  covalent geometry    : angle       0.66520 (11491)
  SS BOND              : bond        0.00366 (    9)
  SS BOND              : angle       1.44993 (   18)
  hydrogen bonds       : bond        0.03836 (  316)
  hydrogen bonds       : angle       5.31195 (  866)
  link_NAG-ASN         : bond        0.01632 (    5)
  link_NAG-ASN         : angle       5.57283 (   15)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 165
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8535 (mt) cc_final: 0.8288 (tt)
REVERT: A  127 TYR cc_start: 0.8377 (t80) cc_final: 0.8092 (t80)
REVERT: A  255 TYR cc_start: 0.7728 (m-80) cc_final: 0.7212 (m-10)
REVERT: E  385 THR cc_start: 0.8711 (p) cc_final: 0.8460 (t)
REVERT: E  430 THR cc_start: 0.8234 (p) cc_final: 0.7998 (t)
REVERT: E  444 LYS cc_start: 0.9081 (pttt) cc_final: 0.8084 (mttm)
REVERT: E  470 THR cc_start: 0.8225 (p) cc_final: 0.7915 (p)
REVERT: E  506 GLN cc_start: 0.7436 (mt0) cc_final: 0.7090 (mt0)
REVERT: H   48 TRP cc_start: 0.8685 (t60) cc_final: 0.7797 (t60)
REVERT: L   34 ASP cc_start: 0.7318 (m-30) cc_final: 0.7012 (m-30)
REVERT: L   80 LEU cc_start: 0.9450 (mt) cc_final: 0.9171 (mt)
REVERT: L   81 GLN cc_start: 0.8667 (mt0) cc_final: 0.8334 (mp10)
REVERT: L   93 TYR cc_start: 0.8007 (t80) cc_final: 0.7531 (t80)
  outliers start: 16
  outliers final: 8
  residues processed: 175
  average time/residue: 0.0708
  time to fit residues: 18.0472
Evaluate side-chains
  130 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 122
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 51 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 71 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 540 HIS
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  40 GLN
L  53 ASN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.117393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.093019 restraints weight = 29524.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.097827 restraints weight = 11415.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.101003 restraints weight = 6251.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.103080 restraints weight = 4182.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.104451 restraints weight = 3195.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3782
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3782 r_free = 0.3782    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3782 r_free = 0.3782    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3782
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8469  Z= 0.144
  Angle     :  0.691  11.238  11524  Z= 0.345
  Chirality :  0.044   0.170   1225
  Planarity :  0.004   0.043   1484
  Dihedral  :  7.012  69.719   1226
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.46 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.26), residues: 1021
  helix: -0.44 (0.25), residues: 394
  sheet: -1.11 (0.40), residues: 159
  loop : -0.80 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  99 
 TYR   0.018   0.002   TYR E 369 
 PHE   0.031   0.002   PHE A 603 
 TRP   0.016   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8455)
  covalent geometry    : angle       0.67568 (11491)
  SS BOND              : bond        0.00396 (    9)
  SS BOND              : angle       1.37558 (   18)
  hydrogen bonds       : bond        0.03697 (  316)
  hydrogen bonds       : angle       5.11828 (  866)
  link_NAG-ASN         : bond        0.00724 (    5)
  link_NAG-ASN         : angle       3.89275 (   15)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8212 (ptm) cc_final: 0.7835 (ptm)
REVERT: A  127 TYR cc_start: 0.8356 (t80) cc_final: 0.8095 (t80)
REVERT: A  222 LEU cc_start: 0.8458 (tp) cc_final: 0.8211 (tp)
REVERT: A  255 TYR cc_start: 0.7545 (m-80) cc_final: 0.6950 (m-10)
REVERT: A  366 MET cc_start: 0.8519 (tpp) cc_final: 0.7790 (tpp)
REVERT: E  385 THR cc_start: 0.8413 (p) cc_final: 0.8168 (t)
REVERT: E  430 THR cc_start: 0.8210 (p) cc_final: 0.7979 (t)
REVERT: E  444 LYS cc_start: 0.9127 (pttt) cc_final: 0.8115 (mttm)
REVERT: E  470 THR cc_start: 0.8390 (p) cc_final: 0.8083 (p)
REVERT: E  506 GLN cc_start: 0.7750 (mt0) cc_final: 0.7314 (mt0)
REVERT: H   55 ILE cc_start: 0.8632 (mp) cc_final: 0.8404 (mt)
REVERT: H   81 TYR cc_start: 0.7757 (m-80) cc_final: 0.7463 (m-80)
REVERT: H   82 MET cc_start: 0.8412 (tmm) cc_final: 0.8174 (tmm)
REVERT: L   34 ASP cc_start: 0.7364 (m-30) cc_final: 0.7125 (m-30)
  outliers start: 17
  outliers final: 13
  residues processed: 147
  average time/residue: 0.0696
  time to fit residues: 15.3049
Evaluate side-chains
  135 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   56 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   41 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 73 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.114446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.092672 restraints weight = 16320.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.096329 restraints weight = 8023.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.098776 restraints weight = 5033.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.100410 restraints weight = 3687.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.101471 restraints weight = 2987.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3739 r_free = 0.3739    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3739 r_free = 0.3739    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3739
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.4081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8469  Z= 0.171
  Angle     :  0.711  11.693  11524  Z= 0.352
  Chirality :  0.046   0.189   1225
  Planarity :  0.004   0.050   1484
  Dihedral  :  7.488  82.388   1226
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 11.80 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.27), residues: 1021
  helix: -0.26 (0.25), residues: 398
  sheet: -0.88 (0.41), residues: 158
  loop : -0.64 (0.31), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 460 
 TYR   0.023   0.002   TYR A 521 
 PHE   0.030   0.002   PHE A 603 
 TRP   0.016   0.002   TRP E 436 
 HIS   0.003   0.001   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 8455)
  covalent geometry    : angle       0.69656 (11491)
  SS BOND              : bond        0.00577 (    9)
  SS BOND              : angle       1.36211 (   18)
  hydrogen bonds       : bond        0.03683 (  316)
  hydrogen bonds       : angle       5.11236 (  866)
  link_NAG-ASN         : bond        0.00959 (    5)
  link_NAG-ASN         : angle       3.78199 (   15)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.8424 (t80) cc_final: 0.8094 (t80)
REVERT: A  222 LEU cc_start: 0.8615 (tp) cc_final: 0.8411 (tp)
REVERT: A  255 TYR cc_start: 0.7588 (m-80) cc_final: 0.6976 (m-10)
REVERT: E  385 THR cc_start: 0.8419 (p) cc_final: 0.8166 (t)
REVERT: E  394 ASN cc_start: 0.7353 (m-40) cc_final: 0.7056 (m-40)
REVERT: E  430 THR cc_start: 0.8214 (p) cc_final: 0.8004 (t)
REVERT: E  432 CYS cc_start: 0.4916 (m) cc_final: 0.4544 (m)
REVERT: E  444 LYS cc_start: 0.9178 (pttt) cc_final: 0.8099 (mttm)
REVERT: E  472 ILE cc_start: 0.8603 (mm) cc_final: 0.8358 (mt)
REVERT: E  507 PRO cc_start: 0.9183 (Cg_endo) cc_final: 0.8955 (Cg_exo)
REVERT: H    5 LEU cc_start: 0.4392 (OUTLIER) cc_final: 0.4173 (mt)
REVERT: H   55 ILE cc_start: 0.8592 (mp) cc_final: 0.8384 (mt)
REVERT: L   34 ASP cc_start: 0.7286 (m-30) cc_final: 0.6987 (m-30)
  outliers start: 20
  outliers final: 15
  residues processed: 139
  average time/residue: 0.0688
  time to fit residues: 14.2965
Evaluate side-chains
  133 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   56 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   41 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   chunk 93 optimal weight:    3.9990
   chunk 12 optimal weight:   20.0000
   chunk 7 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 76 optimal weight:    0.1980
   chunk 85 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  53 ASN
L  91 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.118916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.096837 restraints weight = 20408.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.100754 restraints weight = 9879.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.102863 restraints weight = 5540.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.103396 restraints weight = 4335.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.103508 restraints weight = 3781.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3772
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3772 r_free = 0.3772    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3772 r_free = 0.3772    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3772
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.4277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8469  Z= 0.158
  Angle     :  0.699  10.837  11524  Z= 0.345
  Chirality :  0.046   0.226   1225
  Planarity :  0.004   0.071   1484
  Dihedral  :  7.599  85.952   1226
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 11.35 %
    Favored  : 86.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.69 (0.27), residues: 1021
  helix: -0.06 (0.26), residues: 398
  sheet: -0.81 (0.42), residues: 158
  loop : -0.52 (0.31), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 460 
 TYR   0.023   0.002   TYR A 521 
 PHE   0.030   0.002   PHE A 603 
 TRP   0.015   0.002   TRP A 163 
 HIS   0.003   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 8455)
  covalent geometry    : angle       0.68588 (11491)
  SS BOND              : bond        0.00528 (    9)
  SS BOND              : angle       1.22121 (   18)
  hydrogen bonds       : bond        0.03559 (  316)
  hydrogen bonds       : angle       5.04303 (  866)
  link_NAG-ASN         : bond        0.00938 (    5)
  link_NAG-ASN         : angle       3.61733 (   15)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.8357 (t80) cc_final: 0.8061 (t80)
REVERT: A  222 LEU cc_start: 0.8714 (tp) cc_final: 0.8498 (tp)
REVERT: A  255 TYR cc_start: 0.7674 (m-80) cc_final: 0.7083 (m-10)
REVERT: A  366 MET cc_start: 0.8662 (tpp) cc_final: 0.7933 (tpp)
REVERT: A  375 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8413 (mm-30)
REVERT: E  385 THR cc_start: 0.8544 (p) cc_final: 0.8299 (t)
REVERT: E  432 CYS cc_start: 0.5020 (m) cc_final: 0.4680 (m)
REVERT: E  444 LYS cc_start: 0.9200 (pttt) cc_final: 0.8004 (mttm)
REVERT: E  472 ILE cc_start: 0.8623 (mm) cc_final: 0.8349 (mt)
REVERT: E  508 TYR cc_start: 0.8473 (m-80) cc_final: 0.8239 (m-80)
REVERT: H   55 ILE cc_start: 0.8521 (mp) cc_final: 0.8283 (mt)
REVERT: L   34 ASP cc_start: 0.7281 (m-30) cc_final: 0.7053 (m-30)
  outliers start: 20
  outliers final: 14
  residues processed: 140
  average time/residue: 0.0674
  time to fit residues: 14.4331
Evaluate side-chains
  132 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   56 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   41 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 96 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   chunk 68 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  53 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.119871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.096454 restraints weight = 29160.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.101739 restraints weight = 11950.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.105432 restraints weight = 6272.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.106146 restraints weight = 4232.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.106099 restraints weight = 3734.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3803
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3803 r_free = 0.3803    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3804 r_free = 0.3804    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3804
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.4443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8469  Z= 0.142
  Angle     :  0.693  10.901  11524  Z= 0.340
  Chirality :  0.045   0.228   1225
  Planarity :  0.004   0.071   1484
  Dihedral  :  7.597  89.004   1226
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.03 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.51 (0.27), residues: 1021
  helix:  0.10 (0.26), residues: 399
  sheet: -0.77 (0.42), residues: 160
  loop : -0.40 (0.31), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 460 
 TYR   0.021   0.002   TYR A 521 
 PHE   0.030   0.002   PHE A 603 
 TRP   0.015   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 8455)
  covalent geometry    : angle       0.68027 (11491)
  SS BOND              : bond        0.00492 (    9)
  SS BOND              : angle       1.17149 (   18)
  hydrogen bonds       : bond        0.03439 (  316)
  hydrogen bonds       : angle       4.94002 (  866)
  link_NAG-ASN         : bond        0.00908 (    5)
  link_NAG-ASN         : angle       3.56930 (   15)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.8305 (t80) cc_final: 0.8004 (t80)
REVERT: A  222 LEU cc_start: 0.8690 (tp) cc_final: 0.8481 (tp)
REVERT: A  255 TYR cc_start: 0.7636 (m-80) cc_final: 0.7048 (m-10)
REVERT: A  366 MET cc_start: 0.8632 (tpp) cc_final: 0.8361 (tpt)
REVERT: E  385 THR cc_start: 0.8544 (p) cc_final: 0.8300 (t)
REVERT: E  432 CYS cc_start: 0.4933 (m) cc_final: 0.4608 (m)
REVERT: E  444 LYS cc_start: 0.9207 (pttt) cc_final: 0.7991 (mttm)
REVERT: E  472 ILE cc_start: 0.8604 (mm) cc_final: 0.8387 (mt)
REVERT: H   55 ILE cc_start: 0.8503 (mp) cc_final: 0.8241 (mt)
REVERT: L   34 ASP cc_start: 0.7239 (m-30) cc_final: 0.6991 (m-30)
  outliers start: 20
  outliers final: 15
  residues processed: 142
  average time/residue: 0.0688
  time to fit residues: 14.7777
Evaluate side-chains
  132 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   56 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 77 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    0.1980
   chunk 21 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  16 GLN
L  53 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.119620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.095854 restraints weight = 33891.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.100832 restraints weight = 13306.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.105160 restraints weight = 6726.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.105507 restraints weight = 4329.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.106218 restraints weight = 3644.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3803
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3803 r_free = 0.3803    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3803 r_free = 0.3803    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3803
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8469  Z= 0.143
  Angle     :  0.708  10.699  11524  Z= 0.343
  Chirality :  0.045   0.228   1225
  Planarity :  0.004   0.058   1484
  Dihedral  :  7.627  90.938   1226
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.37 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.39 (0.27), residues: 1021
  helix:  0.16 (0.26), residues: 399
  sheet: -0.64 (0.42), residues: 165
  loop : -0.32 (0.32), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 559 
 TYR   0.019   0.002   TYR A 521 
 PHE   0.031   0.002   PHE A 603 
 TRP   0.014   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8455)
  covalent geometry    : angle       0.69570 (11491)
  SS BOND              : bond        0.00466 (    9)
  SS BOND              : angle       1.14792 (   18)
  hydrogen bonds       : bond        0.03421 (  316)
  hydrogen bonds       : angle       4.96957 (  866)
  link_NAG-ASN         : bond        0.00889 (    5)
  link_NAG-ASN         : angle       3.51818 (   15)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.8338 (t80) cc_final: 0.8021 (t80)
REVERT: A  255 TYR cc_start: 0.7722 (m-80) cc_final: 0.7087 (m-10)
REVERT: A  366 MET cc_start: 0.8668 (tpp) cc_final: 0.8436 (tpt)
REVERT: E  385 THR cc_start: 0.8631 (p) cc_final: 0.8389 (t)
REVERT: E  432 CYS cc_start: 0.5004 (m) cc_final: 0.4666 (m)
REVERT: E  444 LYS cc_start: 0.9208 (pttt) cc_final: 0.7947 (mttm)
REVERT: E  472 ILE cc_start: 0.8630 (mm) cc_final: 0.8412 (mt)
REVERT: H   33 TYR cc_start: 0.8548 (m-80) cc_final: 0.8327 (m-80)
REVERT: H   55 ILE cc_start: 0.8542 (mp) cc_final: 0.8279 (mt)
REVERT: L   34 ASP cc_start: 0.7235 (m-30) cc_final: 0.6986 (m-30)
REVERT: L   83 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8199 (tm-30)
  outliers start: 18
  outliers final: 14
  residues processed: 140
  average time/residue: 0.0707
  time to fit residues: 14.8492
Evaluate side-chains
  131 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   56 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 90 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  53 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.118972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.095436 restraints weight = 27086.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.101030 restraints weight = 11542.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.104757 restraints weight = 5437.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.104798 restraints weight = 3976.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.104979 restraints weight = 3459.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.4679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8469  Z= 0.156
  Angle     :  0.723  10.536  11524  Z= 0.353
  Chirality :  0.046   0.229   1225
  Planarity :  0.004   0.059   1484
  Dihedral  :  7.675  91.791   1226
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 12.83 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.34 (0.27), residues: 1021
  helix:  0.24 (0.26), residues: 399
  sheet: -0.78 (0.41), residues: 164
  loop : -0.25 (0.32), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 460 
 TYR   0.020   0.002   TYR A 521 
 PHE   0.031   0.002   PHE A 603 
 TRP   0.015   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8455)
  covalent geometry    : angle       0.71149 (11491)
  SS BOND              : bond        0.00354 (    9)
  SS BOND              : angle       1.03162 (   18)
  hydrogen bonds       : bond        0.03476 (  316)
  hydrogen bonds       : angle       4.97024 (  866)
  link_NAG-ASN         : bond        0.00906 (    5)
  link_NAG-ASN         : angle       3.50281 (   15)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.8225 (t80) cc_final: 0.7970 (t80)
REVERT: A  255 TYR cc_start: 0.7599 (m-80) cc_final: 0.7002 (m-10)
REVERT: A  366 MET cc_start: 0.8670 (tpp) cc_final: 0.8413 (tpt)
REVERT: E  385 THR cc_start: 0.8566 (p) cc_final: 0.8346 (t)
REVERT: E  432 CYS cc_start: 0.4987 (m) cc_final: 0.4668 (m)
REVERT: E  444 LYS cc_start: 0.9236 (pttt) cc_final: 0.8031 (mttm)
REVERT: E  472 ILE cc_start: 0.8655 (mm) cc_final: 0.8449 (mt)
REVERT: E  508 TYR cc_start: 0.8473 (m-80) cc_final: 0.8204 (m-80)
REVERT: H   55 ILE cc_start: 0.8515 (mp) cc_final: 0.8253 (mt)
REVERT: L   34 ASP cc_start: 0.7288 (m-30) cc_final: 0.7070 (m-30)
  outliers start: 21
  outliers final: 18
  residues processed: 139
  average time/residue: 0.0665
  time to fit residues: 13.9483
Evaluate side-chains
  136 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  340 GLU
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   56 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain H residue  112 PHE
Chi-restraints excluded: chain L residue   41 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0570
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
A 380 GLN
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  53 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.121090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.097174 restraints weight = 33104.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.102380 restraints weight = 13373.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.106837 restraints weight = 6630.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.106939 restraints weight = 4373.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.107150 restraints weight = 3741.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3819
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3819 r_free = 0.3819    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3819 r_free = 0.3819    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3819
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.4801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8469  Z= 0.127
  Angle     :  0.718  12.295  11524  Z= 0.349
  Chirality :  0.045   0.220   1225
  Planarity :  0.004   0.066   1484
  Dihedral  :  7.569  90.550   1226
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.96 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.20 (0.28), residues: 1021
  helix:  0.35 (0.27), residues: 399
  sheet: -0.59 (0.41), residues: 171
  loop : -0.22 (0.32), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  56 
 TYR   0.021   0.002   TYR A 521 
 PHE   0.032   0.002   PHE A 603 
 TRP   0.014   0.001   TRP H 115 
 HIS   0.002   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8455)
  covalent geometry    : angle       0.70664 (11491)
  SS BOND              : bond        0.00405 (    9)
  SS BOND              : angle       1.15581 (   18)
  hydrogen bonds       : bond        0.03395 (  316)
  hydrogen bonds       : angle       4.87821 (  866)
  link_NAG-ASN         : bond        0.00842 (    5)
  link_NAG-ASN         : angle       3.45080 (   15)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 TYR cc_start: 0.7698 (m-80) cc_final: 0.7096 (m-10)
REVERT: E  385 THR cc_start: 0.8648 (p) cc_final: 0.8413 (t)
REVERT: E  432 CYS cc_start: 0.4988 (m) cc_final: 0.4676 (m)
REVERT: E  444 LYS cc_start: 0.9210 (pttt) cc_final: 0.8026 (mttm)
REVERT: E  472 ILE cc_start: 0.8645 (mm) cc_final: 0.8427 (mt)
REVERT: E  508 TYR cc_start: 0.8459 (m-80) cc_final: 0.8204 (m-80)
REVERT: H   55 ILE cc_start: 0.8500 (mp) cc_final: 0.8232 (mt)
REVERT: H   81 TYR cc_start: 0.7732 (m-80) cc_final: 0.7502 (m-80)
REVERT: L   34 ASP cc_start: 0.7228 (m-30) cc_final: 0.7009 (m-30)
  outliers start: 13
  outliers final: 13
  residues processed: 134
  average time/residue: 0.0722
  time to fit residues: 14.3700
Evaluate side-chains
  127 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  340 GLU
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   56 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 23 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0870
   chunk 41 optimal weight:    5.9990
   chunk 88 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    1.1562

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

Flipped N/Q/H residues before XYZ refinement:
A 380 GLN
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.119293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.096138 restraints weight = 24921.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.100909 restraints weight = 10579.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.103234 restraints weight = 5583.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.103352 restraints weight = 4429.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.103698 restraints weight = 4157.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3773
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3773 r_free = 0.3773    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3772 r_free = 0.3772    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3772
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.4835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8469  Z= 0.159
  Angle     :  0.722  10.336  11524  Z= 0.355
  Chirality :  0.046   0.232   1225
  Planarity :  0.004   0.067   1484
  Dihedral  :  7.674  91.788   1226
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.19 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.18 (0.28), residues: 1021
  helix:  0.38 (0.26), residues: 399
  sheet: -0.53 (0.41), residues: 169
  loop : -0.23 (0.32), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H 101 
 TYR   0.022   0.002   TYR A 521 
 PHE   0.032   0.002   PHE A 603 
 TRP   0.016   0.001   TRP H 115 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 8455)
  covalent geometry    : angle       0.71087 (11491)
  SS BOND              : bond        0.00420 (    9)
  SS BOND              : angle       1.20744 (   18)
  hydrogen bonds       : bond        0.03449 (  316)
  hydrogen bonds       : angle       4.91193 (  866)
  link_NAG-ASN         : bond        0.00896 (    5)
  link_NAG-ASN         : angle       3.44730 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1779.55 seconds
wall clock time: 31 minutes 11.30 seconds (1871.30 seconds total)