Starting phenix.real_space_refine
on Sun Jul 27 02:16:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dx4_30895/07_2025/7dx4_30895_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dx4_30895/07_2025/7dx4_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_30895/07_2025/7dx4_30895.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dx4_30895/07_2025/7dx4_30895.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dx4_30895/07_2025/7dx4_30895_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dx4_30895/07_2025/7dx4_30895_neut.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.41, per 1000 atoms: 1.02
  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: 1.97
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  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: 0.90
  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: 2.35

  Time building geometry restraints manager: 2.37 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:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.340
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.050
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.100
-------------------------------------------------------------------------------
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 : 7.28
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.034   0.004   TRP A 302 
 HIS   0.014   0.002   HIS A 401 
 PHE   0.049   0.004   PHE E 497 
 TYR   0.037   0.004   TYR E 495 
 ARG   0.019   0.002   ARG A 169 

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

*********************** 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  : 1.001 
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  204 ARG cc_start: 0.7610 (mtm-85) cc_final: 0.7292 (mtp180)
REVERT: A  255 TYR cc_start: 0.7745 (m-80) cc_final: 0.7154 (m-10)
REVERT: E  385 THR cc_start: 0.8294 (p) cc_final: 0.8018 (t)
REVERT: E  444 LYS cc_start: 0.8917 (pttt) cc_final: 0.8090 (mttm)
REVERT: E  445 VAL cc_start: 0.8876 (t) cc_final: 0.8674 (p)
REVERT: E  470 THR cc_start: 0.8507 (p) cc_final: 0.8304 (p)
REVERT: H   48 TRP cc_start: 0.8687 (t60) cc_final: 0.8091 (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: 0.2133
  time to fit residues: 64.0649
Evaluate side-chains
  132 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 51 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0050
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.7594

-------------------------------------------------------------------------------
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 498 GLN
E 501 ASN
H  40 GLN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.121303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.099146 restraints weight = 28521.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.104858 restraints weight = 11433.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.108099 restraints weight = 5434.876|
|-----------------------------------------------------------------------------|
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) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3797 r_free = 0.3797    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3797
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8469  Z= 0.151
  Angle     :  0.713   9.123  11524  Z= 0.374
  Chirality :  0.046   0.189   1225
  Planarity :  0.006   0.062   1484
  Dihedral  :  8.364  63.762   1226
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  7.95 %
    Favored  : 90.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.24), residues: 1021
  helix: -2.13 (0.21), residues: 392
  sheet: -1.54 (0.42), residues: 142
  loop : -1.20 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 302 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.031   0.002   PHE A 603 
 TYR   0.024   0.002   TYR E 495 
 ARG   0.007   0.001   ARG E 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00186 (    5)
  link_NAG-ASN         : angle       2.01331 (   15)
  hydrogen bonds       : bond        0.04541 (  316)
  hydrogen bonds       : angle       5.85370 (  866)
  SS BOND              : bond        0.00615 (    9)
  SS BOND              : angle       1.62251 (   18)
  covalent geometry    : bond        0.00327 ( 8455)
  covalent geometry    : angle       0.70730 (11491)

*********************** 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
  182 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 166
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 TYR cc_start: 0.7685 (m-80) cc_final: 0.7079 (m-10)
REVERT: A  366 MET cc_start: 0.8136 (tpp) cc_final: 0.7790 (tpp)
REVERT: A  375 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7977 (mm-30)
REVERT: A  484 ILE cc_start: 0.8006 (mm) cc_final: 0.7670 (mm)
REVERT: E  385 THR cc_start: 0.8524 (p) cc_final: 0.8242 (t)
REVERT: E  444 LYS cc_start: 0.9100 (pttt) cc_final: 0.8115 (mttm)
REVERT: E  498 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8126 (mt0)
REVERT: E  506 GLN cc_start: 0.7666 (mt0) cc_final: 0.7317 (mt0)
REVERT: E  507 PRO cc_start: 0.8751 (Cg_exo) cc_final: 0.8551 (Cg_endo)
REVERT: H   48 TRP cc_start: 0.8633 (t60) cc_final: 0.7899 (t60)
REVERT: L   34 ASP cc_start: 0.7492 (m-30) cc_final: 0.7182 (m-30)
  outliers start: 16
  outliers final: 12
  residues processed: 177
  average time/residue: 0.1837
  time to fit residues: 45.8062
Evaluate side-chains
  130 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
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 E residue  498 GLN
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 94 optimal weight:    0.0470
   chunk 83 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 91 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 92 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   overall best weight:    2.2084

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

Flipped N/Q/H residues before XYZ refinement:
A 540 HIS
A 599 ASN
E 498 GLN
H   7 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.110795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.087415 restraints weight = 28701.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.092458 restraints weight = 11949.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.096263 restraints weight = 5789.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.3421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066   8469  Z= 0.250
  Angle     :  0.791  17.638  11524  Z= 0.398
  Chirality :  0.052   0.616   1225
  Planarity :  0.005   0.061   1484
  Dihedral  :  7.280  55.927   1226
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  :  9.31 %
    Favored  : 88.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.25), residues: 1021
  helix: -1.19 (0.23), residues: 395
  sheet: -1.58 (0.41), residues: 142
  loop : -1.03 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP E 436 
 HIS   0.005   0.001   HIS L  36 
 PHE   0.032   0.003   PHE H 112 
 TYR   0.029   0.002   TYR E 453 
 ARG   0.007   0.001   ARG E 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00912 (    5)
  link_NAG-ASN         : angle       6.01204 (   15)
  hydrogen bonds       : bond        0.04318 (  316)
  hydrogen bonds       : angle       5.59093 (  866)
  SS BOND              : bond        0.00519 (    9)
  SS BOND              : angle       1.65641 (   18)
  covalent geometry    : bond        0.00568 ( 8455)
  covalent geometry    : angle       0.75944 (11491)

*********************** 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
  158 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 1.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 TYR cc_start: 0.7801 (m-80) cc_final: 0.7175 (m-10)
REVERT: A  323 MET cc_start: 0.8027 (tpp) cc_final: 0.7089 (mpp)
REVERT: A  366 MET cc_start: 0.8355 (tpp) cc_final: 0.7764 (tpp)
REVERT: E  385 THR cc_start: 0.8714 (p) cc_final: 0.8459 (t)
REVERT: E  430 THR cc_start: 0.8312 (p) cc_final: 0.8108 (t)
REVERT: E  444 LYS cc_start: 0.9177 (pttt) cc_final: 0.7996 (mttm)
REVERT: E  470 THR cc_start: 0.8641 (p) cc_final: 0.8401 (p)
  outliers start: 19
  outliers final: 17
  residues processed: 151
  average time/residue: 0.1793
  time to fit residues: 38.8169
Evaluate side-chains
  136 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
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 A residue  409 SER
Chi-restraints excluded: chain E residue  390 LEU
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  498 GLN
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   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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 91 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 12 optimal weight:   40.0000
   chunk 59 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   chunk 58 optimal weight:    8.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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
** 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 = 0.3935 r_free = 0.3935 target = 0.114629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.092518 restraints weight = 19095.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.096444 restraints weight = 8712.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.099068 restraints weight = 5239.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3698
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3698 r_free = 0.3698    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3698 r_free = 0.3698    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8469  Z= 0.146
  Angle     :  0.693  10.923  11524  Z= 0.350
  Chirality :  0.045   0.207   1225
  Planarity :  0.004   0.043   1484
  Dihedral  :  7.502  75.344   1226
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.67 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.26), residues: 1021
  helix: -0.51 (0.25), residues: 398
  sheet: -1.36 (0.42), residues: 148
  loop : -0.81 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 302 
 HIS   0.003   0.001   HIS A 535 
 PHE   0.034   0.002   PHE H 112 
 TYR   0.028   0.002   TYR A 521 
 ARG   0.006   0.001   ARG E 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01247 (    5)
  link_NAG-ASN         : angle       3.65324 (   15)
  hydrogen bonds       : bond        0.03802 (  316)
  hydrogen bonds       : angle       5.25712 (  866)
  SS BOND              : bond        0.00548 (    9)
  SS BOND              : angle       1.60478 (   18)
  covalent geometry    : bond        0.00331 ( 8455)
  covalent geometry    : angle       0.67789 (11491)

*********************** 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
  160 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8363 (ptm) cc_final: 0.8042 (ptp)
REVERT: A  222 LEU cc_start: 0.8628 (tp) cc_final: 0.8413 (tp)
REVERT: A  255 TYR cc_start: 0.7670 (m-80) cc_final: 0.7065 (m-10)
REVERT: A  323 MET cc_start: 0.7869 (tpp) cc_final: 0.7111 (mpp)
REVERT: A  366 MET cc_start: 0.8305 (tpp) cc_final: 0.7682 (tpp)
REVERT: A  441 LYS cc_start: 0.8397 (tttt) cc_final: 0.7825 (ttmp)
REVERT: E  385 THR cc_start: 0.8546 (p) cc_final: 0.8320 (t)
REVERT: E  444 LYS cc_start: 0.9141 (pttt) cc_final: 0.7915 (mttm)
REVERT: E  470 THR cc_start: 0.8336 (p) cc_final: 0.8029 (p)
REVERT: E  506 GLN cc_start: 0.7744 (mt0) cc_final: 0.7297 (mt0)
REVERT: L   34 ASP cc_start: 0.7374 (m-30) cc_final: 0.7006 (m-30)
REVERT: L   80 LEU cc_start: 0.9484 (mt) cc_final: 0.9184 (mt)
REVERT: L   81 GLN cc_start: 0.8608 (mt0) cc_final: 0.8261 (mp10)
  outliers start: 17
  outliers final: 12
  residues processed: 152
  average time/residue: 0.2100
  time to fit residues: 47.4055
Evaluate side-chains
  133 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 1.729 
-------------------------------------------------------------------------------
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  339 VAL
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   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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 82 optimal weight:    8.9990
   chunk 67 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 80 optimal weight:   30.0000
   chunk 25 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   overall best weight:    1.6784

-------------------------------------------------------------------------------
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**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.116663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.093544 restraints weight = 29477.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.098429 restraints weight = 11765.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.101884 restraints weight = 6388.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3735
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3735 r_free = 0.3735    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3736 r_free = 0.3736    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3736
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.3930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8469  Z= 0.198
  Angle     :  0.717  11.637  11524  Z= 0.361
  Chirality :  0.046   0.189   1225
  Planarity :  0.005   0.048   1484
  Dihedral  :  7.718  85.226   1226
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 11.35 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.27), residues: 1021
  helix: -0.32 (0.25), residues: 399
  sheet: -1.27 (0.41), residues: 158
  loop : -0.76 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 436 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.030   0.002   PHE H 112 
 TYR   0.026   0.002   TYR A 521 
 ARG   0.005   0.001   ARG E 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01015 (    5)
  link_NAG-ASN         : angle       3.87319 (   15)
  hydrogen bonds       : bond        0.03804 (  316)
  hydrogen bonds       : angle       5.21552 (  866)
  SS BOND              : bond        0.00551 (    9)
  SS BOND              : angle       1.53417 (   18)
  covalent geometry    : bond        0.00451 ( 8455)
  covalent geometry    : angle       0.70179 (11491)

*********************** 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
  154 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8188 (tt)
REVERT: A  255 TYR cc_start: 0.7778 (m-80) cc_final: 0.7145 (m-10)
REVERT: A  323 MET cc_start: 0.7812 (tpp) cc_final: 0.7148 (mpp)
REVERT: A  558 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8491 (mt)
REVERT: E  385 THR cc_start: 0.8694 (p) cc_final: 0.8438 (t)
REVERT: E  444 LYS cc_start: 0.9202 (pttt) cc_final: 0.7942 (mttm)
REVERT: E  470 THR cc_start: 0.8572 (p) cc_final: 0.8342 (p)
REVERT: E  506 GLN cc_start: 0.7919 (mt0) cc_final: 0.7708 (mt0)
REVERT: L   80 LEU cc_start: 0.9438 (mt) cc_final: 0.9173 (mt)
REVERT: L   81 GLN cc_start: 0.8558 (mt0) cc_final: 0.8215 (mp10)
  outliers start: 22
  outliers final: 15
  residues processed: 146
  average time/residue: 0.2140
  time to fit residues: 46.0549
Evaluate side-chains
  137 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  558 LEU
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   94 VAL
Chi-restraints excluded: chain L residue   29 ILE
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 6 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0470
   chunk 71 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    0.6278

-------------------------------------------------------------------------------
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**
** L  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.120174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.097042 restraints weight = 34688.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.102349 restraints weight = 14595.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.104726 restraints weight = 6884.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3787 r_free = 0.3787    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3787 r_free = 0.3787    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8469  Z= 0.129
  Angle     :  0.679  10.951  11524  Z= 0.337
  Chirality :  0.045   0.217   1225
  Planarity :  0.004   0.040   1484
  Dihedral  :  7.616  86.471   1226
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.46 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.27), residues: 1021
  helix: -0.04 (0.26), residues: 399
  sheet: -1.01 (0.41), residues: 156
  loop : -0.73 (0.31), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 535 
 PHE   0.031   0.002   PHE H 112 
 TYR   0.021   0.002   TYR A 521 
 ARG   0.005   0.001   ARG E 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00908 (    5)
  link_NAG-ASN         : angle       3.64684 (   15)
  hydrogen bonds       : bond        0.03456 (  316)
  hydrogen bonds       : angle       4.98180 (  866)
  SS BOND              : bond        0.00408 (    9)
  SS BOND              : angle       1.32128 (   18)
  covalent geometry    : bond        0.00290 ( 8455)
  covalent geometry    : angle       0.66461 (11491)

*********************** 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
  155 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8331 (tt)
REVERT: A  127 TYR cc_start: 0.8240 (t80) cc_final: 0.8001 (t80)
REVERT: A  255 TYR cc_start: 0.7612 (m-80) cc_final: 0.6989 (m-10)
REVERT: A  558 LEU cc_start: 0.8626 (mt) cc_final: 0.8395 (mt)
REVERT: E  385 THR cc_start: 0.8625 (p) cc_final: 0.8379 (t)
REVERT: E  432 CYS cc_start: 0.4984 (m) cc_final: 0.4698 (m)
REVERT: E  444 LYS cc_start: 0.9163 (pttt) cc_final: 0.8028 (mttm)
REVERT: E  470 THR cc_start: 0.8317 (p) cc_final: 0.8001 (p)
REVERT: E  472 ILE cc_start: 0.8621 (mm) cc_final: 0.8329 (mt)
REVERT: E  506 GLN cc_start: 0.7724 (mt0) cc_final: 0.7521 (mt0)
REVERT: H   81 TYR cc_start: 0.7854 (m-80) cc_final: 0.7641 (m-80)
REVERT: L   81 GLN cc_start: 0.8508 (mt0) cc_final: 0.8294 (mp10)
REVERT: L   93 TYR cc_start: 0.8186 (t80) cc_final: 0.7745 (t80)
  outliers start: 16
  outliers final: 12
  residues processed: 147
  average time/residue: 0.1803
  time to fit residues: 39.5907
Evaluate side-chains
  136 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  149 ASN
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 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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 80 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 89 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.117276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.093776 restraints weight = 27902.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.099412 restraints weight = 11421.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.102852 restraints weight = 5558.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3756 r_free = 0.3756    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3756 r_free = 0.3756    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.4315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8469  Z= 0.182
  Angle     :  0.702  10.953  11524  Z= 0.351
  Chirality :  0.046   0.228   1225
  Planarity :  0.004   0.044   1484
  Dihedral  :  7.827  90.502   1226
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 11.35 %
    Favored  : 85.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.27), residues: 1021
  helix:  0.07 (0.26), residues: 399
  sheet: -1.01 (0.41), residues: 158
  loop : -0.67 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.030   0.002   PHE A 603 
 TYR   0.025   0.002   TYR A 521 
 ARG   0.004   0.001   ARG E 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00981 (    5)
  link_NAG-ASN         : angle       3.68181 (   15)
  hydrogen bonds       : bond        0.03577 (  316)
  hydrogen bonds       : angle       5.02838 (  866)
  SS BOND              : bond        0.00515 (    9)
  SS BOND              : angle       1.28948 (   18)
  covalent geometry    : bond        0.00415 ( 8455)
  covalent geometry    : angle       0.68876 (11491)

*********************** 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
  154 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8268 (tt)
REVERT: A  127 TYR cc_start: 0.8253 (t80) cc_final: 0.7989 (t80)
REVERT: A  255 TYR cc_start: 0.7762 (m-80) cc_final: 0.7192 (m-10)
REVERT: A  375 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8065 (mm-30)
REVERT: A  558 LEU cc_start: 0.8737 (mt) cc_final: 0.8502 (mt)
REVERT: E  385 THR cc_start: 0.8600 (p) cc_final: 0.8371 (t)
REVERT: E  432 CYS cc_start: 0.4994 (m) cc_final: 0.4698 (m)
REVERT: E  444 LYS cc_start: 0.9168 (pttt) cc_final: 0.8026 (mttm)
REVERT: E  472 ILE cc_start: 0.8619 (mm) cc_final: 0.8340 (mt)
REVERT: E  484 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7887 (mm-30)
REVERT: L   93 TYR cc_start: 0.8266 (t80) cc_final: 0.7813 (t80)
  outliers start: 22
  outliers final: 17
  residues processed: 142
  average time/residue: 0.1848
  time to fit residues: 39.0004
Evaluate side-chains
  144 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  149 ASN
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 E residue  468 ILE
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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0970
   chunk 0 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 8 optimal weight:    0.2980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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**
** L  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.120464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.097079 restraints weight = 32537.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.102091 restraints weight = 12823.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.106208 restraints weight = 6620.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3806
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3806 r_free = 0.3806    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3806 r_free = 0.3806    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3806
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.4567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8469  Z= 0.132
  Angle     :  0.683  10.842  11524  Z= 0.337
  Chirality :  0.044   0.225   1225
  Planarity :  0.004   0.037   1484
  Dihedral  :  7.670  90.566   1226
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.92 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.27), residues: 1021
  helix:  0.25 (0.26), residues: 399
  sheet: -0.85 (0.41), residues: 164
  loop : -0.46 (0.31), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A 535 
 PHE   0.030   0.002   PHE A 603 
 TYR   0.022   0.001   TYR A 521 
 ARG   0.004   0.001   ARG E 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00889 (    5)
  link_NAG-ASN         : angle       3.60563 (   15)
  hydrogen bonds       : bond        0.03397 (  316)
  hydrogen bonds       : angle       4.82337 (  866)
  SS BOND              : bond        0.00486 (    9)
  SS BOND              : angle       1.21941 (   18)
  covalent geometry    : bond        0.00297 ( 8455)
  covalent geometry    : angle       0.67006 (11491)

*********************** 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
  161 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 1.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8238 (tt)
REVERT: A  127 TYR cc_start: 0.8186 (t80) cc_final: 0.7983 (t80)
REVERT: A  255 TYR cc_start: 0.7695 (m-80) cc_final: 0.7157 (m-10)
REVERT: A  375 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8121 (mm-30)
REVERT: A  558 LEU cc_start: 0.8653 (mt) cc_final: 0.8429 (mt)
REVERT: E  385 THR cc_start: 0.8625 (p) cc_final: 0.8382 (t)
REVERT: E  432 CYS cc_start: 0.4980 (m) cc_final: 0.4693 (m)
REVERT: E  444 LYS cc_start: 0.9197 (pttt) cc_final: 0.7973 (mttm)
REVERT: E  466 ARG cc_start: 0.8336 (ttm110) cc_final: 0.7632 (ptm160)
REVERT: E  472 ILE cc_start: 0.8672 (mm) cc_final: 0.8466 (mt)
REVERT: E  484 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7855 (mm-30)
REVERT: E  506 GLN cc_start: 0.7754 (mt0) cc_final: 0.7246 (mt0)
REVERT: L   81 GLN cc_start: 0.8418 (mp10) cc_final: 0.8081 (mp10)
REVERT: L   93 TYR cc_start: 0.7935 (t80) cc_final: 0.7646 (t80)
  outliers start: 16
  outliers final: 14
  residues processed: 156
  average time/residue: 0.2585
  time to fit residues: 59.5091
Evaluate side-chains
  141 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  340 GLU
Chi-restraints excluded: chain E residue  359 SER
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain H residue    5 LEU
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   51 TYR
Chi-restraints excluded: chain L residue   78 THR
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 15 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 90 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 89 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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**
** L  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.118160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.095167 restraints weight = 30065.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.099523 restraints weight = 12642.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.103574 restraints weight = 6889.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3766
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3766 r_free = 0.3766    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 = 0.3766 r_free = 0.3766    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3766
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.4650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8469  Z= 0.172
  Angle     :  0.715  10.765  11524  Z= 0.357
  Chirality :  0.046   0.231   1225
  Planarity :  0.004   0.056   1484
  Dihedral  :  7.825  92.173   1226
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.28), residues: 1021
  helix:  0.30 (0.27), residues: 399
  sheet: -0.96 (0.41), residues: 162
  loop : -0.40 (0.32), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E 436 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.032   0.002   PHE A 603 
 TYR   0.022   0.002   TYR A 521 
 ARG   0.008   0.001   ARG L  63 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00961 (    5)
  link_NAG-ASN         : angle       3.60369 (   15)
  hydrogen bonds       : bond        0.03488 (  316)
  hydrogen bonds       : angle       4.93984 (  866)
  SS BOND              : bond        0.00484 (    9)
  SS BOND              : angle       1.25889 (   18)
  covalent geometry    : bond        0.00395 ( 8455)
  covalent geometry    : angle       0.70247 (11491)

*********************** 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
  145 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8294 (tt)
REVERT: A  255 TYR cc_start: 0.7736 (m-80) cc_final: 0.7186 (m-10)
REVERT: A  261 CYS cc_start: 0.7496 (m) cc_final: 0.7271 (m)
REVERT: A  375 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7751 (mm-30)
REVERT: A  558 LEU cc_start: 0.8734 (mt) cc_final: 0.8514 (mt)
REVERT: E  385 THR cc_start: 0.8638 (p) cc_final: 0.8425 (t)
REVERT: E  432 CYS cc_start: 0.5014 (m) cc_final: 0.4717 (m)
REVERT: E  444 LYS cc_start: 0.9170 (pttt) cc_final: 0.7973 (mttm)
REVERT: E  484 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7976 (mm-30)
REVERT: E  508 TYR cc_start: 0.8510 (m-80) cc_final: 0.8299 (m-80)
  outliers start: 18
  outliers final: 16
  residues processed: 137
  average time/residue: 0.1695
  time to fit residues: 34.7887
Evaluate side-chains
  138 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  222 LEU
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  359 SER
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   23 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 77 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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**
L  53 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.120008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.096764 restraints weight = 27068.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.101967 restraints weight = 11365.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.105462 restraints weight = 5819.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3797
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3797 r_free = 0.3797    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3797 r_free = 0.3797    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3797
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
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   0.042   8469  Z= 0.143
  Angle     :  0.709  13.000  11524  Z= 0.351
  Chirality :  0.045   0.224   1225
  Planarity :  0.004   0.054   1484
  Dihedral  :  7.724  90.747   1226
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.49 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.28), residues: 1021
  helix:  0.37 (0.27), residues: 396
  sheet: -0.80 (0.41), residues: 162
  loop : -0.38 (0.32), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A 535 
 PHE   0.032   0.002   PHE A 603 
 TYR   0.020   0.002   TYR A 521 
 ARG   0.007   0.001   ARG L  63 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00913 (    5)
  link_NAG-ASN         : angle       3.53786 (   15)
  hydrogen bonds       : bond        0.03337 (  316)
  hydrogen bonds       : angle       4.84179 (  866)
  SS BOND              : bond        0.00479 (    9)
  SS BOND              : angle       1.23659 (   18)
  covalent geometry    : bond        0.00332 ( 8455)
  covalent geometry    : angle       0.69710 (11491)

********************** 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
  144 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8272 (tt)
REVERT: A  127 TYR cc_start: 0.7954 (t80) cc_final: 0.7548 (t80)
REVERT: A  255 TYR cc_start: 0.7678 (m-80) cc_final: 0.7144 (m-10)
REVERT: A  375 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8062 (mm-30)
REVERT: A  558 LEU cc_start: 0.8671 (mt) cc_final: 0.8446 (mt)
REVERT: E  385 THR cc_start: 0.8586 (p) cc_final: 0.8376 (t)
REVERT: E  432 CYS cc_start: 0.5016 (m) cc_final: 0.4716 (m)
REVERT: E  444 LYS cc_start: 0.9201 (pttt) cc_final: 0.8016 (mttm)
REVERT: E  508 TYR cc_start: 0.8469 (m-80) cc_final: 0.8255 (m-80)
REVERT: H  115 TRP cc_start: 0.8799 (m-10) cc_final: 0.8320 (m-10)
  outliers start: 17
  outliers final: 16
  residues processed: 138
  average time/residue: 0.1697
  time to fit residues: 34.4459
Evaluate side-chains
  139 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  132 VAL
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  359 SER
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   23 THR
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 96 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 69 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 501 ASN
** 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 = 0.3960 r_free = 0.3960 target = 0.116390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.092843 restraints weight = 28536.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.097845 restraints weight = 11921.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.101428 restraints weight = 6058.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.4765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8469  Z= 0.220
  Angle     :  0.764  11.774  11524  Z= 0.380
  Chirality :  0.048   0.246   1225
  Planarity :  0.005   0.059   1484
  Dihedral  :  8.013  93.727   1226
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.83 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.28), residues: 1021
  helix:  0.34 (0.27), residues: 396
  sheet: -0.97 (0.41), residues: 164
  loop : -0.32 (0.32), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 436 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.040   0.003   PHE E 392 
 TYR   0.025   0.002   TYR E 453 
 ARG   0.009   0.001   ARG L  63 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01051 (    5)
  link_NAG-ASN         : angle       3.59658 (   15)
  hydrogen bonds       : bond        0.03549 (  316)
  hydrogen bonds       : angle       5.00922 (  866)
  SS BOND              : bond        0.00522 (    9)
  SS BOND              : angle       1.30775 (   18)
  covalent geometry    : bond        0.00503 ( 8455)
  covalent geometry    : angle       0.75184 (11491)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4004.35 seconds
wall clock time: 72 minutes 0.47 seconds (4320.47 seconds total)