Starting phenix.real_space_refine
on Sat Aug 23 04:27:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kc9_37097/08_2025/8kc9_37097.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kc9_37097/08_2025/8kc9_37097.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kc9_37097/08_2025/8kc9_37097.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kc9_37097/08_2025/8kc9_37097.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kc9_37097/08_2025/8kc9_37097.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kc9_37097/08_2025/8kc9_37097.cif"
  }
  resolution = 3.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 sd=   0.088
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     S      51      5.16       5
     C    6193      2.51       5
     N    1648      2.21       5
     O    1821      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9714
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 642, 5162
          Classifications: {'peptide': 642}
          Link IDs: {'PTRANS': 33, 'TRANS': 608}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2994
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2994
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 18, 'TRANS': 343}
    Chain: "C"
      Number of atoms: 1416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1416
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 6, 'TRANS': 175}
    Chain: "E"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 85
          Classifications: {'peptide': 11}
          Modifications used: {'PEPT-D': 1}
          Link IDs: {'NMTRANS': 7, 'TRANS': 3}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 16
          Planarities with less than four sites: {'MLE:plan-1': 4, 'MVA:plan-1': 1, 'BMT:plan-1': 1, 'ABA:plan-1': 1, 'SAR:plan-1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' FE': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.64, per 1000 atoms: 0.27
  Number of scatterers: 9714
  At special positions: 0
  Unit cell: (94.6, 113.3, 126.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      1     26.01
     S      51     16.00
     O    1821      8.00
     N    1648      7.00
     C    6193      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  75 " - pdb=" SG  CYS A 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  79 " - pdb=" SG  CYS A 119 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 242 " - pdb=" SG  CYS A 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 246 " - pdb=" SG  CYS A 278 " 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 801 " - " ASN A 540 "
      " NAG A 802 " - " ASN A 316 "
      " NAG B 501 " - " ASN B  87 "
      " NAG B 502 " - " ASN B 363 "
    TRANS
      " DAL E   1 " - " ALA E  11 "
  Time building additional restraints: 1.11
  Conformation dependent library (CDL) restraints added in 380.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DAL E   1 "
  Number of C-beta restraints generated:  2250

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 9 sheets defined
      57.4% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 49
      removed outlier: 3.894A  pdb=" N   LEU A  38 " --> pdb=" O   THR A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 82
    Processing helix  chain 'A' and resid 94 through 98
      removed outlier: 3.620A  pdb=" N   ALA A  98 " --> pdb=" O   PRO A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 125
      removed outlier: 3.826A  pdb=" N   GLY A 125 " --> pdb=" O   ARG A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 131
      removed outlier: 3.511A  pdb=" N   ALA A 129 " --> pdb=" O   PRO A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 143
      removed outlier: 3.630A  pdb=" N   GLU A 137 " --> pdb=" O   SER A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 157
    Processing helix  chain 'A' and resid 158 through 173
    Processing helix  chain 'A' and resid 176 through 189
    Processing helix  chain 'A' and resid 203 through 218
      removed outlier: 3.590A  pdb=" N   GLN A 207 " --> pdb=" O   GLN A 203 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLU A 208 " --> pdb=" O   PRO A 204 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   PHE A 209 " --> pdb=" O   HIS A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 244
      removed outlier: 3.549A  pdb=" N   VAL A 225 " --> pdb=" O   PRO A 221 " (cutoff:3.500A)
      Proline residue:  A 226  - end of helix
      removed outlier: 3.599A  pdb=" N   ALA A 244 " --> pdb=" O   GLU A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 286
      removed outlier: 3.553A  pdb=" N   CYS A 282 " --> pdb=" O   CYS A 278 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   THR A 284 " --> pdb=" O   GLN A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 315
      removed outlier: 3.567A  pdb=" N   TYR A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 331
      removed outlier: 3.724A  pdb=" N   PHE A 330 " --> pdb=" O   THR A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 348
    Processing helix  chain 'A' and resid 349 through 356
    Processing helix  chain 'A' and resid 359 through 384
    Processing helix  chain 'A' and resid 395 through 399
      removed outlier: 3.684A  pdb=" N   VAL A 398 " --> pdb=" O   PRO A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 428
      removed outlier: 3.705A  pdb=" N   LYS A 406 " --> pdb=" O   ARG A 402 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU A 424 " --> pdb=" O   GLU A 420 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   MET A 425 " --> pdb=" O   ILE A 421 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   LYS A 426 " --> pdb=" O   GLY A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 467
      removed outlier: 3.534A  pdb=" N   LEU A 466 " --> pdb=" O   ASN A 462 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ASN A 467 " --> pdb=" O   SER A 463 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 462 through 467'
    Processing helix  chain 'A' and resid 479 through 493
      removed outlier: 3.999A  pdb=" N   GLN A 484 " --> pdb=" O   ASP A 480 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   GLU A 485 " --> pdb=" O   HIS A 481 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LEU A 486 " --> pdb=" O   GLU A 482 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A 493 " --> pdb=" O   LEU A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 528
    Processing helix  chain 'A' and resid 531 through 553
      removed outlier: 3.797A  pdb=" N   ALA A 535 " --> pdb=" O   PRO A 531 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   PHE A 553 " --> pdb=" O   MET A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 698
    Processing helix  chain 'B' and resid 37 through 41
      removed outlier: 3.886A  pdb=" N   GLU B  40 " --> pdb=" O   PRO B  37 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU B  41 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 37 through 41'
    Processing helix  chain 'B' and resid 43 through 57
    Processing helix  chain 'B' and resid 60 through 87
      removed outlier: 3.946A  pdb=" N   ASN B  87 " --> pdb=" O   PHE B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 102
      removed outlier: 3.592A  pdb=" N   SER B 102 " --> pdb=" O   GLY B  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 99 through 102'
    Processing helix  chain 'B' and resid 103 through 124
      removed outlier: 3.808A  pdb=" N   GLN B 124 " --> pdb=" O   LYS B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 131
      removed outlier: 6.136A  pdb=" N   ALA B 128 " --> pdb=" O   GLY B 125 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   GLN B 131 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 144
    Processing helix  chain 'B' and resid 147 through 157
    Processing helix  chain 'B' and resid 160 through 175
      removed outlier: 3.606A  pdb=" N   LYS B 174 " --> pdb=" O   THR B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 191
    Processing helix  chain 'B' and resid 204 through 219
    Processing helix  chain 'B' and resid 222 through 246
      Proline residue:  B 234  - end of helix
    Processing helix  chain 'B' and resid 258 through 275
      removed outlier: 3.669A  pdb=" N   ASP B 265 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   HIS B 266 " --> pdb=" O   SER B 262 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   TYR B 267 " --> pdb=" O   ILE B 263 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   VAL B 268 " --> pdb=" O   ALA B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 281
      removed outlier: 3.540A  pdb=" N   LEU B 281 " --> pdb=" O   CYS B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 308
    Processing helix  chain 'B' and resid 310 through 325
      Proline residue:  B 316  - end of helix
    Processing helix  chain 'B' and resid 329 through 341
    Processing helix  chain 'B' and resid 348 through 353
      removed outlier: 3.569A  pdb=" N   PHE B 352 " --> pdb=" O   ASP B 349 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   GLN B 353 " --> pdb=" O   GLU B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 379
      removed outlier: 3.732A  pdb=" N   GLN B 368 " --> pdb=" O   VAL B 364 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   GLU B 377 " --> pdb=" O   ASP B 373 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ASN B 378 " --> pdb=" O   PHE B 374 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 81
    Processing helix  chain 'C' and resid 175 through 183
      removed outlier: 3.809A  pdb=" N   VAL C 179 " --> pdb=" O   GLY C 175 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 471 through 475
      removed outlier: 4.380A  pdb=" N   ARG A 647 " --> pdb=" O   TYR A 617 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR A 563 " --> pdb=" O   TRP A 675 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   THR A 677 " --> pdb=" O   PHE A 561 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   PHE A 561 " --> pdb=" O   THR A 677 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 475
      removed outlier: 4.380A  pdb=" N   ARG A 647 " --> pdb=" O   TYR A 617 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ASP A 623 " --> pdb=" O   THR A 665 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 592 through 593
      removed outlier: 3.661A  pdb=" N   ILE A 592 " --> pdb=" O   VAL A 601 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   VAL A 601 " --> pdb=" O   ILE A 592 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 637 through 641
      removed outlier: 6.588A  pdb=" N   PHE A 629 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   GLU A 640 " --> pdb=" O   PHE A 627 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   PHE A 627 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 284 through 285
    Processing sheet with id=AA6, first strand: chain 'B' and resid 384 through 386
      removed outlier: 3.561A  pdb=" N   GLY C  39 " --> pdb=" O   GLY B 385 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 44 through 45
    Processing sheet with id=AA8, first strand: chain 'C' and resid 55 through 56
      removed outlier: 3.605A  pdb=" N   ASP C 201 " --> pdb=" O   ASP C  49 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   ARG C  51 " --> pdb=" O   ILE C 199 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   ILE C 199 " --> pdb=" O   ARG C  51 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 152 through 154
      removed outlier: 6.837A  pdb=" N   MET C 140 " --> pdb=" O   VAL C 168 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL C 168 " --> pdb=" O   MET C 140 " (cutoff:3.500A)

    510 hydrogen bonds defined for protein.
    1497 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.59

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3179
        1.34 -     1.46: 2368
        1.46 -     1.59: 4323
        1.59 -     1.71: 0
        1.71 -     1.83: 77
  Bond restraints: 9947
  Sorted by residual:
  bond pdb=" N   MLE E   3 "
       pdb=" CN  MLE E   3 "
    ideal  model  delta    sigma   weight residual
    1.451  1.518 -0.067 2.00e-02 2.50e+03 1.11e+01
  bond pdb=" N   MLE E  10 "
       pdb=" CN  MLE E  10 "
    ideal  model  delta    sigma   weight residual
    1.451  1.513 -0.062 2.00e-02 2.50e+03 9.67e+00
  bond pdb=" N   SAR E   7 "
       pdb=" CN  SAR E   7 "
    ideal  model  delta    sigma   weight residual
    1.443  1.502 -0.059 2.00e-02 2.50e+03 8.78e+00
  bond pdb=" CA  SER A 699 "
       pdb=" CB  SER A 699 "
    ideal  model  delta    sigma   weight residual
    1.529  1.496  0.033 1.13e-02 7.83e+03 8.61e+00
  bond pdb=" N   MVA E   4 "
       pdb=" CN  MVA E   4 "
    ideal  model  delta    sigma   weight residual
    1.449  1.506 -0.057 2.00e-02 2.50e+03 8.05e+00
  ... (remaining 9942 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 13101
        2.25 -     4.49: 289
        4.49 -     6.74: 50
        6.74 -     8.99: 9
        8.99 -    11.23: 3
  Bond angle restraints: 13452
  Sorted by residual:
  angle pdb=" CA  LYS C  98 "
        pdb=" C   LYS C  98 "
        pdb=" N   ASP C  99 "
      ideal   model   delta    sigma   weight residual
     117.22  123.43   -6.21 1.17e+00 7.31e-01 2.81e+01
  angle pdb=" N   PHE C 107 "
        pdb=" CA  PHE C 107 "
        pdb=" C   PHE C 107 "
      ideal   model   delta    sigma   weight residual
     113.41  107.65    5.76 1.22e+00 6.72e-01 2.23e+01
  angle pdb=" N   LYS C 165 "
        pdb=" CA  LYS C 165 "
        pdb=" C   LYS C 165 "
      ideal   model   delta    sigma   weight residual
     113.72  108.33    5.39 1.30e+00 5.92e-01 1.72e+01
  angle pdb=" N   TRP C 161 "
        pdb=" CA  TRP C 161 "
        pdb=" C   TRP C 161 "
      ideal   model   delta    sigma   weight residual
     111.11  106.60    4.51 1.20e+00 6.94e-01 1.41e+01
  angle pdb=" CA  LYS C  98 "
        pdb=" C   LYS C  98 "
        pdb=" O   LYS C  98 "
      ideal   model   delta    sigma   weight residual
     120.63  116.57    4.06 1.08e+00 8.57e-01 1.41e+01
  ... (remaining 13447 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.97: 5338
       22.97 -    45.94: 561
       45.94 -    68.91: 92
       68.91 -    91.88: 13
       91.88 -   114.85: 17
  Dihedral angle restraints: 6021
    sinusoidal: 2514
      harmonic: 3507
  Sorted by residual:
  dihedral pdb=" CB  CYS A 246 "
           pdb=" SG  CYS A 246 "
           pdb=" SG  CYS A 278 "
           pdb=" CB  CYS A 278 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.26  -63.26     1      1.00e+01 1.00e-02 5.28e+01
  dihedral pdb=" CA  CYS A  79 "
           pdb=" C   CYS A  79 "
           pdb=" N   ALA A  80 "
           pdb=" CA  ALA A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.95   26.05     0      5.00e+00 4.00e-02 2.71e+01
  dihedral pdb=" CB  CYS A  79 "
           pdb=" SG  CYS A  79 "
           pdb=" SG  CYS A 119 "
           pdb=" CB  CYS A 119 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -125.87   39.87     1      1.00e+01 1.00e-02 2.23e+01
  ... (remaining 6018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1226
       0.062 -    0.124: 167
       0.124 -    0.185: 20
       0.185 -    0.247: 5
       0.247 -    0.309: 3
  Chirality restraints: 1421
  Sorted by residual:
  chirality pdb=" CB  BMT E   5 "
            pdb=" CA  BMT E   5 "
            pdb=" OG1 BMT E   5 "
            pdb=" CG2 BMT E   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.37    2.68   -0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" C1  NAG B 502 "
            pdb=" ND2 ASN B 363 "
            pdb=" C2  NAG B 502 "
            pdb=" O5  NAG B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-01 2.50e+01 2.33e+00
  chirality pdb=" CA  MVA E   4 "
            pdb=" N   MVA E   4 "
            pdb=" C   MVA E   4 "
            pdb=" CB  MVA E   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.25 2.00e-01 2.50e+01 1.62e+00
  ... (remaining 1418 not shown)

  Planarity restraints: 1770
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 155 "   -0.015 2.00e-02 2.50e+03   2.96e-02 8.76e+00
        pdb=" C   THR C 155 "    0.051 2.00e-02 2.50e+03
        pdb=" O   THR C 155 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR C 156 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 123 "    0.042 5.00e-02 4.00e+02   6.40e-02 6.55e+00
        pdb=" N   PRO C 124 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO C 124 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C 124 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 604 "    0.033 5.00e-02 4.00e+02   4.99e-02 3.99e+00
        pdb=" N   PRO A 605 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 605 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 605 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1767 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 325
        2.71 -     3.26: 9807
        3.26 -     3.81: 15727
        3.81 -     4.35: 17583
        4.35 -     4.90: 30112
  Nonbonded interactions: 73554
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 258 "
            pdb=" N   PHE B 259 "
     model   vdw
     2.168 3.120
  nonbonded pdb=" NE2 HIS A 659 "
            pdb="FE    FE A 803 "
     model   vdw
     2.178 2.340
  nonbonded pdb=" O   MET B 180 "
            pdb=" ND2 ASN B 184 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   GLU A 351 "
            pdb=" OG  SER A 355 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   TYR B 187 "
            pdb=" OG  SER B 190 "
     model   vdw
     2.244 3.040
  ... (remaining 73549 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     11.150
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6197
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      :  0.004   0.067   9956  Z= 0.215
  Angle     :  0.801  11.232  13475  Z= 0.445
  Chirality :  0.047   0.309   1421
  Planarity :  0.004   0.064   1765
  Dihedral  : 18.981 114.850   3756
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  4.34 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 22.93 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.26), residues: 1176
  helix:  2.13 (0.21), residues: 613
  sheet: -0.27 (0.75), residues: 50
  loop : -2.03 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 190 
 TYR   0.026   0.001   TYR B 267 
 PHE   0.017   0.001   PHE C 153 
 TRP   0.033   0.001   TRP A  91 
 HIS   0.003   0.000   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 9947)
  covalent geometry    : angle       0.79472 (13452)
  SS BOND              : bond        0.00255 (    4)
  SS BOND              : angle       2.91884 (    8)
  hydrogen bonds       : bond        0.17221 (  495)
  hydrogen bonds       : angle       5.70491 ( 1497)
  link_NAG-ASN         : bond        0.00457 (    4)
  link_NAG-ASN         : angle       2.30289 (   12)
  link_TRANS           : bond        0.00081 (    1)
  link_TRANS           : angle       1.67063 (    3)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 240
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.7426 (t0) cc_final: 0.7063 (t0)
REVERT: A  322 GLU cc_start: 0.7897 (tt0) cc_final: 0.7122 (tm-30)
REVERT: A  323 CYS cc_start: 0.8139 (t) cc_final: 0.7590 (t)
REVERT: A  334 ASP cc_start: 0.7394 (t0) cc_final: 0.7012 (t0)
REVERT: A  423 ASN cc_start: 0.7424 (m-40) cc_final: 0.6579 (t0)
REVERT: A  487 GLN cc_start: 0.8205 (mt0) cc_final: 0.7785 (mm110)
REVERT: A  488 ARG cc_start: 0.7847 (mtp-110) cc_final: 0.7623 (ptp-110)
REVERT: A  635 LYS cc_start: 0.8787 (tppt) cc_final: 0.8529 (mmtp)
REVERT: A  668 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7121 (mm-40)
REVERT: A  702 GLU cc_start: 0.5134 (OUTLIER) cc_final: 0.4880 (pm20)
REVERT: A  703 MET cc_start: 0.6026 (OUTLIER) cc_final: 0.5807 (mtt)
REVERT: B   88 CYS cc_start: 0.8789 (m) cc_final: 0.7314 (m)
REVERT: B  184 ASN cc_start: 0.8962 (m-40) cc_final: 0.8596 (m110)
REVERT: B  199 LYS cc_start: 0.7445 (mttt) cc_final: 0.7232 (mmtm)
REVERT: B  202 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7109 (mm-30)
REVERT: B  215 ARG cc_start: 0.8835 (tpt-90) cc_final: 0.8629 (mmm-85)
REVERT: B  228 ASP cc_start: 0.9052 (m-30) cc_final: 0.8822 (m-30)
REVERT: B  278 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7845 (tm-30)
REVERT: B  329 LYS cc_start: 0.9398 (mppt) cc_final: 0.9086 (mmtm)
REVERT: B  351 HIS cc_start: 0.6434 (m-70) cc_final: 0.6226 (m90)
REVERT: B  381 ASP cc_start: 0.8689 (m-30) cc_final: 0.8109 (p0)
REVERT: B  382 ASP cc_start: 0.7827 (m-30) cc_final: 0.6811 (p0)
REVERT: C   97 ILE cc_start: 0.7293 (tt) cc_final: 0.7049 (mt)
REVERT: C  159 THR cc_start: 0.7893 (p) cc_final: 0.7345 (p)
REVERT: C  171 LYS cc_start: 0.7028 (tttm) cc_final: 0.6718 (tttp)
REVERT: C  174 GLU cc_start: 0.7999 (tp30) cc_final: 0.7602 (tp30)
REVERT: C  176 MET cc_start: 0.7185 (mmp) cc_final: 0.6961 (mmt)
  outliers start: 12
  outliers final: 3
  residues processed: 248
  average time/residue: 0.1207
  time to fit residues: 40.2997
Evaluate side-chains
  149 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 144
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  702 GLU
Chi-restraints excluded: chain A residue  703 MET
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  162 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    0.7980
   chunk 117 optimal weight:    5.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.136658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.097366 restraints weight = 16574.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.101705 restraints weight = 9080.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.104741 restraints weight = 6171.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.106674 restraints weight = 4754.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.108118 restraints weight = 4019.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   9956  Z= 0.209
  Angle     :  0.712   9.572  13475  Z= 0.364
  Chirality :  0.046   0.342   1421
  Planarity :  0.005   0.053   1765
  Dihedral  :  8.882  95.202   1431
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.12 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 22.34 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.25), residues: 1176
  helix:  2.09 (0.21), residues: 625
  sheet:  0.27 (0.64), residues: 60
  loop : -2.09 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 214 
 TYR   0.030   0.002   TYR B 267 
 PHE   0.026   0.002   PHE C 153 
 TRP   0.026   0.002   TRP B 345 
 HIS   0.006   0.001   HIS C 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 9947)
  covalent geometry    : angle       0.70538 (13452)
  SS BOND              : bond        0.00318 (    4)
  SS BOND              : angle       2.81139 (    8)
  hydrogen bonds       : bond        0.06144 (  495)
  hydrogen bonds       : angle       4.35891 ( 1497)
  link_NAG-ASN         : bond        0.00381 (    4)
  link_NAG-ASN         : angle       2.45221 (   12)
  link_TRANS           : bond        0.00042 (    1)
  link_TRANS           : angle       0.11695 (    3)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 144
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.7582 (t0) cc_final: 0.7260 (t0)
REVERT: A  139 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.6842 (mp0)
REVERT: A  156 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7556 (tt)
REVERT: A  202 THR cc_start: 0.7185 (m) cc_final: 0.6609 (p)
REVERT: A  322 GLU cc_start: 0.8307 (tt0) cc_final: 0.7407 (tm-30)
REVERT: A  323 CYS cc_start: 0.8228 (t) cc_final: 0.7485 (t)
REVERT: A  374 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7995 (tm-30)
REVERT: A  423 ASN cc_start: 0.7930 (m-40) cc_final: 0.7286 (p0)
REVERT: A  488 ARG cc_start: 0.8034 (mtp-110) cc_final: 0.7787 (ptp90)
REVERT: A  600 CYS cc_start: 0.7696 (m) cc_final: 0.6602 (t)
REVERT: A  668 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7393 (mm-40)
REVERT: B  146 GLU cc_start: 0.8780 (pt0) cc_final: 0.7572 (pt0)
REVERT: B  198 ILE cc_start: 0.7996 (mm) cc_final: 0.7620 (mp)
REVERT: B  199 LYS cc_start: 0.8235 (mttt) cc_final: 0.7919 (mmtt)
REVERT: B  202 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7373 (mm-30)
REVERT: B  252 GLU cc_start: 0.7926 (pm20) cc_final: 0.7712 (pm20)
REVERT: B  382 ASP cc_start: 0.7676 (m-30) cc_final: 0.6768 (p0)
REVERT: C  171 LYS cc_start: 0.8586 (tttm) cc_final: 0.8355 (tttp)
REVERT: C  208 GLU cc_start: 0.8715 (pm20) cc_final: 0.8473 (pm20)
  outliers start: 46
  outliers final: 23
  residues processed: 178
  average time/residue: 0.1026
  time to fit residues: 25.8527
Evaluate side-chains
  145 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  123 CYS
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  177 ASP
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  255 ASP
Chi-restraints excluded: chain B residue  277 CYS
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   94 HIS
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain E residue    9 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 100 optimal weight:    0.1980
   chunk 24 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.142314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.100579 restraints weight = 16168.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.105250 restraints weight = 8652.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.108454 restraints weight = 5830.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.110674 restraints weight = 4467.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.112033 restraints weight = 3727.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9956  Z= 0.118
  Angle     :  0.597   8.486  13475  Z= 0.302
  Chirality :  0.041   0.217   1421
  Planarity :  0.004   0.065   1765
  Dihedral  :  6.821  77.880   1423
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.34 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 24.90 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.25), residues: 1176
  helix:  2.17 (0.20), residues: 616
  sheet:  0.24 (0.64), residues: 60
  loop : -1.89 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 292 
 TYR   0.021   0.001   TYR A 628 
 PHE   0.015   0.001   PHE C 153 
 TRP   0.013   0.001   TRP C 161 
 HIS   0.003   0.001   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9947)
  covalent geometry    : angle       0.59026 (13452)
  SS BOND              : bond        0.00487 (    4)
  SS BOND              : angle       2.72766 (    8)
  hydrogen bonds       : bond        0.04503 (  495)
  hydrogen bonds       : angle       3.88310 ( 1497)
  link_NAG-ASN         : bond        0.00457 (    4)
  link_NAG-ASN         : angle       2.24539 (   12)
  link_TRANS           : bond        0.00066 (    1)
  link_TRANS           : angle       0.06579 (    3)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 157
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 LEU cc_start: 0.7727 (tt) cc_final: 0.7487 (tp)
REVERT: A  139 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6698 (mp0)
REVERT: A  156 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7328 (tt)
REVERT: A  322 GLU cc_start: 0.8295 (tt0) cc_final: 0.7387 (tm-30)
REVERT: A  374 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7995 (tm-30)
REVERT: A  423 ASN cc_start: 0.7914 (m-40) cc_final: 0.7055 (t0)
REVERT: A  482 GLU cc_start: 0.8415 (mp0) cc_final: 0.8201 (mp0)
REVERT: A  488 ARG cc_start: 0.8014 (mtp-110) cc_final: 0.7774 (ptp90)
REVERT: B  146 GLU cc_start: 0.8480 (pt0) cc_final: 0.8089 (pt0)
REVERT: B  198 ILE cc_start: 0.7907 (mm) cc_final: 0.7484 (mp)
REVERT: B  199 LYS cc_start: 0.8223 (mttt) cc_final: 0.7880 (mmtm)
REVERT: B  202 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7473 (mm-30)
REVERT: B  252 GLU cc_start: 0.8005 (pm20) cc_final: 0.7734 (pm20)
REVERT: B  278 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8627 (tm-30)
REVERT: B  282 THR cc_start: 0.9451 (m) cc_final: 0.9007 (p)
REVERT: B  382 ASP cc_start: 0.7711 (m-30) cc_final: 0.6718 (t0)
REVERT: C   59 ARG cc_start: 0.7647 (ttm110) cc_final: 0.6968 (ptm160)
REVERT: C  208 GLU cc_start: 0.8783 (pm20) cc_final: 0.8561 (pm20)
  outliers start: 33
  outliers final: 16
  residues processed: 181
  average time/residue: 0.0987
  time to fit residues: 25.7456
Evaluate side-chains
  143 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain C residue   94 HIS
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain E residue    9 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 35 optimal weight:    0.6980
   chunk 83 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 487 GLN
B 339 GLN
B 368 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.138081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.098117 restraints weight = 16763.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.102415 restraints weight = 9162.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.105401 restraints weight = 6233.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.107476 restraints weight = 4839.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.108771 restraints weight = 4064.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9956  Z= 0.147
  Angle     :  0.616   8.101  13475  Z= 0.309
  Chirality :  0.042   0.209   1421
  Planarity :  0.004   0.065   1765
  Dihedral  :  6.409  68.599   1423
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.36 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 25.39 %
    Favored  : 70.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.25), residues: 1176
  helix:  2.23 (0.20), residues: 613
  sheet:  0.45 (0.72), residues: 49
  loop : -1.84 (0.26), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 354 
 TYR   0.022   0.001   TYR A 628 
 PHE   0.021   0.001   PHE C 153 
 TRP   0.011   0.001   TRP C 161 
 HIS   0.004   0.001   HIS A 565 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9947)
  covalent geometry    : angle       0.60235 (13452)
  SS BOND              : bond        0.00299 (    4)
  SS BOND              : angle       2.64382 (    8)
  hydrogen bonds       : bond        0.04835 (  495)
  hydrogen bonds       : angle       3.85187 ( 1497)
  link_NAG-ASN         : bond        0.00309 (    4)
  link_NAG-ASN         : angle       3.83129 (   12)
  link_TRANS           : bond        0.00049 (    1)
  link_TRANS           : angle       0.06913 (    3)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 137
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6854 (mp0)
REVERT: A  156 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7409 (tt)
REVERT: A  202 THR cc_start: 0.7292 (m) cc_final: 0.6797 (p)
REVERT: A  206 MET cc_start: 0.7736 (tpp) cc_final: 0.7525 (mmm)
REVERT: A  322 GLU cc_start: 0.8398 (tt0) cc_final: 0.7669 (tm-30)
REVERT: A  323 CYS cc_start: 0.8969 (m) cc_final: 0.7923 (t)
REVERT: A  374 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8008 (tm-30)
REVERT: A  423 ASN cc_start: 0.7935 (m-40) cc_final: 0.6936 (t0)
REVERT: A  479 SER cc_start: 0.5679 (OUTLIER) cc_final: 0.4599 (t)
REVERT: A  488 ARG cc_start: 0.8067 (mtp-110) cc_final: 0.7836 (ptp90)
REVERT: A  689 GLN cc_start: 0.7433 (mm-40) cc_final: 0.7045 (mm-40)
REVERT: B  146 GLU cc_start: 0.8481 (pt0) cc_final: 0.8107 (pt0)
REVERT: B  198 ILE cc_start: 0.7902 (mm) cc_final: 0.7383 (mp)
REVERT: B  243 CYS cc_start: 0.8968 (t) cc_final: 0.8523 (t)
REVERT: B  252 GLU cc_start: 0.8224 (pm20) cc_final: 0.7916 (pm20)
REVERT: B  382 ASP cc_start: 0.7782 (m-30) cc_final: 0.6758 (t0)
REVERT: C   59 ARG cc_start: 0.7726 (ttm110) cc_final: 0.6943 (ptm160)
REVERT: C  113 THR cc_start: 0.8572 (m) cc_final: 0.8332 (p)
REVERT: C  190 ARG cc_start: 0.8077 (mtp180) cc_final: 0.7642 (mmm-85)
REVERT: C  208 GLU cc_start: 0.8723 (pm20) cc_final: 0.8474 (pm20)
  outliers start: 43
  outliers final: 32
  residues processed: 170
  average time/residue: 0.0957
  time to fit residues: 23.7530
Evaluate side-chains
  161 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 126
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  123 CYS
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   94 HIS
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain E residue    9 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 99 optimal weight:    0.5980
   chunk 83 optimal weight:    9.9990
   chunk 90 optimal weight:    0.9980
   chunk 93 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 368 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.140518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.099306 restraints weight = 16576.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.103865 restraints weight = 8928.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.106870 restraints weight = 6030.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.109126 restraints weight = 4655.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.110481 restraints weight = 3899.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9956  Z= 0.112
  Angle     :  0.582   9.150  13475  Z= 0.288
  Chirality :  0.040   0.167   1421
  Planarity :  0.004   0.066   1765
  Dihedral  :  5.961  59.835   1423
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.08 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 26.48 %
    Favored  : 69.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.25), residues: 1176
  helix:  2.27 (0.20), residues: 616
  sheet: -0.40 (0.61), residues: 71
  loop : -1.69 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 666 
 TYR   0.021   0.001   TYR A 628 
 PHE   0.016   0.001   PHE C 153 
 TRP   0.011   0.001   TRP C 161 
 HIS   0.003   0.001   HIS A 536 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 9947)
  covalent geometry    : angle       0.57011 (13452)
  SS BOND              : bond        0.00305 (    4)
  SS BOND              : angle       2.47910 (    8)
  hydrogen bonds       : bond        0.04120 (  495)
  hydrogen bonds       : angle       3.68013 ( 1497)
  link_NAG-ASN         : bond        0.00538 (    4)
  link_NAG-ASN         : angle       3.37750 (   12)
  link_TRANS           : bond        0.00010 (    1)
  link_TRANS           : angle       0.07880 (    3)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 136
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6831 (mp0)
REVERT: A  156 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7394 (tt)
REVERT: A  322 GLU cc_start: 0.8362 (tt0) cc_final: 0.7767 (tm-30)
REVERT: A  323 CYS cc_start: 0.8889 (m) cc_final: 0.7815 (t)
REVERT: A  374 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8066 (tm-30)
REVERT: A  423 ASN cc_start: 0.8064 (m-40) cc_final: 0.7729 (m110)
REVERT: A  482 GLU cc_start: 0.8412 (pm20) cc_final: 0.8181 (pm20)
REVERT: A  488 ARG cc_start: 0.8071 (mtp-110) cc_final: 0.7836 (ptp90)
REVERT: A  600 CYS cc_start: 0.7984 (m) cc_final: 0.7762 (m)
REVERT: B  146 GLU cc_start: 0.8376 (pt0) cc_final: 0.7980 (pt0)
REVERT: B  180 MET cc_start: 0.6503 (ttt) cc_final: 0.5460 (tpt)
REVERT: B  243 CYS cc_start: 0.8907 (t) cc_final: 0.8356 (t)
REVERT: B  252 GLU cc_start: 0.8260 (pm20) cc_final: 0.7967 (pm20)
REVERT: B  297 MET cc_start: 0.8302 (ttm) cc_final: 0.8055 (mtp)
REVERT: B  382 ASP cc_start: 0.7763 (m-30) cc_final: 0.6812 (t70)
REVERT: C  113 THR cc_start: 0.8598 (m) cc_final: 0.8364 (p)
REVERT: C  190 ARG cc_start: 0.8047 (mtp180) cc_final: 0.7297 (mmm160)
REVERT: C  208 GLU cc_start: 0.8756 (pm20) cc_final: 0.8541 (pm20)
  outliers start: 40
  outliers final: 26
  residues processed: 167
  average time/residue: 0.0919
  time to fit residues: 22.6775
Evaluate side-chains
  154 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 126
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  123 CYS
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   94 HIS
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain E residue    9 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 83 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9980
   chunk 102 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 59 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 115 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.141606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.106229 restraints weight = 17449.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.110952 restraints weight = 10633.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.111143 restraints weight = 8307.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.111575 restraints weight = 6621.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.112690 restraints weight = 6060.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9956  Z= 0.113
  Angle     :  0.579   9.434  13475  Z= 0.287
  Chirality :  0.040   0.158   1421
  Planarity :  0.004   0.067   1765
  Dihedral  :  5.362  48.871   1423
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.68 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 25.69 %
    Favored  : 69.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.25), residues: 1176
  helix:  2.31 (0.20), residues: 618
  sheet: -0.38 (0.61), residues: 71
  loop : -1.67 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 666 
 TYR   0.023   0.001   TYR C 133 
 PHE   0.017   0.001   PHE C 153 
 TRP   0.012   0.001   TRP C 161 
 HIS   0.003   0.001   HIS C 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 9947)
  covalent geometry    : angle       0.56655 (13452)
  SS BOND              : bond        0.00323 (    4)
  SS BOND              : angle       2.93509 (    8)
  hydrogen bonds       : bond        0.04058 (  495)
  hydrogen bonds       : angle       3.65427 ( 1497)
  link_NAG-ASN         : bond        0.00375 (    4)
  link_NAG-ASN         : angle       3.22999 (   12)
  link_TRANS           : bond        0.00017 (    1)
  link_TRANS           : angle       0.03726 (    3)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 135
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5566 (mmm)
REVERT: A   58 MET cc_start: 0.8879 (mmm) cc_final: 0.8468 (mpp)
REVERT: A  139 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6744 (mp0)
REVERT: A  156 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7171 (tt)
REVERT: A  202 THR cc_start: 0.7004 (m) cc_final: 0.6494 (p)
REVERT: A  322 GLU cc_start: 0.8440 (tt0) cc_final: 0.7774 (tm-30)
REVERT: A  323 CYS cc_start: 0.8994 (m) cc_final: 0.7851 (t)
REVERT: A  374 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8231 (tm-30)
REVERT: A  423 ASN cc_start: 0.8215 (m-40) cc_final: 0.7803 (m110)
REVERT: A  471 ARG cc_start: 0.5998 (mtm-85) cc_final: 0.5562 (mtm-85)
REVERT: A  488 ARG cc_start: 0.8035 (mtp-110) cc_final: 0.7732 (ptp90)
REVERT: B  146 GLU cc_start: 0.8391 (pt0) cc_final: 0.7937 (pt0)
REVERT: B  180 MET cc_start: 0.6674 (ttt) cc_final: 0.5547 (tpt)
REVERT: B  243 CYS cc_start: 0.8898 (t) cc_final: 0.8317 (t)
REVERT: B  252 GLU cc_start: 0.8290 (pm20) cc_final: 0.7921 (pm20)
REVERT: B  382 ASP cc_start: 0.7976 (m-30) cc_final: 0.6938 (t70)
REVERT: C  171 LYS cc_start: 0.8017 (tttp) cc_final: 0.7695 (tttm)
REVERT: C  190 ARG cc_start: 0.8096 (mtp180) cc_final: 0.7273 (mmm160)
  outliers start: 48
  outliers final: 30
  residues processed: 171
  average time/residue: 0.0921
  time to fit residues: 23.2532
Evaluate side-chains
  158 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  123 CYS
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  572 ILE
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  277 CYS
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   94 HIS
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain E residue    9 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 111 optimal weight:    3.9990
   chunk 114 optimal weight:    0.0570
   chunk 65 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    1.4104

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

Flipped N/Q/H residues before XYZ refinement:
** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.138227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.099459 restraints weight = 16821.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.103071 restraints weight = 9215.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.104802 restraints weight = 5858.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107139 restraints weight = 4942.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.107640 restraints weight = 4241.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.3835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9956  Z= 0.137
  Angle     :  0.614  10.124  13475  Z= 0.305
  Chirality :  0.041   0.175   1421
  Planarity :  0.004   0.068   1765
  Dihedral  :  5.040  46.048   1423
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.59 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 26.57 %
    Favored  : 68.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.25), residues: 1176
  helix:  2.31 (0.20), residues: 618
  sheet: -0.29 (0.60), residues: 73
  loop : -1.80 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 212 
 TYR   0.019   0.001   TYR A 628 
 PHE   0.020   0.001   PHE C 153 
 TRP   0.012   0.001   TRP C 161 
 HIS   0.004   0.001   HIS A 565 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9947)
  covalent geometry    : angle       0.60387 (13452)
  SS BOND              : bond        0.00320 (    4)
  SS BOND              : angle       2.81873 (    8)
  hydrogen bonds       : bond        0.04509 (  495)
  hydrogen bonds       : angle       3.79367 ( 1497)
  link_NAG-ASN         : bond        0.00294 (    4)
  link_NAG-ASN         : angle       3.04312 (   12)
  link_TRANS           : bond        0.00014 (    1)
  link_TRANS           : angle       0.05411 (    3)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 129
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.6800 (mp0)
REVERT: A  156 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7460 (tt)
REVERT: A  286 LEU cc_start: 0.8423 (mt) cc_final: 0.8155 (mp)
REVERT: A  322 GLU cc_start: 0.8367 (tt0) cc_final: 0.7815 (tm-30)
REVERT: A  323 CYS cc_start: 0.8986 (m) cc_final: 0.7893 (t)
REVERT: A  374 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8342 (tm-30)
REVERT: A  471 ARG cc_start: 0.6436 (mtm-85) cc_final: 0.5644 (mtm-85)
REVERT: A  482 GLU cc_start: 0.8413 (pm20) cc_final: 0.8142 (pm20)
REVERT: A  488 ARG cc_start: 0.8057 (mtp-110) cc_final: 0.7712 (ptp90)
REVERT: B  146 GLU cc_start: 0.8432 (pt0) cc_final: 0.8056 (pt0)
REVERT: B  180 MET cc_start: 0.6517 (ttt) cc_final: 0.5485 (tpt)
REVERT: B  243 CYS cc_start: 0.8907 (t) cc_final: 0.8254 (t)
REVERT: B  252 GLU cc_start: 0.8326 (pm20) cc_final: 0.7979 (pm20)
REVERT: B  297 MET cc_start: 0.8333 (ttm) cc_final: 0.8068 (mtp)
REVERT: B  382 ASP cc_start: 0.7796 (m-30) cc_final: 0.6895 (t70)
REVERT: C   59 ARG cc_start: 0.8001 (ptp-110) cc_final: 0.7750 (ptp-110)
REVERT: C  171 LYS cc_start: 0.8633 (tttp) cc_final: 0.8265 (tttm)
REVERT: C  190 ARG cc_start: 0.7982 (mtp180) cc_final: 0.7256 (mmm160)
  outliers start: 47
  outliers final: 35
  residues processed: 165
  average time/residue: 0.0931
  time to fit residues: 22.5567
Evaluate side-chains
  160 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 123
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  123 CYS
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  572 ILE
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  277 CYS
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   86 PHE
Chi-restraints excluded: chain C residue   94 HIS
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain E residue    9 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 115 optimal weight:    0.1980
   chunk 30 optimal weight:    0.7980
   chunk 114 optimal weight:    0.9980
   chunk 81 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 60 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 423 ASN
** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.140017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.099227 restraints weight = 16801.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.103674 restraints weight = 9092.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.106774 restraints weight = 6178.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.108866 restraints weight = 4774.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.110198 restraints weight = 4024.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.3922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9956  Z= 0.109
  Angle     :  0.602  10.805  13475  Z= 0.293
  Chirality :  0.041   0.170   1421
  Planarity :  0.004   0.068   1765
  Dihedral  :  4.792  45.338   1423
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.42 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 27.26 %
    Favored  : 68.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.25), residues: 1176
  helix:  2.34 (0.20), residues: 620
  sheet: -0.19 (0.59), residues: 73
  loop : -1.78 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 107 
 TYR   0.019   0.001   TYR A 628 
 PHE   0.016   0.001   PHE C 153 
 TRP   0.010   0.001   TRP C 161 
 HIS   0.003   0.000   HIS C  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9947)
  covalent geometry    : angle       0.59228 (13452)
  SS BOND              : bond        0.00333 (    4)
  SS BOND              : angle       2.58319 (    8)
  hydrogen bonds       : bond        0.03938 (  495)
  hydrogen bonds       : angle       3.67724 ( 1497)
  link_NAG-ASN         : bond        0.00361 (    4)
  link_NAG-ASN         : angle       2.97592 (   12)
  link_TRANS           : bond        0.00006 (    1)
  link_TRANS           : angle       0.03748 (    3)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 130
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 LEU cc_start: 0.7786 (tt) cc_final: 0.7489 (tp)
REVERT: A   88 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7517 (p0)
REVERT: A  139 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6709 (mp0)
REVERT: A  156 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7383 (tt)
REVERT: A  202 THR cc_start: 0.7015 (m) cc_final: 0.6524 (p)
REVERT: A  218 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7278 (mp0)
REVERT: A  286 LEU cc_start: 0.8441 (mt) cc_final: 0.8181 (mp)
REVERT: A  322 GLU cc_start: 0.8331 (tt0) cc_final: 0.7782 (tm-30)
REVERT: A  374 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8360 (tm-30)
REVERT: A  471 ARG cc_start: 0.6247 (mtm-85) cc_final: 0.5644 (mtm-85)
REVERT: A  482 GLU cc_start: 0.8405 (pm20) cc_final: 0.8112 (pm20)
REVERT: A  488 ARG cc_start: 0.8044 (mtp-110) cc_final: 0.7713 (ptp90)
REVERT: B  146 GLU cc_start: 0.8422 (pt0) cc_final: 0.8054 (pt0)
REVERT: B  180 MET cc_start: 0.6375 (ttt) cc_final: 0.5414 (tpt)
REVERT: B  191 LEU cc_start: 0.8939 (mm) cc_final: 0.8734 (mp)
REVERT: B  243 CYS cc_start: 0.8852 (t) cc_final: 0.8191 (t)
REVERT: B  252 GLU cc_start: 0.8334 (pm20) cc_final: 0.8000 (pm20)
REVERT: B  288 TYR cc_start: 0.6987 (m-80) cc_final: 0.6784 (m-80)
REVERT: B  382 ASP cc_start: 0.7760 (m-30) cc_final: 0.6907 (t70)
REVERT: C   59 ARG cc_start: 0.8019 (ptp-110) cc_final: 0.7817 (ptp-110)
REVERT: C  190 ARG cc_start: 0.7922 (mtp180) cc_final: 0.7267 (mmm160)
  outliers start: 40
  outliers final: 30
  residues processed: 160
  average time/residue: 0.0950
  time to fit residues: 22.2102
Evaluate side-chains
  158 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 124
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  123 CYS
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  343 TYR
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  572 ILE
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain E residue    9 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 52 optimal weight:    6.9990
   chunk 80 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 30 optimal weight:    0.4980
   chunk 28 optimal weight:    9.9990
   chunk 55 optimal weight:    0.0980
   chunk 44 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.139511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.098756 restraints weight = 16587.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.103040 restraints weight = 9181.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.105991 restraints weight = 6304.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.108020 restraints weight = 4931.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.109381 restraints weight = 4172.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9956  Z= 0.120
  Angle     :  0.607  11.319  13475  Z= 0.297
  Chirality :  0.041   0.166   1421
  Planarity :  0.004   0.068   1765
  Dihedral  :  4.676  44.636   1423
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.85 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 27.07 %
    Favored  : 68.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.25), residues: 1176
  helix:  2.31 (0.20), residues: 625
  sheet: -0.15 (0.60), residues: 73
  loop : -1.82 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 212 
 TYR   0.018   0.001   TYR A 628 
 PHE   0.018   0.001   PHE C 153 
 TRP   0.010   0.001   TRP C 161 
 HIS   0.003   0.001   HIS A 565 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9947)
  covalent geometry    : angle       0.59810 (13452)
  SS BOND              : bond        0.00317 (    4)
  SS BOND              : angle       2.60574 (    8)
  hydrogen bonds       : bond        0.04099 (  495)
  hydrogen bonds       : angle       3.70732 ( 1497)
  link_NAG-ASN         : bond        0.00319 (    4)
  link_NAG-ASN         : angle       2.84592 (   12)
  link_TRANS           : bond        0.00003 (    1)
  link_TRANS           : angle       0.05231 (    3)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 125
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 LEU cc_start: 0.7747 (tt) cc_final: 0.7450 (tp)
REVERT: A  139 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6738 (mp0)
REVERT: A  156 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7397 (tt)
REVERT: A  202 THR cc_start: 0.7161 (m) cc_final: 0.6688 (p)
REVERT: A  218 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7289 (mp0)
REVERT: A  286 LEU cc_start: 0.8455 (mt) cc_final: 0.8193 (mp)
REVERT: A  322 GLU cc_start: 0.8379 (tt0) cc_final: 0.7797 (tm-30)
REVERT: A  323 CYS cc_start: 0.8919 (m) cc_final: 0.7843 (t)
REVERT: A  374 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8356 (tm-30)
REVERT: A  471 ARG cc_start: 0.6370 (mtm-85) cc_final: 0.5702 (mtm-85)
REVERT: A  488 ARG cc_start: 0.8038 (mtp-110) cc_final: 0.7696 (ptp90)
REVERT: A  600 CYS cc_start: 0.7506 (m) cc_final: 0.6876 (t)
REVERT: B  146 GLU cc_start: 0.8429 (pt0) cc_final: 0.8037 (pt0)
REVERT: B  180 MET cc_start: 0.6375 (ttt) cc_final: 0.5416 (tpt)
REVERT: B  191 LEU cc_start: 0.8955 (mm) cc_final: 0.8737 (mp)
REVERT: B  243 CYS cc_start: 0.8880 (t) cc_final: 0.8201 (t)
REVERT: B  252 GLU cc_start: 0.8297 (pm20) cc_final: 0.7956 (pm20)
REVERT: B  288 TYR cc_start: 0.7042 (m-80) cc_final: 0.6840 (m-80)
REVERT: B  382 ASP cc_start: 0.7768 (m-30) cc_final: 0.6923 (t70)
REVERT: C   59 ARG cc_start: 0.8044 (ptp-110) cc_final: 0.7833 (ptp-110)
REVERT: C  107 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7172 (p90)
REVERT: C  190 ARG cc_start: 0.7982 (mtp180) cc_final: 0.7602 (mmm-85)
  outliers start: 42
  outliers final: 33
  residues processed: 154
  average time/residue: 0.0924
  time to fit residues: 20.9182
Evaluate side-chains
  157 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 120
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  123 CYS
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  136 MET
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  343 TYR
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  572 ILE
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  696 MET
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain E residue    9 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0060
   chunk 82 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0970
   chunk 27 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0010
   chunk 55 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   overall best weight:    0.3600

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

Flipped N/Q/H residues before XYZ refinement:
** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.142451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.101841 restraints weight = 16536.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.106453 restraints weight = 8771.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.109607 restraints weight = 5893.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.111781 restraints weight = 4532.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.113224 restraints weight = 3799.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.4121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9956  Z= 0.105
  Angle     :  0.606  11.783  13475  Z= 0.292
  Chirality :  0.040   0.186   1421
  Planarity :  0.004   0.068   1765
  Dihedral  :  4.483  44.286   1423
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.59 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 27.95 %
    Favored  : 68.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.25), residues: 1176
  helix:  2.33 (0.20), residues: 626
  sheet: -0.18 (0.54), residues: 80
  loop : -1.85 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 666 
 TYR   0.016   0.001   TYR A 628 
 PHE   0.014   0.001   PHE C 153 
 TRP   0.007   0.001   TRP C 161 
 HIS   0.003   0.000   HIS A 565 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 9947)
  covalent geometry    : angle       0.59769 (13452)
  SS BOND              : bond        0.00322 (    4)
  SS BOND              : angle       2.51405 (    8)
  hydrogen bonds       : bond        0.03470 (  495)
  hydrogen bonds       : angle       3.60600 ( 1497)
  link_NAG-ASN         : bond        0.00402 (    4)
  link_NAG-ASN         : angle       2.82563 (   12)
  link_TRANS           : bond        0.00017 (    1)
  link_TRANS           : angle       0.06565 (    3)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 134
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.8949 (mmm) cc_final: 0.8536 (mpp)
REVERT: A   73 LEU cc_start: 0.7695 (tt) cc_final: 0.7430 (tp)
REVERT: A  139 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6771 (mp0)
REVERT: A  156 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7292 (tt)
REVERT: A  198 LYS cc_start: 0.8923 (mmtm) cc_final: 0.8646 (mmtt)
REVERT: A  218 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7248 (mp0)
REVERT: A  286 LEU cc_start: 0.8455 (mt) cc_final: 0.8169 (mp)
REVERT: A  322 GLU cc_start: 0.8356 (tt0) cc_final: 0.7799 (tm-30)
REVERT: A  347 MET cc_start: 0.8345 (tpp) cc_final: 0.7786 (mmp)
REVERT: A  374 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8394 (tm-30)
REVERT: A  471 ARG cc_start: 0.6110 (mtm-85) cc_final: 0.5570 (mtm-85)
REVERT: A  488 ARG cc_start: 0.8001 (mtp-110) cc_final: 0.7665 (ptp90)
REVERT: A  600 CYS cc_start: 0.7448 (m) cc_final: 0.6793 (t)
REVERT: B  146 GLU cc_start: 0.8247 (pt0) cc_final: 0.7828 (pt0)
REVERT: B  180 MET cc_start: 0.6338 (ttt) cc_final: 0.5409 (tpt)
REVERT: B  243 CYS cc_start: 0.8847 (t) cc_final: 0.8239 (t)
REVERT: B  252 GLU cc_start: 0.8248 (pm20) cc_final: 0.7906 (pm20)
REVERT: B  382 ASP cc_start: 0.7727 (m-30) cc_final: 0.6907 (t70)
REVERT: C   48 PHE cc_start: 0.7468 (m-80) cc_final: 0.7156 (m-10)
REVERT: C   59 ARG cc_start: 0.8051 (ptp-110) cc_final: 0.7755 (ptp-110)
REVERT: C  122 ARG cc_start: 0.8039 (mmt180) cc_final: 0.7830 (mmt180)
REVERT: C  190 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7601 (mmm-85)
  outliers start: 35
  outliers final: 26
  residues processed: 156
  average time/residue: 0.1028
  time to fit residues: 22.8680
Evaluate side-chains
  153 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  572 ILE
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  696 MET
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain E residue    9 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0670
   chunk 98 optimal weight:    0.7980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.142085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.101214 restraints weight = 16831.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.105805 restraints weight = 9039.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.108956 restraints weight = 6096.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.111096 restraints weight = 4700.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.112536 restraints weight = 3941.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.4193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9956  Z= 0.110
  Angle     :  0.621  11.868  13475  Z= 0.300
  Chirality :  0.040   0.186   1421
  Planarity :  0.004   0.068   1765
  Dihedral  :  4.385  43.872   1423
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.34 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 28.25 %
    Favored  : 68.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.25), residues: 1176
  helix:  2.38 (0.20), residues: 625
  sheet: -0.00 (0.56), residues: 71
  loop : -1.86 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 666 
 TYR   0.015   0.001   TYR A 628 
 PHE   0.016   0.001   PHE C 153 
 TRP   0.008   0.001   TRP C 161 
 HIS   0.002   0.000   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9947)
  covalent geometry    : angle       0.61279 (13452)
  SS BOND              : bond        0.00300 (    4)
  SS BOND              : angle       2.51135 (    8)
  hydrogen bonds       : bond        0.03566 (  495)
  hydrogen bonds       : angle       3.61528 ( 1497)
  link_NAG-ASN         : bond        0.00371 (    4)
  link_NAG-ASN         : angle       2.70433 (   12)
  link_TRANS           : bond        0.00029 (    1)
  link_TRANS           : angle       0.07621 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1840.38 seconds
wall clock time: 32 minutes 38.34 seconds (1958.34 seconds total)