Starting phenix.real_space_refine
on Sat May  2 21:01:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y6i_33641/05_2026/7y6i_33641_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y6i_33641/05_2026/7y6i_33641.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y6i_33641/05_2026/7y6i_33641_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y6i_33641/05_2026/7y6i_33641_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y6i_33641/05_2026/7y6i_33641.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y6i_33641/05_2026/7y6i_33641.map"
  }
  resolution = 2.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.102
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: 7
    Type Number    sf(0)   Gaussians
     P      17      5.49       5
     S      42      5.16       5
     Cl      4      4.86       5
     Na      4      4.78       5
     C    5544      2.51       5
     N    1137      2.21       5
     O    1428      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8176
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3564
          Classifications: {'peptide': 469}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 450}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 3564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3564
          Classifications: {'peptide': 469}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 450}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      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
    Chain: "D"
      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
    Chain: "A"
      Number of atoms: 519
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 519
          Unusual residues: {' CL': 2, ' NA': 2, 'LPE': 4, 'NAG': 1, 'POV': 5, 'Y01': 3}
          Classifications: {'undetermined': 17}
          Link IDs: {None: 16}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 467
          Unusual residues: {' CL': 2, ' NA': 2, 'LPE': 4, 'NAG': 1, 'POV': 4, 'Y01': 3}
          Classifications: {'undetermined': 16}
          Link IDs: {None: 15}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.04, per 1000 atoms: 0.25
  Number of scatterers: 8176
  At special positions: 0
  Unit cell: (80.542, 109.83, 94.14, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Cl      4     17.00
     S      42     16.00
     P      17     15.00
     Na      4     11.00
     O    1428      8.00
     N    1137      7.00
     C    5544      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 416 " - pdb=" SG  CYS A 421 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 430 " - pdb=" SG  CYS A 436 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 416 " - pdb=" SG  CYS B 421 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 430 " - pdb=" SG  CYS B 436 " distance=2.04

  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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A1117 " - " ASN A 406 "
      " NAG B1116 " - " ASN B 406 "
      " NAG C   1 " - " ASN A 426 "
      " NAG D   1 " - " ASN B 426 "
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 285.9 milliseconds
  

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1700

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 0 sheets defined
      78.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 142 through 151
    Processing helix  chain 'A' and resid 153 through 158
    Processing helix  chain 'A' and resid 158 through 194
      removed outlier: 6.786A  pdb=" N   ILE A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 9.201A  pdb=" N   VAL A 169 " --> pdb=" O   GLN A 165 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LEU A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 212
    Processing helix  chain 'A' and resid 212 through 249
      removed outlier: 3.718A  pdb=" N   ALA A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA A 232 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 277
      removed outlier: 3.600A  pdb=" N   ILE A 260 " --> pdb=" O   PRO A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 306
      removed outlier: 3.547A  pdb=" N   LEU A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 316
    Processing helix  chain 'A' and resid 321 through 329
    Processing helix  chain 'A' and resid 339 through 348
      removed outlier: 3.644A  pdb=" N   ILE A 346 " --> pdb=" O   GLY A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 351
      No H-bonds generated for 'chain 'A' and resid 349 through 351'
    Processing helix  chain 'A' and resid 353 through 361
      removed outlier: 4.212A  pdb=" N   GLY A 357 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA A 358 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 395
      Proline residue:  A 372  - end of helix
    Processing helix  chain 'A' and resid 418 through 424
      removed outlier: 3.559A  pdb=" N   CYS A 421 " --> pdb=" O   GLY A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 434
    Processing helix  chain 'A' and resid 445 through 451
    Processing helix  chain 'A' and resid 453 through 486
      removed outlier: 3.758A  pdb=" N   ILE A 457 " --> pdb=" O   PHE A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 497
      removed outlier: 3.645A  pdb=" N   PHE A 494 " --> pdb=" O   LEU A 491 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLY A 496 " --> pdb=" O   GLY A 493 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   LYS A 497 " --> pdb=" O   PHE A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 521
    Processing helix  chain 'A' and resid 524 through 553
      Proline residue:  A 530  - end of helix
    Processing helix  chain 'A' and resid 566 through 585
      removed outlier: 3.628A  pdb=" N   THR A 585 " --> pdb=" O   MET A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 605
      removed outlier: 3.611A  pdb=" N   ALA A 589 " --> pdb=" O   THR A 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 151
      removed outlier: 4.504A  pdb=" N   ILE B 144 " --> pdb=" O   LYS B 140 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   ARG B 145 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASN B 149 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 158
      removed outlier: 4.105A  pdb=" N   TYR B 156 " --> pdb=" O   GLY B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 166
    Processing helix  chain 'B' and resid 167 through 194
      removed outlier: 3.528A  pdb=" N   VAL B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 211
    Processing helix  chain 'B' and resid 212 through 249
      removed outlier: 3.760A  pdb=" N   SER B 218 " --> pdb=" O   GLU B 214 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B 232 " --> pdb=" O   ALA B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 277
    Processing helix  chain 'B' and resid 281 through 306
      removed outlier: 4.696A  pdb=" N   VAL B 287 " --> pdb=" O   SER B 283 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU B 288 " --> pdb=" O   LYS B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 316
    Processing helix  chain 'B' and resid 321 through 330
      removed outlier: 4.211A  pdb=" N   VAL B 330 " --> pdb=" O   VAL B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 348
      removed outlier: 3.627A  pdb=" N   ILE B 346 " --> pdb=" O   GLY B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 351
      No H-bonds generated for 'chain 'B' and resid 349 through 351'
    Processing helix  chain 'B' and resid 353 through 358
    Processing helix  chain 'B' and resid 366 through 394
      Proline residue:  B 372  - end of helix
    Processing helix  chain 'B' and resid 418 through 424
    Processing helix  chain 'B' and resid 428 through 434
    Processing helix  chain 'B' and resid 445 through 451
      removed outlier: 3.692A  pdb=" N   MET B 449 " --> pdb=" O   GLN B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 486
      removed outlier: 3.841A  pdb=" N   ILE B 457 " --> pdb=" O   PHE B 453 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU B 470 " --> pdb=" O   LEU B 466 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LYS B 478 " --> pdb=" O   VAL B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 505 through 521
    Processing helix  chain 'B' and resid 524 through 553
      Proline residue:  B 530  - end of helix
    Processing helix  chain 'B' and resid 566 through 585
      removed outlier: 3.631A  pdb=" N   THR B 585 " --> pdb=" O   MET B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 605
      removed outlier: 3.618A  pdb=" N   ALA B 589 " --> pdb=" O   THR B 585 " (cutoff:3.500A)

    520 hydrogen bonds defined for protein.
    1515 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: 1.23

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 1120
        1.28 -     1.41: 2011
        1.41 -     1.54: 5101
        1.54 -     1.68: 58
        1.68 -     1.81: 63
  Bond restraints: 8353
  Sorted by residual:
  bond pdb="C310 POV A1116 "
       pdb="C311 POV A1116 "
    ideal  model  delta    sigma   weight residual
    1.523  1.375  0.148 2.00e-02 2.50e+03 5.49e+01
  bond pdb=" C31 POV B1115 "
       pdb=" O31 POV B1115 "
    ideal  model  delta    sigma   weight residual
    1.327  1.471 -0.144 2.00e-02 2.50e+03 5.16e+01
  bond pdb=" C31 POV B1101 "
       pdb=" O31 POV B1101 "
    ideal  model  delta    sigma   weight residual
    1.327  1.467 -0.140 2.00e-02 2.50e+03 4.92e+01
  bond pdb=" C21 POV A1116 "
       pdb=" O21 POV A1116 "
    ideal  model  delta    sigma   weight residual
    1.330  1.464 -0.134 2.00e-02 2.50e+03 4.50e+01
  bond pdb=" C21 POV B1102 "
       pdb=" O21 POV B1102 "
    ideal  model  delta    sigma   weight residual
    1.330  1.464 -0.134 2.00e-02 2.50e+03 4.49e+01
  ... (remaining 8348 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.21: 10978
        5.21 -    10.41: 205
       10.41 -    15.62: 76
       15.62 -    20.82: 22
       20.82 -    26.03: 10
  Bond angle restraints: 11291
  Sorted by residual:
  angle pdb=" O32 LPE B1110 "
        pdb=" P   LPE B1110 "
        pdb=" O33 LPE B1110 "
      ideal   model   delta    sigma   weight residual
     110.64   84.61   26.03 3.00e+00 1.11e-01 7.53e+01
  angle pdb=" O11 POV A1116 "
        pdb=" P   POV A1116 "
        pdb=" O12 POV A1116 "
      ideal   model   delta    sigma   weight residual
      97.67  123.02  -25.35 3.00e+00 1.11e-01 7.14e+01
  angle pdb=" C37 POV A1116 "
        pdb=" C38 POV A1116 "
        pdb=" C39 POV A1116 "
      ideal   model   delta    sigma   weight residual
     113.94   89.39   24.55 3.00e+00 1.11e-01 6.70e+01
  angle pdb=" C27 POV B1115 "
        pdb=" C28 POV B1115 "
        pdb=" C29 POV B1115 "
      ideal   model   delta    sigma   weight residual
     112.18   87.68   24.50 3.00e+00 1.11e-01 6.67e+01
  angle pdb=" O3  LPE B1110 "
        pdb=" P   LPE B1110 "
        pdb=" O32 LPE B1110 "
      ideal   model   delta    sigma   weight residual
     103.09  126.46  -23.37 3.00e+00 1.11e-01 6.07e+01
  ... (remaining 11286 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.67: 4818
       26.67 -    53.35: 456
       53.35 -    80.02: 67
       80.02 -   106.70: 37
      106.70 -   133.37: 7
  Dihedral angle restraints: 5385
    sinusoidal: 2711
      harmonic: 2674
  Sorted by residual:
  dihedral pdb=" CB  CYS B 416 "
           pdb=" SG  CYS B 416 "
           pdb=" SG  CYS B 421 "
           pdb=" CB  CYS B 421 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  151.35  -58.35     1      1.00e+01 1.00e-02 4.56e+01
  dihedral pdb=" C39 POV A1112 "
           pdb="C310 POV A1112 "
           pdb="C311 POV A1112 "
           pdb="C312 POV A1112 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.49   47.12  133.37     1      3.00e+01 1.11e-03 1.80e+01
  dihedral pdb=" C39 POV A1116 "
           pdb="C310 POV A1116 "
           pdb="C311 POV A1116 "
           pdb="C312 POV A1116 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.49   47.43  133.06     1      3.00e+01 1.11e-03 1.79e+01
  ... (remaining 5382 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.164: 1260
       0.164 -    0.328: 8
       0.328 -    0.492: 1
       0.492 -    0.656: 1
       0.656 -    0.820: 1
  Chirality restraints: 1271
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN B 426 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.58   -0.82 2.00e-01 2.50e+01 1.68e+01
  chirality pdb=" C2  LPE B1111 "
            pdb=" C1  LPE B1111 "
            pdb=" C3  LPE B1111 "
            pdb=" O2H LPE B1111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.86    0.57 2.00e-01 2.50e+01 8.22e+00
  chirality pdb=" CA  ARG B 334 "
            pdb=" N   ARG B 334 "
            pdb=" C   ARG B 334 "
            pdb=" CB  ARG B 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.03e+00
  ... (remaining 1268 not shown)

  Planarity restraints: 1271
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.336 2.00e-02 2.50e+03   2.89e-01 1.05e+03
        pdb=" C7  NAG D   1 "    0.077 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.036 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.504 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.209 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A1117 "   -0.176 2.00e-02 2.50e+03   1.49e-01 2.76e+02
        pdb=" C7  NAG A1117 "    0.037 2.00e-02 2.50e+03
        pdb=" C8  NAG A1117 "    0.039 2.00e-02 2.50e+03
        pdb=" N2  NAG A1117 "    0.239 2.00e-02 2.50e+03
        pdb=" O7  NAG A1117 "   -0.139 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "    0.112 2.00e-02 2.50e+03   9.26e-02 1.07e+02
        pdb=" C7  NAG D   2 "   -0.031 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.084 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "   -0.148 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1268 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 81
        2.60 -     3.18: 6983
        3.18 -     3.75: 13049
        3.75 -     4.33: 19250
        4.33 -     4.90: 31498
  Nonbonded interactions: 70861
  Sorted by model distance:
  nonbonded pdb=" O2H LPE B1110 "
            pdb=" O31 LPE B1110 "
     model   vdw
     2.025 3.040
  nonbonded pdb=" O   SER A 345 "
            pdb=" OG  SER A 533 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   SER B 345 "
            pdb=" OG  SER B 533 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OH  TYR A 156 "
            pdb=" OG  SER A 296 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OH  TYR B 156 "
            pdb=" OG  SER B 296 "
     model   vdw
     2.234 3.040
  ... (remaining 70856 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 137 through 605 or resid 1103 through 1104 or resid 1107 o \ 
r resid 1110 through 1111 or resid 1114 through 1115))
  selection = (chain 'B' and (resid 137 through 605 or resid 1103 through 1104 or resid 1107 o \ 
r resid 1110 through 1111 or resid 1114 through 1115))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.080
  Find NCS groups from input model:        0.130
  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:6.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
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      :  0.015   0.148   8363  Z= 0.782
  Angle     :  2.020  26.030  11317  Z= 0.757
  Chirality :  0.054   0.820   1271
  Planarity :  0.010   0.289   1267
  Dihedral  : 20.978 133.370   3673
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 20.73
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.21 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 19.28 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.28), residues: 934
  helix:  1.65 (0.20), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.62 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 559 
 TYR   0.017   0.001   TYR B 320 
 PHE   0.011   0.001   PHE B 494 
 TRP   0.016   0.001   TRP A 161 
 HIS   0.002   0.000   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.01547 ( 8353)
  covalent geometry    : angle       2.01515 (11291)
  SS BOND              : bond        0.00499 (    4)
  SS BOND              : angle       0.77202 (    8)
  hydrogen bonds       : bond        0.13169 (  520)
  hydrogen bonds       : angle       5.22888 ( 1515)
  link_BETA1-4         : bond        0.01471 (    2)
  link_BETA1-4         : angle       2.97374 (    6)
  link_NAG-ASN         : bond        0.01238 (    4)
  link_NAG-ASN         : angle       4.63220 (   12)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A  497 LYS cc_start: 0.7538 (ptmt) cc_final: 0.6013 (mmtm)
REVERT: A  581 MET cc_start: 0.8921 (ttm) cc_final: 0.8645 (ttm)
  outliers start: 8
  outliers final: 5
  residues processed: 82
  average time/residue: 0.4406
  time to fit residues: 39.1727
Evaluate side-chains
  73 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain B residue  292 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.168864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.131412 restraints weight = 7404.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.58
r_work: 0.3227 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   8363  Z= 0.143
  Angle     :  0.617   7.231  11317  Z= 0.288
  Chirality :  0.042   0.235   1271
  Planarity :  0.004   0.048   1267
  Dihedral  : 20.373 140.384   2212
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.95 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.28), residues: 934
  helix:  1.62 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.58 (0.35), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 243 
 TYR   0.010   0.001   TYR A 204 
 PHE   0.015   0.001   PHE A 545 
 TRP   0.013   0.001   TRP B 425 
 HIS   0.008   0.002   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8353)
  covalent geometry    : angle       0.60729 (11291)
  SS BOND              : bond        0.00396 (    4)
  SS BOND              : angle       1.00909 (    8)
  hydrogen bonds       : bond        0.04276 (  520)
  hydrogen bonds       : angle       4.24137 ( 1515)
  link_BETA1-4         : bond        0.00097 (    2)
  link_BETA1-4         : angle       0.84061 (    6)
  link_NAG-ASN         : bond        0.00551 (    4)
  link_NAG-ASN         : angle       3.27756 (   12)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A  147 MET cc_start: 0.8421 (mtt) cc_final: 0.8175 (mtt)
REVERT: A  497 LYS cc_start: 0.7587 (ptmt) cc_final: 0.5973 (mmtm)
REVERT: A  581 MET cc_start: 0.8797 (ttm) cc_final: 0.8531 (ttm)
REVERT: B  248 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6681 (pp20)
REVERT: B  492 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7278 (pp)
  outliers start: 20
  outliers final: 10
  residues processed: 86
  average time/residue: 0.4191
  time to fit residues: 39.3008
Evaluate side-chains
  77 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain A residue  448 SER
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain B residue  248 GLU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  561 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3807 r_free = 0.3807 target = 0.160959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.121384 restraints weight = 7422.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 1.66
r_work: 0.3111 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   8363  Z= 0.183
  Angle     :  0.591   6.934  11317  Z= 0.289
  Chirality :  0.042   0.182   1271
  Planarity :  0.005   0.046   1267
  Dihedral  : 18.731 129.266   2208
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.35 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.28), residues: 934
  helix:  1.48 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.50 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 243 
 TYR   0.012   0.002   TYR A 204 
 PHE   0.015   0.002   PHE A 535 
 TRP   0.010   0.001   TRP B 281 
 HIS   0.007   0.002   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 8353)
  covalent geometry    : angle       0.58490 (11291)
  SS BOND              : bond        0.00361 (    4)
  SS BOND              : angle       1.08886 (    8)
  hydrogen bonds       : bond        0.04520 (  520)
  hydrogen bonds       : angle       4.28133 ( 1515)
  link_BETA1-4         : bond        0.00337 (    2)
  link_BETA1-4         : angle       1.10504 (    6)
  link_NAG-ASN         : bond        0.00556 (    4)
  link_NAG-ASN         : angle       2.51948 (   12)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  497 LYS cc_start: 0.7633 (ptmt) cc_final: 0.5988 (mmtm)
REVERT: A  581 MET cc_start: 0.8698 (ttm) cc_final: 0.8444 (ttm)
REVERT: B  248 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6670 (pp20)
REVERT: B  343 MET cc_start: 0.8777 (mmt) cc_final: 0.8362 (mmt)
REVERT: B  405 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7992 (mp)
REVERT: B  488 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8141 (mp)
REVERT: B  559 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7103 (mmt180)
  outliers start: 21
  outliers final: 10
  residues processed: 91
  average time/residue: 0.4476
  time to fit residues: 44.1293
Evaluate side-chains
  85 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain A residue  561 SER
Chi-restraints excluded: chain B residue  243 ARG
Chi-restraints excluded: chain B residue  248 GLU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  483 LEU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  559 ARG
Chi-restraints excluded: chain B residue  561 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 82 optimal weight:    0.0020
   chunk 20 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
B 359 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.166576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.128696 restraints weight = 7471.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 1.59
r_work: 0.3198 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8363  Z= 0.123
  Angle     :  0.503   5.456  11317  Z= 0.252
  Chirality :  0.039   0.184   1271
  Planarity :  0.004   0.047   1267
  Dihedral  : 17.781 123.727   2208
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 19.15 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.28), residues: 934
  helix:  1.68 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.53 (0.35), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 145 
 TYR   0.013   0.001   TYR B 320 
 PHE   0.014   0.001   PHE B 494 
 TRP   0.010   0.001   TRP A 161 
 HIS   0.005   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8353)
  covalent geometry    : angle       0.49606 (11291)
  SS BOND              : bond        0.00254 (    4)
  SS BOND              : angle       0.91707 (    8)
  hydrogen bonds       : bond        0.03816 (  520)
  hydrogen bonds       : angle       4.03965 ( 1515)
  link_BETA1-4         : bond        0.00406 (    2)
  link_BETA1-4         : angle       1.44180 (    6)
  link_NAG-ASN         : bond        0.00533 (    4)
  link_NAG-ASN         : angle       2.40646 (   12)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 ILE cc_start: 0.7868 (mt) cc_final: 0.7614 (mm)
REVERT: A  497 LYS cc_start: 0.7567 (ptmt) cc_final: 0.5980 (mmtm)
REVERT: A  581 MET cc_start: 0.8647 (ttm) cc_final: 0.8425 (ttm)
REVERT: B  248 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6709 (pp20)
REVERT: B  343 MET cc_start: 0.8744 (mmt) cc_final: 0.8447 (mmt)
REVERT: B  405 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8014 (mp)
REVERT: B  559 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7080 (mmt180)
  outliers start: 21
  outliers final: 8
  residues processed: 87
  average time/residue: 0.4132
  time to fit residues: 39.2065
Evaluate side-chains
  79 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain A residue  448 SER
Chi-restraints excluded: chain A residue  561 SER
Chi-restraints excluded: chain B residue  248 GLU
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  559 ARG
Chi-restraints excluded: chain B residue  561 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0770
   chunk 51 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   overall best weight:    0.7340

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

Flipped N/Q/H residues before XYZ refinement:
A 299 ASN
B 566 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.165442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.127460 restraints weight = 7468.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.57
r_work: 0.3185 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   8363  Z= 0.136
  Angle     :  0.527   5.570  11317  Z= 0.261
  Chirality :  0.040   0.263   1271
  Planarity :  0.004   0.049   1267
  Dihedral  : 17.503 119.163   2207
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 19.28 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.28), residues: 934
  helix:  1.69 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.51 (0.35), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 145 
 TYR   0.011   0.001   TYR A 204 
 PHE   0.013   0.002   PHE B 494 
 TRP   0.010   0.001   TRP B 425 
 HIS   0.004   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8353)
  covalent geometry    : angle       0.51605 (11291)
  SS BOND              : bond        0.00297 (    4)
  SS BOND              : angle       1.43501 (    8)
  hydrogen bonds       : bond        0.03934 (  520)
  hydrogen bonds       : angle       4.05093 ( 1515)
  link_BETA1-4         : bond        0.00148 (    2)
  link_BETA1-4         : angle       2.44832 (    6)
  link_NAG-ASN         : bond        0.00757 (    4)
  link_NAG-ASN         : angle       2.67985 (   12)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7697 (mm)
REVERT: A  371 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7582 (mt)
REVERT: A  497 LYS cc_start: 0.7603 (ptmt) cc_final: 0.5977 (mmtm)
REVERT: B  248 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6724 (pp20)
REVERT: B  405 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7864 (OUTLIER)
REVERT: B  559 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7093 (mmt180)
REVERT: B  566 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8111 (t0)
  outliers start: 23
  outliers final: 9
  residues processed: 87
  average time/residue: 0.4527
  time to fit residues: 42.5551
Evaluate side-chains
  83 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  561 SER
Chi-restraints excluded: chain B residue  243 ARG
Chi-restraints excluded: chain B residue  248 GLU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  559 ARG
Chi-restraints excluded: chain B residue  561 SER
Chi-restraints excluded: chain B residue  566 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 82 optimal weight:    6.9990
   chunk 91 optimal weight:    0.8980
   chunk 47 optimal weight:    0.2980
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 149 ASN
B 566 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.164187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.126444 restraints weight = 7412.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.56
r_work: 0.3197 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8363  Z= 0.129
  Angle     :  0.515   6.405  11317  Z= 0.258
  Chirality :  0.039   0.232   1271
  Planarity :  0.004   0.048   1267
  Dihedral  : 17.302 118.010   2207
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 19.81 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.28), residues: 934
  helix:  1.74 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.51 (0.35), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 158 
 TYR   0.010   0.001   TYR A 204 
 PHE   0.013   0.001   PHE B 494 
 TRP   0.010   0.001   TRP B 425 
 HIS   0.003   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8353)
  covalent geometry    : angle       0.50539 (11291)
  SS BOND              : bond        0.00233 (    4)
  SS BOND              : angle       1.73475 (    8)
  hydrogen bonds       : bond        0.03856 (  520)
  hydrogen bonds       : angle       4.02254 ( 1515)
  link_BETA1-4         : bond        0.00417 (    2)
  link_BETA1-4         : angle       1.89473 (    6)
  link_NAG-ASN         : bond        0.00710 (    4)
  link_NAG-ASN         : angle       2.50521 (   12)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7694 (mm)
REVERT: A  497 LYS cc_start: 0.7606 (ptmt) cc_final: 0.5971 (mmtm)
REVERT: B  343 MET cc_start: 0.8456 (mmt) cc_final: 0.8112 (mmt)
REVERT: B  559 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7076 (mmt180)
REVERT: B  566 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8023 (t0)
  outliers start: 21
  outliers final: 9
  residues processed: 83
  average time/residue: 0.4417
  time to fit residues: 39.7521
Evaluate side-chains
  78 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain A residue  561 SER
Chi-restraints excluded: chain B residue  243 ARG
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  559 ARG
Chi-restraints excluded: chain B residue  561 SER
Chi-restraints excluded: chain B residue  566 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 30 optimal weight:    0.4980
   chunk 39 optimal weight:    0.8980
   chunk 84 optimal weight:    0.6980
   chunk 56 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 359 ASN
B 566 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.165979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.128349 restraints weight = 7420.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.56
r_work: 0.3196 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8363  Z= 0.128
  Angle     :  0.509   5.693  11317  Z= 0.254
  Chirality :  0.039   0.208   1271
  Planarity :  0.004   0.047   1267
  Dihedral  : 17.072 116.382   2205
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 20.61 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.28), residues: 934
  helix:  1.76 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.50 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 145 
 TYR   0.010   0.001   TYR A 204 
 PHE   0.012   0.001   PHE B 494 
 TRP   0.011   0.001   TRP B 425 
 HIS   0.003   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8353)
  covalent geometry    : angle       0.49923 (11291)
  SS BOND              : bond        0.00304 (    4)
  SS BOND              : angle       1.85402 (    8)
  hydrogen bonds       : bond        0.03822 (  520)
  hydrogen bonds       : angle       4.00994 ( 1515)
  link_BETA1-4         : bond        0.00418 (    2)
  link_BETA1-4         : angle       1.81733 (    6)
  link_NAG-ASN         : bond        0.00699 (    4)
  link_NAG-ASN         : angle       2.42128 (   12)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7729 (mm)
REVERT: A  371 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7603 (mt)
REVERT: A  497 LYS cc_start: 0.7617 (ptmt) cc_final: 0.5977 (mmtm)
REVERT: A  566 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8176 (t0)
REVERT: B  559 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7078 (mmt180)
REVERT: B  566 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7953 (t0)
  outliers start: 19
  outliers final: 8
  residues processed: 82
  average time/residue: 0.4401
  time to fit residues: 39.0777
Evaluate side-chains
  79 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain A residue  561 SER
Chi-restraints excluded: chain A residue  566 ASN
Chi-restraints excluded: chain B residue  243 ARG
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  559 ARG
Chi-restraints excluded: chain B residue  561 SER
Chi-restraints excluded: chain B residue  566 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 75 optimal weight:    0.8980
   chunk 78 optimal weight:    0.6980
   chunk 22 optimal weight:    9.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 359 ASN
B 566 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.165550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.127714 restraints weight = 7390.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 1.57
r_work: 0.3187 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3029 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8363  Z= 0.138
  Angle     :  0.515   5.710  11317  Z= 0.257
  Chirality :  0.039   0.196   1271
  Planarity :  0.004   0.047   1267
  Dihedral  : 16.899 114.671   2205
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 20.35 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.28), residues: 934
  helix:  1.91 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.62 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 145 
 TYR   0.011   0.001   TYR A 204 
 PHE   0.012   0.002   PHE B 347 
 TRP   0.010   0.001   TRP B 425 
 HIS   0.003   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8353)
  covalent geometry    : angle       0.50564 (11291)
  SS BOND              : bond        0.00334 (    4)
  SS BOND              : angle       1.72667 (    8)
  hydrogen bonds       : bond        0.03903 (  520)
  hydrogen bonds       : angle       4.02344 ( 1515)
  link_BETA1-4         : bond        0.00381 (    2)
  link_BETA1-4         : angle       1.77276 (    6)
  link_NAG-ASN         : bond        0.00686 (    4)
  link_NAG-ASN         : angle       2.43226 (   12)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7707 (mm)
REVERT: A  320 TYR cc_start: 0.8302 (m-80) cc_final: 0.8061 (m-80)
REVERT: A  371 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7622 (mt)
REVERT: A  497 LYS cc_start: 0.7587 (ptmt) cc_final: 0.5963 (mmtm)
REVERT: A  566 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8190 (t0)
REVERT: B  429 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6811 (mm-30)
REVERT: B  559 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7070 (mmt180)
REVERT: B  566 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7947 (t0)
  outliers start: 22
  outliers final: 11
  residues processed: 83
  average time/residue: 0.4668
  time to fit residues: 41.8607
Evaluate side-chains
  85 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain A residue  561 SER
Chi-restraints excluded: chain A residue  566 ASN
Chi-restraints excluded: chain B residue  243 ARG
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  429 GLU
Chi-restraints excluded: chain B residue  559 ARG
Chi-restraints excluded: chain B residue  561 SER
Chi-restraints excluded: chain B residue  566 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 83 optimal weight:    0.8980
   chunk 39 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 359 ASN
B 566 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.167572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.129784 restraints weight = 7415.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 1.57
r_work: 0.3242 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8363  Z= 0.139
  Angle     :  0.515   5.732  11317  Z= 0.257
  Chirality :  0.039   0.190   1271
  Planarity :  0.004   0.047   1267
  Dihedral  : 16.719 113.471   2205
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.48 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.28), residues: 934
  helix:  1.89 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.62 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 145 
 TYR   0.012   0.001   TYR B 320 
 PHE   0.012   0.002   PHE B 347 
 TRP   0.011   0.001   TRP B 425 
 HIS   0.003   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8353)
  covalent geometry    : angle       0.50607 (11291)
  SS BOND              : bond        0.00329 (    4)
  SS BOND              : angle       1.64496 (    8)
  hydrogen bonds       : bond        0.03907 (  520)
  hydrogen bonds       : angle       4.02581 ( 1515)
  link_BETA1-4         : bond        0.00363 (    2)
  link_BETA1-4         : angle       1.74601 (    6)
  link_NAG-ASN         : bond        0.00679 (    4)
  link_NAG-ASN         : angle       2.44333 (   12)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7761 (mm)
REVERT: A  189 ILE cc_start: 0.7826 (mt) cc_final: 0.7561 (mm)
REVERT: A  320 TYR cc_start: 0.8391 (m-80) cc_final: 0.8158 (m-80)
REVERT: A  371 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7614 (mt)
REVERT: A  497 LYS cc_start: 0.7598 (ptmt) cc_final: 0.5981 (mmtm)
REVERT: A  566 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8202 (t0)
REVERT: B  429 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6953 (mm-30)
REVERT: B  559 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7081 (mmt180)
REVERT: B  566 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.7960 (t0)
  outliers start: 21
  outliers final: 10
  residues processed: 84
  average time/residue: 0.4729
  time to fit residues: 42.8920
Evaluate side-chains
  86 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain A residue  561 SER
Chi-restraints excluded: chain A residue  566 ASN
Chi-restraints excluded: chain B residue  243 ARG
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  429 GLU
Chi-restraints excluded: chain B residue  559 ARG
Chi-restraints excluded: chain B residue  561 SER
Chi-restraints excluded: chain B residue  566 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 47 optimal weight:    0.5980
   chunk 82 optimal weight:    0.0270
   chunk 11 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 80 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
B 359 ASN
B 566 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.166038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.128411 restraints weight = 7411.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 1.56
r_work: 0.3174 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8363  Z= 0.120
  Angle     :  0.495   5.833  11317  Z= 0.248
  Chirality :  0.039   0.187   1271
  Planarity :  0.004   0.047   1267
  Dihedral  : 16.468 113.164   2205
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 20.88 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.28), residues: 934
  helix:  1.98 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.58 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 145 
 TYR   0.014   0.001   TYR B 320 
 PHE   0.011   0.001   PHE B 494 
 TRP   0.011   0.001   TRP B 425 
 HIS   0.003   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8353)
  covalent geometry    : angle       0.48603 (11291)
  SS BOND              : bond        0.00317 (    4)
  SS BOND              : angle       1.57658 (    8)
  hydrogen bonds       : bond        0.03751 (  520)
  hydrogen bonds       : angle       3.97233 ( 1515)
  link_BETA1-4         : bond        0.00376 (    2)
  link_BETA1-4         : angle       1.70306 (    6)
  link_NAG-ASN         : bond        0.00663 (    4)
  link_NAG-ASN         : angle       2.47655 (   12)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7725 (mm)
REVERT: A  189 ILE cc_start: 0.7793 (mt) cc_final: 0.7524 (mm)
REVERT: A  320 TYR cc_start: 0.8345 (m-80) cc_final: 0.8064 (m-80)
REVERT: A  371 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7590 (mt)
REVERT: A  497 LYS cc_start: 0.7605 (ptmt) cc_final: 0.5981 (mmtm)
REVERT: A  566 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8198 (t0)
REVERT: B  343 MET cc_start: 0.9021 (mmp) cc_final: 0.8600 (mmt)
REVERT: B  429 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6948 (mm-30)
REVERT: B  559 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7075 (mmt180)
REVERT: B  566 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7949 (t0)
  outliers start: 20
  outliers final: 10
  residues processed: 82
  average time/residue: 0.5042
  time to fit residues: 44.5018
Evaluate side-chains
  85 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain A residue  561 SER
Chi-restraints excluded: chain A residue  566 ASN
Chi-restraints excluded: chain B residue  243 ARG
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  429 GLU
Chi-restraints excluded: chain B residue  559 ARG
Chi-restraints excluded: chain B residue  561 SER
Chi-restraints excluded: chain B residue  566 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
B 359 ASN
B 566 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.161525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.121087 restraints weight = 7529.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.70
r_work: 0.3084 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8363  Z= 0.138
  Angle     :  0.508   5.757  11317  Z= 0.254
  Chirality :  0.039   0.183   1271
  Planarity :  0.004   0.047   1267
  Dihedral  : 16.364 111.955   2205
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.74 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.28), residues: 934
  helix:  1.94 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.59 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 145 
 TYR   0.014   0.001   TYR B 320 
 PHE   0.012   0.001   PHE B 347 
 TRP   0.010   0.001   TRP B 425 
 HIS   0.003   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8353)
  covalent geometry    : angle       0.49871 (11291)
  SS BOND              : bond        0.00337 (    4)
  SS BOND              : angle       1.58319 (    8)
  hydrogen bonds       : bond        0.03868 (  520)
  hydrogen bonds       : angle       4.00814 ( 1515)
  link_BETA1-4         : bond        0.00385 (    2)
  link_BETA1-4         : angle       1.67047 (    6)
  link_NAG-ASN         : bond        0.00667 (    4)
  link_NAG-ASN         : angle       2.46960 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2553.64 seconds
wall clock time: 44 minutes 21.87 seconds (2661.87 seconds total)