Starting phenix.real_space_refine
on Sun May 11 03:31:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ylp_39388/05_2025/8ylp_39388_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ylp_39388/05_2025/8ylp_39388.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ylp_39388/05_2025/8ylp_39388.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ylp_39388/05_2025/8ylp_39388.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ylp_39388/05_2025/8ylp_39388_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ylp_39388/05_2025/8ylp_39388_neut.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
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: 4
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     C    4821      2.51       5
     N    1203      2.21       5
     O    1347      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7397
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 471, 3670
          Classifications: {'peptide': 471}
          Link IDs: {'PTRANS': 22, 'TRANS': 448}
    Chain: "B"
      Number of atoms: 3603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 464, 3603
          Classifications: {'peptide': 464}
          Link IDs: {'PTRANS': 20, 'TRANS': 443}
    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: "E"
      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: "F"
      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: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 4.77, per 1000 atoms: 0.64
  Number of scatterers: 7397
  At special positions: 0
  Unit cell: (82.612, 84.786, 125.005, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      26     16.00
     O    1347      8.00
     N    1203      7.00
     C    4821      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 151 " distance=2.02

  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 E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 507 "
      " NAG D   1 " - " ASN A 366 "
      " NAG E   1 " - " ASN A 382 "
      " NAG F   1 " - " ASN A 425 "
  Time building additional restraints: 1.86
  Conformation dependent library (CDL) restraints added in 938.8 milliseconds
  

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1728

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      61.2% alpha, 6.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 174
    Processing helix  chain 'A' and resid 179 through 206
    Processing helix  chain 'A' and resid 218 through 222
      removed outlier: 3.887A  pdb=" N   THR A 222 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.608A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 247
    Processing helix  chain 'A' and resid 248 through 256
      removed outlier: 3.593A  pdb=" N   LEU A 255 " --> pdb=" O   TYR A 251 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 301
      removed outlier: 3.861A  pdb=" N   PHE A 291 " --> pdb=" O   SER A 287 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ASP A 292 " --> pdb=" O   LYS A 288 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LYS A 301 " --> pdb=" O   SER A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 342
      removed outlier: 3.593A  pdb=" N   ALA A 328 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 354
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.522A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ALA A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 392
    Processing helix  chain 'A' and resid 412 through 428
      removed outlier: 3.672A  pdb=" N   THR A 416 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 445
    Processing helix  chain 'A' and resid 447 through 449
      No H-bonds generated for 'chain 'A' and resid 447 through 449'
    Processing helix  chain 'A' and resid 450 through 460
      removed outlier: 3.565A  pdb=" N   PHE A 459 " --> pdb=" O   GLN A 455 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   THR A 460 " --> pdb=" O   LEU A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 514
    Processing helix  chain 'A' and resid 519 through 532
      removed outlier: 3.591A  pdb=" N   LEU A 523 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   SER A 532 " --> pdb=" O   SER A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 539
    Processing helix  chain 'A' and resid 585 through 589
      removed outlier: 3.890A  pdb=" N   SER A 589 " --> pdb=" O   ALA A 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 51
    Processing helix  chain 'B' and resid 53 through 58
      removed outlier: 3.560A  pdb=" N   SER B  58 " --> pdb=" O   GLY B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 67
    Processing helix  chain 'B' and resid 68 through 98
      removed outlier: 3.645A  pdb=" N   GLY B  86 " --> pdb=" O   PHE B  82 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   CYS B  89 " --> pdb=" O   PHE B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 112
    Processing helix  chain 'B' and resid 113 through 126
    Processing helix  chain 'B' and resid 126 through 144
      removed outlier: 3.861A  pdb=" N   THR B 130 " --> pdb=" O   ILE B 126 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   VAL B 144 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 176
      removed outlier: 3.804A  pdb=" N   SER B 158 " --> pdb=" O   PRO B 154 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ARG B 159 " --> pdb=" O   TYR B 155 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   TYR B 176 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 209
      removed outlier: 3.772A  pdb=" N   GLY B 180 " --> pdb=" O   TYR B 176 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   GLY B 209 " --> pdb=" O   ARG B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 239
      removed outlier: 3.709A  pdb=" N   LEU B 230 " --> pdb=" O   GLY B 226 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   TYR B 239 " --> pdb=" O   ALA B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 252
      removed outlier: 4.065A  pdb=" N   THR B 249 " --> pdb=" O   ASN B 246 " (cutoff:3.500A)
      removed outlier: 5.762A  pdb=" N   GLU B 250 " --> pdb=" O   TYR B 247 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE B 252 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 285
      removed outlier: 3.779A  pdb=" N   LEU B 259 " --> pdb=" O   PRO B 255 " (cutoff:3.500A)
      Proline residue:  B 260  - end of helix
      Proline residue:  B 268  - end of helix
      removed outlier: 3.569A  pdb=" N   ASN B 278 " --> pdb=" O   TYR B 274 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL B 284 " --> pdb=" O   ALA B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 291
      removed outlier: 3.551A  pdb=" N   ILE B 290 " --> pdb=" O   ASP B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 305
    Processing helix  chain 'B' and resid 310 through 341
      removed outlier: 3.733A  pdb=" N   ASN B 325 " --> pdb=" O   PHE B 321 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ALA B 326 " --> pdb=" O   GLY B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 350
    Processing helix  chain 'B' and resid 358 through 373
    Processing helix  chain 'B' and resid 378 through 384
      removed outlier: 3.808A  pdb=" N   ILE B 382 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 407
      removed outlier: 3.618A  pdb=" N   TYR B 389 " --> pdb=" O   TYR B 385 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   TRP B 390 " --> pdb=" O   SER B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 438
      removed outlier: 3.517A  pdb=" N   ILE B 422 " --> pdb=" O   VAL B 418 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   VAL B 434 " --> pdb=" O   PHE B 430 " (cutoff:3.500A)
      Proline residue:  B 435  - end of helix
    Processing helix  chain 'B' and resid 439 through 452
      removed outlier: 3.908A  pdb=" N   SER B 443 " --> pdb=" O   ASP B 439 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU B 444 " --> pdb=" O   THR B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 460
      removed outlier: 3.575A  pdb=" N   LEU B 459 " --> pdb=" O   PRO B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 488
      removed outlier: 3.601A  pdb=" N   ILE B 475 " --> pdb=" O   TYR B 471 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402
      removed outlier: 6.515A  pdb=" N   LEU A 377 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 7.954A  pdb=" N   THR A 402 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ALA A 379 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   GLY A 345 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   LEU A 260 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
      removed outlier: 7.374A  pdb=" N   ASP A 308 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   LEU A 262 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   TYR A 226 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267
      removed outlier: 7.124A  pdb=" N   GLN A 280 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545
      removed outlier: 4.622A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576
    Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 594
    Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 352

    393 hydrogen bonds defined for protein.
    1110 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.15

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1814
        1.33 -     1.45: 1550
        1.45 -     1.57: 4173
        1.57 -     1.69: 0
        1.69 -     1.80: 38
  Bond restraints: 7575
  Sorted by residual:
  bond pdb=" N   PRO A 481 "
       pdb=" CD  PRO A 481 "
    ideal  model  delta    sigma   weight residual
    1.473  1.534 -0.061 1.40e-02 5.10e+03 1.87e+01
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.453 -0.047 2.00e-02 2.50e+03 5.57e+00
  bond pdb=" C   LEU A 480 "
       pdb=" N   PRO A 481 "
    ideal  model  delta    sigma   weight residual
    1.334  1.389 -0.055 2.34e-02 1.83e+03 5.51e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.452 -0.046 2.00e-02 2.50e+03 5.39e+00
  bond pdb=" C   HIS A 539 "
       pdb=" N   GLY A 540 "
    ideal  model  delta    sigma   weight residual
    1.328  1.298  0.031 1.34e-02 5.57e+03 5.29e+00
  ... (remaining 7570 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 9954
        2.54 -     5.08: 295
        5.08 -     7.62: 38
        7.62 -    10.16: 13
       10.16 -    12.70: 2
  Bond angle restraints: 10302
  Sorted by residual:
  angle pdb=" N   ASP A 272 "
        pdb=" CA  ASP A 272 "
        pdb=" C   ASP A 272 "
      ideal   model   delta    sigma   weight residual
     109.59  100.37    9.22 1.47e+00 4.63e-01 3.93e+01
  angle pdb=" N   ARG B 288 "
        pdb=" CA  ARG B 288 "
        pdb=" C   ARG B 288 "
      ideal   model   delta    sigma   weight residual
     111.28  115.88   -4.60 1.09e+00 8.42e-01 1.78e+01
  angle pdb=" C   LEU A 480 "
        pdb=" N   PRO A 481 "
        pdb=" CA  PRO A 481 "
      ideal   model   delta    sigma   weight residual
     119.84  114.62    5.22 1.25e+00 6.40e-01 1.75e+01
  angle pdb=" N   ASP A 271 "
        pdb=" CA  ASP A 271 "
        pdb=" C   ASP A 271 "
      ideal   model   delta    sigma   weight residual
     110.80  119.09   -8.29 2.13e+00 2.20e-01 1.52e+01
  angle pdb=" CA  ARG B 355 "
        pdb=" CB  ARG B 355 "
        pdb=" CG  ARG B 355 "
      ideal   model   delta    sigma   weight residual
     114.10  121.77   -7.67 2.00e+00 2.50e-01 1.47e+01
  ... (remaining 10297 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.48: 4162
       20.48 -    40.96: 309
       40.96 -    61.44: 55
       61.44 -    81.92: 11
       81.92 -   102.41: 12
  Dihedral angle restraints: 4549
    sinusoidal: 1856
      harmonic: 2693
  Sorted by residual:
  dihedral pdb=" CA  VAL B 353 "
           pdb=" C   VAL B 353 "
           pdb=" N   GLU B 354 "
           pdb=" CA  GLU B 354 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.72   25.28     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  ASN A 317 "
           pdb=" C   ASN A 317 "
           pdb=" N   SER A 318 "
           pdb=" CA  SER A 318 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.99  -25.01     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  PRO B 345 "
           pdb=" C   PRO B 345 "
           pdb=" N   ASP B 346 "
           pdb=" CA  ASP B 346 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.66  -24.34     0      5.00e+00 4.00e-02 2.37e+01
  ... (remaining 4546 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.144: 1184
       0.144 -    0.288: 18
       0.288 -    0.432: 1
       0.432 -    0.576: 0
       0.576 -    0.720: 1
  Chirality restraints: 1204
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 366 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.68   -0.72 2.00e-01 2.50e+01 1.29e+01
  chirality pdb=" C4  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" C5  NAG D   1 "
            pdb=" O4  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.16   -0.37 2.00e-01 2.50e+01 3.39e+00
  chirality pdb=" CA  ASP A 272 "
            pdb=" N   ASP A 272 "
            pdb=" C   ASP A 272 "
            pdb=" CB  ASP A 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.64e+00
  ... (remaining 1201 not shown)

  Planarity restraints: 1285
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 214 "   -0.058 5.00e-02 4.00e+02   8.75e-02 1.23e+01
        pdb=" N   PRO A 215 "    0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO A 215 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 215 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 454 "   -0.048 5.00e-02 4.00e+02   7.21e-02 8.31e+00
        pdb=" N   PRO B 455 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO B 455 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 455 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 454 "   -0.013 2.00e-02 2.50e+03   1.87e-02 6.96e+00
        pdb=" CG  TYR A 454 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 454 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 454 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 454 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 454 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 454 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 454 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1282 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2213
        2.82 -     3.34: 6431
        3.34 -     3.86: 11909
        3.86 -     4.38: 13952
        4.38 -     4.90: 24169
  Nonbonded interactions: 58674
  Sorted by model distance:
  nonbonded pdb=" O   SER B 211 "
            pdb=" OG  SER B 211 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   LEU A 255 "
            pdb=" OG  SER A 528 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OH  TYR A 251 "
            pdb=" OE2 GLU A 472 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O   SER A 302 "
            pdb=" OG  SER A 302 "
     model   vdw
     2.331 3.040
  nonbonded pdb=" ND1 HIS B 352 "
            pdb=" O   GLU B 354 "
     model   vdw
     2.333 3.120
  ... (remaining 58669 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 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             1.000
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.220
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
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      :  0.008   0.083   7584  Z= 0.377
  Angle     :  1.061  12.700  10328  Z= 0.560
  Chirality :  0.061   0.720   1204
  Planarity :  0.007   0.088   1281
  Dihedral  : 15.871 102.405   2818
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  8.49 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  5.62 %
    Favored  : 93.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.15 (0.22), residues: 931
  helix: -1.62 (0.18), residues: 501
  sheet: -0.67 (0.63), residues: 66
  loop : -2.95 (0.26), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP A 220 
 HIS   0.010   0.002   HIS B 466 
 PHE   0.025   0.003   PHE A 627 
 TYR   0.045   0.003   TYR A 454 
 ARG   0.005   0.001   ARG A 452 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00767 (    4)
  link_NAG-ASN         : angle       4.45150 (   12)
  link_BETA1-4         : bond        0.01568 (    4)
  link_BETA1-4         : angle       4.40590 (   12)
  hydrogen bonds       : bond        0.17961 (  393)
  hydrogen bonds       : angle       6.51126 ( 1110)
  SS BOND              : bond        0.00709 (    1)
  SS BOND              : angle       3.26987 (    2)
  covalent geometry    : bond        0.00845 ( 7575)
  covalent geometry    : angle       1.04003 (10302)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 136
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 ARG cc_start: 0.6800 (mtp-110) cc_final: 0.6369 (mtp-110)
REVERT: A  398 ASP cc_start: 0.7437 (t70) cc_final: 0.7093 (t0)
REVERT: A  457 MET cc_start: 0.9052 (ttp) cc_final: 0.8794 (ttp)
REVERT: A  511 LYS cc_start: 0.6554 (ttpp) cc_final: 0.6320 (pttp)
REVERT: B  178 LYS cc_start: 0.7931 (mmmm) cc_final: 0.7540 (pttt)
REVERT: B  256 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7293 (pm20)
REVERT: B  267 MET cc_start: 0.8437 (mmp) cc_final: 0.8207 (mmm)
REVERT: B  481 ARG cc_start: 0.7386 (ttm110) cc_final: 0.6892 (mtm110)
  outliers start: 4
  outliers final: 1
  residues processed: 140
  average time/residue: 1.0776
  time to fit residues: 160.1817
Evaluate side-chains
  85 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  151 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 221 HIS
** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 353 ASN
A 483 GLN
B 216 ASN
B 254 ASN
B 258 ASN
B 278 ASN
B 383 ASN
B 484 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.160467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.126893 restraints weight = 8893.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.87
r_work: 0.3203 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7584  Z= 0.142
  Angle     :  0.670   8.469  10328  Z= 0.334
  Chirality :  0.044   0.373   1204
  Planarity :  0.005   0.055   1281
  Dihedral  : 11.056  81.495   1175
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.30 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.77 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.26), residues: 931
  helix:  0.19 (0.22), residues: 514
  sheet: -0.55 (0.65), residues: 65
  loop : -2.20 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 220 
 HIS   0.005   0.001   HIS B 466 
 PHE   0.018   0.001   PHE B 187 
 TYR   0.023   0.002   TYR B  90 
 ARG   0.008   0.001   ARG B 474 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00219 (    4)
  link_NAG-ASN         : angle       3.14809 (   12)
  link_BETA1-4         : bond        0.00616 (    4)
  link_BETA1-4         : angle       2.01106 (   12)
  hydrogen bonds       : bond        0.05508 (  393)
  hydrogen bonds       : angle       4.55939 ( 1110)
  SS BOND              : bond        0.00194 (    1)
  SS BOND              : angle       1.95228 (    2)
  covalent geometry    : bond        0.00304 ( 7575)
  covalent geometry    : angle       0.65787 (10302)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.738 
Fit side-chains
REVERT: A  207 ARG cc_start: 0.7271 (mtp-110) cc_final: 0.6795 (mtp-110)
REVERT: A  330 LYS cc_start: 0.7806 (mmtp) cc_final: 0.7212 (mmtm)
REVERT: A  398 ASP cc_start: 0.7744 (t70) cc_final: 0.7430 (t0)
REVERT: A  457 MET cc_start: 0.9166 (ttp) cc_final: 0.8963 (ttp)
REVERT: A  511 LYS cc_start: 0.6376 (ttpp) cc_final: 0.6059 (pttp)
REVERT: A  580 GLN cc_start: 0.6887 (pt0) cc_final: 0.6395 (mp10)
REVERT: B  109 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7780 (mp0)
REVERT: B  178 LYS cc_start: 0.8503 (mmmm) cc_final: 0.8137 (pttt)
REVERT: B  481 ARG cc_start: 0.8014 (ttm110) cc_final: 0.7535 (mtm-85)
  outliers start: 18
  outliers final: 6
  residues processed: 101
  average time/residue: 1.0759
  time to fit residues: 116.0692
Evaluate side-chains
  86 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  593 LYS
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain B residue  109 GLU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  204 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 68 optimal weight:    0.2980
   chunk 55 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0030
   chunk 38 optimal weight:    0.9990
   overall best weight:    1.0596

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 ASN
B 365 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.159684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.125733 restraints weight = 9042.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.86
r_work: 0.3180 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7584  Z= 0.139
  Angle     :  0.648   7.862  10328  Z= 0.318
  Chirality :  0.043   0.331   1204
  Planarity :  0.004   0.052   1281
  Dihedral  :  9.566  70.006   1174
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.06 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 15.33 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.28), residues: 931
  helix:  0.98 (0.23), residues: 514
  sheet: -0.29 (0.65), residues: 63
  loop : -1.88 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 220 
 HIS   0.005   0.001   HIS B 466 
 PHE   0.021   0.001   PHE B 187 
 TYR   0.023   0.002   TYR B  90 
 ARG   0.004   0.000   ARG B 474 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00225 (    4)
  link_NAG-ASN         : angle       2.85050 (   12)
  link_BETA1-4         : bond        0.00735 (    4)
  link_BETA1-4         : angle       1.98641 (   12)
  hydrogen bonds       : bond        0.05235 (  393)
  hydrogen bonds       : angle       4.27616 ( 1110)
  SS BOND              : bond        0.01008 (    1)
  SS BOND              : angle       2.98833 (    2)
  covalent geometry    : bond        0.00306 ( 7575)
  covalent geometry    : angle       0.63651 (10302)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  207 ARG cc_start: 0.7364 (mtp-110) cc_final: 0.6898 (mtp-110)
REVERT: A  272 ASP cc_start: 0.7458 (p0) cc_final: 0.7031 (p0)
REVERT: A  280 GLN cc_start: 0.7380 (tt0) cc_final: 0.6788 (tm-30)
REVERT: A  330 LYS cc_start: 0.7657 (mmtp) cc_final: 0.7215 (mmtm)
REVERT: A  398 ASP cc_start: 0.7766 (t70) cc_final: 0.7438 (t0)
REVERT: A  457 MET cc_start: 0.9191 (ttp) cc_final: 0.8986 (ttp)
REVERT: A  511 LYS cc_start: 0.6645 (ttpp) cc_final: 0.6331 (pttp)
REVERT: A  580 GLN cc_start: 0.6997 (pt0) cc_final: 0.6382 (mp10)
REVERT: B  178 LYS cc_start: 0.8539 (mmmm) cc_final: 0.8149 (pttt)
REVERT: B  481 ARG cc_start: 0.8052 (ttm110) cc_final: 0.7589 (mtm-85)
  outliers start: 15
  outliers final: 8
  residues processed: 99
  average time/residue: 1.1193
  time to fit residues: 117.9403
Evaluate side-chains
  87 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  204 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 89 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0970
   chunk 77 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.160536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.127466 restraints weight = 8992.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 1.92
r_work: 0.3206 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7584  Z= 0.116
  Angle     :  0.604   8.495  10328  Z= 0.295
  Chirality :  0.042   0.316   1204
  Planarity :  0.004   0.048   1281
  Dihedral  :  8.232  59.509   1174
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.30 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.35 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.28), residues: 931
  helix:  1.49 (0.23), residues: 513
  sheet: -0.39 (0.64), residues: 64
  loop : -1.69 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 220 
 HIS   0.004   0.001   HIS B 466 
 PHE   0.016   0.001   PHE B 187 
 TYR   0.016   0.001   TYR B  90 
 ARG   0.007   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00160 (    4)
  link_NAG-ASN         : angle       2.61597 (   12)
  link_BETA1-4         : bond        0.00810 (    4)
  link_BETA1-4         : angle       2.16395 (   12)
  hydrogen bonds       : bond        0.04471 (  393)
  hydrogen bonds       : angle       4.09159 ( 1110)
  SS BOND              : bond        0.00763 (    1)
  SS BOND              : angle       3.23465 (    2)
  covalent geometry    : bond        0.00243 ( 7575)
  covalent geometry    : angle       0.59170 (10302)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.798 
Fit side-chains
REVERT: A  207 ARG cc_start: 0.7260 (mtp-110) cc_final: 0.6854 (mtp-110)
REVERT: A  272 ASP cc_start: 0.7283 (p0) cc_final: 0.6868 (p0)
REVERT: A  280 GLN cc_start: 0.7257 (tt0) cc_final: 0.6714 (tm-30)
REVERT: A  390 LEU cc_start: 0.8911 (mt) cc_final: 0.8665 (mm)
REVERT: A  398 ASP cc_start: 0.7744 (t70) cc_final: 0.7346 (t0)
REVERT: A  457 MET cc_start: 0.9223 (ttp) cc_final: 0.8971 (ttp)
REVERT: A  511 LYS cc_start: 0.6607 (ttpp) cc_final: 0.6381 (pttp)
REVERT: A  572 ASP cc_start: 0.8340 (p0) cc_final: 0.8001 (p0)
REVERT: A  580 GLN cc_start: 0.7127 (pt0) cc_final: 0.6461 (mp10)
REVERT: B  109 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7863 (mp0)
REVERT: B  178 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8079 (pttt)
REVERT: B  481 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7668 (ttm-80)
  outliers start: 15
  outliers final: 7
  residues processed: 103
  average time/residue: 1.0354
  time to fit residues: 113.6031
Evaluate side-chains
  86 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  109 GLU
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  463 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 55 optimal weight:    0.4980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.159050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.126510 restraints weight = 8922.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.81
r_work: 0.3193 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7584  Z= 0.148
  Angle     :  0.642   8.415  10328  Z= 0.314
  Chirality :  0.043   0.307   1204
  Planarity :  0.004   0.050   1281
  Dihedral  :  7.627  59.760   1174
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.49 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.73 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.28), residues: 931
  helix:  1.54 (0.23), residues: 512
  sheet: -0.22 (0.65), residues: 63
  loop : -1.61 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 220 
 HIS   0.004   0.001   HIS B 466 
 PHE   0.020   0.001   PHE B 187 
 TYR   0.014   0.002   TYR B 142 
 ARG   0.004   0.000   ARG B 205 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00187 (    4)
  link_NAG-ASN         : angle       2.54471 (   12)
  link_BETA1-4         : bond        0.00762 (    4)
  link_BETA1-4         : angle       2.28525 (   12)
  hydrogen bonds       : bond        0.05134 (  393)
  hydrogen bonds       : angle       4.12824 ( 1110)
  SS BOND              : bond        0.01185 (    1)
  SS BOND              : angle       3.05471 (    2)
  covalent geometry    : bond        0.00335 ( 7575)
  covalent geometry    : angle       0.63082 (10302)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.825 
Fit side-chains
REVERT: A  207 ARG cc_start: 0.7278 (mtp-110) cc_final: 0.6846 (mtp-110)
REVERT: A  272 ASP cc_start: 0.7258 (p0) cc_final: 0.6841 (p0)
REVERT: A  280 GLN cc_start: 0.7337 (tt0) cc_final: 0.6672 (tm-30)
REVERT: A  398 ASP cc_start: 0.7678 (t70) cc_final: 0.7284 (t0)
REVERT: A  457 MET cc_start: 0.9244 (ttp) cc_final: 0.8974 (ttp)
REVERT: A  511 LYS cc_start: 0.6543 (ttpp) cc_final: 0.6279 (pttp)
REVERT: A  515 GLU cc_start: 0.7791 (mp0) cc_final: 0.7480 (mp0)
REVERT: A  580 GLN cc_start: 0.6999 (pt0) cc_final: 0.6378 (mp10)
REVERT: B   98 LYS cc_start: 0.8271 (ttmm) cc_final: 0.7942 (mtpt)
REVERT: B  109 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7795 (mp0)
REVERT: B  178 LYS cc_start: 0.8567 (mmmm) cc_final: 0.8146 (pttt)
REVERT: B  481 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7245 (mtm110)
  outliers start: 17
  outliers final: 8
  residues processed: 101
  average time/residue: 1.0584
  time to fit residues: 113.8443
Evaluate side-chains
  95 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  109 GLU
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  463 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 45 optimal weight:    0.3980
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B 254 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.158007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.123829 restraints weight = 8850.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.84
r_work: 0.3164 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7584  Z= 0.146
  Angle     :  0.642   7.538  10328  Z= 0.313
  Chirality :  0.043   0.298   1204
  Planarity :  0.004   0.050   1281
  Dihedral  :  7.080  59.750   1174
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.84 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.48 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.28), residues: 931
  helix:  1.58 (0.23), residues: 513
  sheet: -0.26 (0.64), residues: 63
  loop : -1.47 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 220 
 HIS   0.003   0.001   HIS B 466 
 PHE   0.019   0.001   PHE B 187 
 TYR   0.013   0.002   TYR B 142 
 ARG   0.003   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00227 (    4)
  link_NAG-ASN         : angle       2.63847 (   12)
  link_BETA1-4         : bond        0.00791 (    4)
  link_BETA1-4         : angle       2.20675 (   12)
  hydrogen bonds       : bond        0.05125 (  393)
  hydrogen bonds       : angle       4.11034 ( 1110)
  SS BOND              : bond        0.00516 (    1)
  SS BOND              : angle       3.01799 (    2)
  covalent geometry    : bond        0.00331 ( 7575)
  covalent geometry    : angle       0.63029 (10302)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: A  272 ASP cc_start: 0.7269 (p0) cc_final: 0.6845 (p0)
REVERT: A  280 GLN cc_start: 0.7341 (tt0) cc_final: 0.6684 (tm-30)
REVERT: A  398 ASP cc_start: 0.7723 (t70) cc_final: 0.7337 (t0)
REVERT: A  457 MET cc_start: 0.9263 (ttp) cc_final: 0.8992 (ttp)
REVERT: A  511 LYS cc_start: 0.6405 (ttpp) cc_final: 0.6151 (pttp)
REVERT: A  572 ASP cc_start: 0.8519 (p0) cc_final: 0.8178 (p0)
REVERT: A  580 GLN cc_start: 0.6947 (pt0) cc_final: 0.6279 (mp10)
REVERT: B   36 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.5479 (pm20)
REVERT: B  109 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7834 (mp0)
REVERT: B  481 ARG cc_start: 0.8128 (ttm110) cc_final: 0.7325 (mtm110)
  outliers start: 23
  outliers final: 10
  residues processed: 104
  average time/residue: 1.0434
  time to fit residues: 115.7523
Evaluate side-chains
  89 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 GLU
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  109 GLU
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  463 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0020
   chunk 54 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 35 optimal weight:    0.3980
   chunk 49 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
B 254 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.160172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.126226 restraints weight = 8845.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.99
r_work: 0.3193 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7584  Z= 0.117
  Angle     :  0.605   6.959  10328  Z= 0.296
  Chirality :  0.041   0.303   1204
  Planarity :  0.004   0.046   1281
  Dihedral  :  6.406  54.336   1174
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.63 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 17.62 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.29), residues: 931
  helix:  1.80 (0.23), residues: 513
  sheet: -0.35 (0.64), residues: 64
  loop : -1.35 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 220 
 HIS   0.003   0.001   HIS B 466 
 PHE   0.014   0.001   PHE B 187 
 TYR   0.011   0.001   TYR B  90 
 ARG   0.006   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00251 (    4)
  link_NAG-ASN         : angle       2.61639 (   12)
  link_BETA1-4         : bond        0.00832 (    4)
  link_BETA1-4         : angle       2.12488 (   12)
  hydrogen bonds       : bond        0.04333 (  393)
  hydrogen bonds       : angle       4.00806 ( 1110)
  SS BOND              : bond        0.01392 (    1)
  SS BOND              : angle       2.97745 (    2)
  covalent geometry    : bond        0.00249 ( 7575)
  covalent geometry    : angle       0.59339 (10302)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
REVERT: A  280 GLN cc_start: 0.7350 (tt0) cc_final: 0.6700 (tm-30)
REVERT: A  390 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8571 (mm)
REVERT: A  398 ASP cc_start: 0.7693 (t70) cc_final: 0.7292 (t0)
REVERT: A  457 MET cc_start: 0.9221 (ttp) cc_final: 0.8975 (ttp)
REVERT: A  515 GLU cc_start: 0.7910 (mp0) cc_final: 0.7539 (mp0)
REVERT: A  572 ASP cc_start: 0.8544 (p0) cc_final: 0.8239 (p0)
REVERT: A  580 GLN cc_start: 0.7105 (pt0) cc_final: 0.6403 (mp10)
REVERT: B  109 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7871 (mp0)
REVERT: B  481 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7350 (mtm110)
  outliers start: 15
  outliers final: 8
  residues processed: 98
  average time/residue: 0.9642
  time to fit residues: 101.3823
Evaluate side-chains
  88 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  109 GLU
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  463 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0370
   chunk 70 optimal weight:    0.9980
   chunk 88 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0470
   chunk 82 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
B 254 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.160872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.126619 restraints weight = 8947.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.07
r_work: 0.3202 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7584  Z= 0.110
  Angle     :  0.596   7.072  10328  Z= 0.292
  Chirality :  0.040   0.301   1204
  Planarity :  0.004   0.044   1281
  Dihedral  :  5.935  47.196   1174
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.84 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 18.77 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.29), residues: 931
  helix:  1.99 (0.23), residues: 508
  sheet: -0.29 (0.65), residues: 64
  loop : -1.33 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 219 
 HIS   0.003   0.001   HIS B 466 
 PHE   0.014   0.001   PHE B 187 
 TYR   0.009   0.001   TYR B 142 
 ARG   0.006   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00255 (    4)
  link_NAG-ASN         : angle       2.65329 (   12)
  link_BETA1-4         : bond        0.00819 (    4)
  link_BETA1-4         : angle       2.13352 (   12)
  hydrogen bonds       : bond        0.04120 (  393)
  hydrogen bonds       : angle       3.93060 ( 1110)
  SS BOND              : bond        0.00483 (    1)
  SS BOND              : angle       3.00831 (    2)
  covalent geometry    : bond        0.00228 ( 7575)
  covalent geometry    : angle       0.58422 (10302)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A  280 GLN cc_start: 0.7387 (tt0) cc_final: 0.6728 (tm-30)
REVERT: A  398 ASP cc_start: 0.7685 (t70) cc_final: 0.7286 (t0)
REVERT: A  457 MET cc_start: 0.9218 (ttp) cc_final: 0.8985 (ttp)
REVERT: A  511 LYS cc_start: 0.6682 (ttpp) cc_final: 0.6115 (pttp)
REVERT: A  572 ASP cc_start: 0.8562 (p0) cc_final: 0.8279 (p0)
REVERT: A  580 GLN cc_start: 0.7042 (pt0) cc_final: 0.6252 (mp10)
REVERT: B   92 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7917 (tt0)
REVERT: B  109 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7877 (mp0)
REVERT: B  481 ARG cc_start: 0.8172 (ttm110) cc_final: 0.7733 (ttm-80)
  outliers start: 13
  outliers final: 9
  residues processed: 98
  average time/residue: 0.9095
  time to fit residues: 95.9589
Evaluate side-chains
  91 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain B residue  109 GLU
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  463 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 32 optimal weight:    0.3980
   chunk 53 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0470
   chunk 16 optimal weight:    4.9990
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
B 254 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.161081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.128103 restraints weight = 9033.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.04
r_work: 0.3216 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7584  Z= 0.114
  Angle     :  0.601   7.428  10328  Z= 0.294
  Chirality :  0.041   0.302   1204
  Planarity :  0.004   0.044   1281
  Dihedral  :  5.602  41.481   1174
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.06 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 18.52 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.29), residues: 931
  helix:  2.04 (0.23), residues: 507
  sheet: -0.22 (0.64), residues: 65
  loop : -1.30 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 220 
 HIS   0.003   0.001   HIS B 466 
 PHE   0.015   0.001   PHE B 187 
 TYR   0.023   0.001   TYR A 469 
 ARG   0.006   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00251 (    4)
  link_NAG-ASN         : angle       2.69887 (   12)
  link_BETA1-4         : bond        0.00781 (    4)
  link_BETA1-4         : angle       2.10080 (   12)
  hydrogen bonds       : bond        0.04219 (  393)
  hydrogen bonds       : angle       3.92412 ( 1110)
  SS BOND              : bond        0.00787 (    1)
  SS BOND              : angle       2.70974 (    2)
  covalent geometry    : bond        0.00241 ( 7575)
  covalent geometry    : angle       0.58885 (10302)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.841 
Fit side-chains
REVERT: A  280 GLN cc_start: 0.7366 (tt0) cc_final: 0.6705 (tm-30)
REVERT: A  398 ASP cc_start: 0.7574 (t70) cc_final: 0.7125 (t0)
REVERT: A  457 MET cc_start: 0.9249 (ttp) cc_final: 0.9007 (ttp)
REVERT: A  572 ASP cc_start: 0.8516 (p0) cc_final: 0.8235 (p0)
REVERT: A  580 GLN cc_start: 0.6896 (pt0) cc_final: 0.6282 (mp10)
REVERT: A  583 ASP cc_start: 0.6120 (m-30) cc_final: 0.5620 (t0)
REVERT: B  109 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7849 (mp0)
REVERT: B  481 ARG cc_start: 0.8099 (ttm110) cc_final: 0.7652 (ttm-80)
  outliers start: 14
  outliers final: 9
  residues processed: 97
  average time/residue: 1.0507
  time to fit residues: 109.3887
Evaluate side-chains
  92 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain B residue  109 GLU
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  463 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0570
   chunk 35 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
B 254 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.161168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.129904 restraints weight = 9032.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.97
r_work: 0.3188 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7584  Z= 0.114
  Angle     :  0.612   7.719  10328  Z= 0.298
  Chirality :  0.041   0.302   1204
  Planarity :  0.004   0.044   1281
  Dihedral  :  5.420  38.117   1174
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.84 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 19.03 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.29), residues: 931
  helix:  2.05 (0.23), residues: 509
  sheet: -0.22 (0.64), residues: 65
  loop : -1.24 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 220 
 HIS   0.003   0.001   HIS B 466 
 PHE   0.015   0.001   PHE B  82 
 TYR   0.023   0.001   TYR A 469 
 ARG   0.005   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00257 (    4)
  link_NAG-ASN         : angle       2.72383 (   12)
  link_BETA1-4         : bond        0.00796 (    4)
  link_BETA1-4         : angle       2.04354 (   12)
  hydrogen bonds       : bond        0.04127 (  393)
  hydrogen bonds       : angle       3.90433 ( 1110)
  SS BOND              : bond        0.00465 (    1)
  SS BOND              : angle       2.83664 (    2)
  covalent geometry    : bond        0.00242 ( 7575)
  covalent geometry    : angle       0.60032 (10302)

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.742 
Fit side-chains
REVERT: A  168 GLU cc_start: 0.6404 (mm-30) cc_final: 0.6118 (tm-30)
REVERT: A  280 GLN cc_start: 0.7419 (tt0) cc_final: 0.6778 (tm-30)
REVERT: A  398 ASP cc_start: 0.7548 (t70) cc_final: 0.7140 (t0)
REVERT: A  457 MET cc_start: 0.9237 (ttp) cc_final: 0.8997 (ttp)
REVERT: A  511 LYS cc_start: 0.6864 (ttpp) cc_final: 0.6219 (pttp)
REVERT: A  572 ASP cc_start: 0.8535 (p0) cc_final: 0.8289 (p0)
REVERT: A  580 GLN cc_start: 0.6586 (pt0) cc_final: 0.6232 (mp10)
REVERT: A  583 ASP cc_start: 0.6250 (m-30) cc_final: 0.5725 (t0)
REVERT: B   92 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8058 (tt0)
REVERT: B  109 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7847 (mp0)
  outliers start: 14
  outliers final: 8
  residues processed: 96
  average time/residue: 1.0144
  time to fit residues: 104.1262
Evaluate side-chains
  92 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain B residue  109 GLU
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  463 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 72 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9980
   chunk 43 optimal weight:    8.9990
   chunk 2 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0010
   chunk 42 optimal weight:    0.1980
   chunk 69 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.4386

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

Flipped N/Q/H residues before XYZ refinement:
B 254 ASN
B 365 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.162218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.129375 restraints weight = 8907.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 1.82
r_work: 0.3206 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7584  Z= 0.110
  Angle     :  0.615   7.832  10328  Z= 0.299
  Chirality :  0.041   0.306   1204
  Planarity :  0.004   0.043   1281
  Dihedral  :  5.189  33.688   1174
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.95 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 19.67 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.29), residues: 931
  helix:  2.11 (0.24), residues: 509
  sheet: -0.22 (0.64), residues: 65
  loop : -1.20 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 219 
 HIS   0.003   0.001   HIS B 466 
 PHE   0.014   0.001   PHE B  82 
 TYR   0.024   0.001   TYR A 469 
 ARG   0.004   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00264 (    4)
  link_NAG-ASN         : angle       2.78368 (   12)
  link_BETA1-4         : bond        0.00751 (    4)
  link_BETA1-4         : angle       1.98604 (   12)
  hydrogen bonds       : bond        0.03852 (  393)
  hydrogen bonds       : angle       3.86928 ( 1110)
  SS BOND              : bond        0.00515 (    1)
  SS BOND              : angle       2.57987 (    2)
  covalent geometry    : bond        0.00230 ( 7575)
  covalent geometry    : angle       0.60307 (10302)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5419.39 seconds
wall clock time: 94 minutes 2.39 seconds (5642.39 seconds total)