Starting phenix.real_space_refine
on Fri Jul 25 10:09:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j8l_36073/07_2025/8j8l_36073_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j8l_36073/07_2025/8j8l_36073.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j8l_36073/07_2025/8j8l_36073.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j8l_36073/07_2025/8j8l_36073.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j8l_36073/07_2025/8j8l_36073_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j8l_36073/07_2025/8j8l_36073_neut.cif"
  }
  resolution = 3.56
  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=  -0.003 sd=   0.039
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      27      5.16       5
     C    4809      2.51       5
     N    1187      2.21       5
     O    1338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7361
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3656
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 22, 'TRANS': 446}
    Chain: "B"
      Number of atoms: 3579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 463, 3579
          Classifications: {'peptide': 463}
          Link IDs: {'PTRANS': 24, 'TRANS': 438}
    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: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Classifications: {'peptide': 1}
  Time building chain proxies: 5.50, per 1000 atoms: 0.75
  Number of scatterers: 7361
  At special positions: 0
  Unit cell: (99.645, 83.22, 129.21, 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      27     16.00
     O    1338      8.00
     N    1187      7.00
     C    4809      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 164 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    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: 2.35
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1718

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 5 sheets defined
      58.7% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 174
    Processing helix  chain 'A' and resid 179 through 207
    Processing helix  chain 'A' and resid 218 through 222
      removed outlier: 3.756A  pdb=" N   HIS A 221 " --> pdb=" O   LYS A 218 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR A 222 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 218 through 222'
    Processing helix  chain 'A' and resid 230 through 235
      removed outlier: 4.445A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
    Processing helix  chain 'A' and resid 248 through 256
    Processing helix  chain 'A' and resid 287 through 302
    Processing helix  chain 'A' and resid 324 through 342
      removed outlier: 3.575A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLN A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ALA A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 354
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.728A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE A 371 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   SER A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
      removed outlier: 3.624A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A 393 " --> pdb=" O   ILE A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 428
      removed outlier: 3.615A  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 450 through 460
      removed outlier: 3.628A  pdb=" N   PHE A 459 " --> pdb=" O   GLN A 455 " (cutoff:3.500A)
      removed outlier: 3.698A  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
    Processing helix  chain 'A' and resid 534 through 540
    Processing helix  chain 'A' and resid 585 through 589
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 70
      removed outlier: 3.660A  pdb=" N   VAL B  70 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 79
      removed outlier: 3.946A  pdb=" N   LEU B  76 " --> pdb=" O   PRO B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 3.536A  pdb=" N   VAL B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   GLU B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   THR B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 124
      removed outlier: 4.000A  pdb=" N   GLU B 122 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 158
      removed outlier: 4.789A  pdb=" N   ARG B 141 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      Proline residue:  B 142  - end of helix
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.756A  pdb=" N   ALA B 171 " --> pdb=" O   PRO B 167 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LYS B 172 " --> pdb=" O   GLU B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 221
      removed outlier: 3.678A  pdb=" N   ALA B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE B 219 " --> pdb=" O   GLY B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 245
      No H-bonds generated for 'chain 'B' and resid 243 through 245'
    Processing helix  chain 'B' and resid 246 through 251
    Processing helix  chain 'B' and resid 269 through 298
      removed outlier: 3.627A  pdb=" N   ASN B 273 " --> pdb=" O   ASN B 269 " (cutoff:3.500A)
      Proline residue:  B 275  - end of helix
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 301 through 307
    Processing helix  chain 'B' and resid 310 through 321
      removed outlier: 3.645A  pdb=" N   HIS B 319 " --> pdb=" O   PHE B 315 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLY B 321 " --> pdb=" O   ASN B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 357
      removed outlier: 4.647A  pdb=" N   ARG B 348 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ARG B 355 " --> pdb=" O   PHE B 351 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLU B 356 " --> pdb=" O   VAL B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 389
      removed outlier: 4.003A  pdb=" N   PHE B 389 " --> pdb=" O   LEU B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 422
      removed outlier: 3.929A  pdb=" N   SER B 401 " --> pdb=" O   ILE B 397 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   PHE B 402 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE B 416 " --> pdb=" O   ILE B 412 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TRP B 417 " --> pdb=" O   ILE B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 451
      removed outlier: 4.270A  pdb=" N   PHE B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE B 439 " --> pdb=" O   LEU B 435 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ILE B 447 " --> pdb=" O   CYS B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 476
      removed outlier: 3.865A  pdb=" N   ILE B 464 " --> pdb=" O   ILE B 460 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE B 465 " --> pdb=" O   GLY B 461 " (cutoff:3.500A)
      Proline residue:  B 470  - end of helix
      removed outlier: 3.895A  pdb=" N   GLY B 475 " --> pdb=" O   VAL B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 500
    Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 227
      removed outlier: 3.590A  pdb=" N   PHE A 467 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 262
      removed outlier: 6.853A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 8.722A  pdb=" N   ARG A 349 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 400 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 267
    Processing sheet with id=AA4, first strand: chain 'A' and resid 541 through 545
      removed outlier: 3.568A  pdb=" N   PHE A 545 " --> pdb=" O   SER A 553 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLU A 621 " --> pdb=" O   ASN A 569 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   GLY A 622 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   SER A 599 " --> pdb=" O   GLY A 622 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   LEU A 624 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU A 597 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG A 626 " --> pdb=" O   ASP A 595 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 575 through 576
      removed outlier: 3.569A  pdb=" N   LEU A 575 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)

    379 hydrogen bonds defined for protein.
    1095 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: 2.19

  Time building geometry restraints manager: 2.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2166
        1.34 -     1.46: 1276
        1.46 -     1.58: 4060
        1.58 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 7542
  Sorted by residual:
  bond pdb=" C   DAH B 601 "
       pdb=" OXT DAH B 601 "
    ideal  model  delta    sigma   weight residual
    1.360  1.257  0.103 2.00e-02 2.50e+03 2.64e+01
  bond pdb=" C4  NAG F   1 "
       pdb=" O4  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.409  1.477 -0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.64e+00
  bond pdb=" C3  NAG F   1 "
       pdb=" O3  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.403  1.435 -0.032 2.00e-02 2.50e+03 2.49e+00
  bond pdb=" CB  DAH B 601 "
       pdb=" CG  DAH B 601 "
    ideal  model  delta    sigma   weight residual
    1.487  1.517 -0.030 2.00e-02 2.50e+03 2.24e+00
  ... (remaining 7537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 10027
        2.03 -     4.06: 197
        4.06 -     6.09: 37
        6.09 -     8.12: 7
        8.12 -    10.15: 3
  Bond angle restraints: 10271
  Sorted by residual:
  angle pdb=" C   LEU B 138 "
        pdb=" N   ILE B 139 "
        pdb=" CA  ILE B 139 "
      ideal   model   delta    sigma   weight residual
     123.16  119.05    4.11 1.06e+00 8.90e-01 1.50e+01
  angle pdb=" N   ILE B 429 "
        pdb=" CA  ILE B 429 "
        pdb=" C   ILE B 429 "
      ideal   model   delta    sigma   weight residual
     113.22  117.46   -4.24 1.23e+00 6.61e-01 1.19e+01
  angle pdb=" CA  DAH B 601 "
        pdb=" C   DAH B 601 "
        pdb=" O   DAH B 601 "
      ideal   model   delta    sigma   weight residual
     128.96  118.81   10.15 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" N   PRO B 428 "
        pdb=" CA  PRO B 428 "
        pdb=" C   PRO B 428 "
      ideal   model   delta    sigma   weight residual
     112.47  119.32   -6.85 2.06e+00 2.36e-01 1.11e+01
  angle pdb=" N   GLU B  78 "
        pdb=" CA  GLU B  78 "
        pdb=" C   GLU B  78 "
      ideal   model   delta    sigma   weight residual
     114.31  110.14    4.17 1.29e+00 6.01e-01 1.05e+01
  ... (remaining 10266 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.38: 4227
       25.38 -    50.76: 234
       50.76 -    76.14: 31
       76.14 -   101.53: 15
      101.53 -   126.91: 11
  Dihedral angle restraints: 4518
    sinusoidal: 1845
      harmonic: 2673
  Sorted by residual:
  dihedral pdb=" C2  NAG D   2 "
           pdb=" C1  NAG D   2 "
           pdb=" O5  NAG D   2 "
           pdb=" C5  NAG D   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   63.95 -126.91     1      3.00e+01 1.11e-03 1.71e+01
  dihedral pdb=" C2  NAG D   1 "
           pdb=" C3  NAG D   1 "
           pdb=" C4  NAG D   1 "
           pdb=" O4  NAG D   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   56.03  119.08     1      3.00e+01 1.11e-03 1.59e+01
  dihedral pdb=" O3  NAG D   1 "
           pdb=" C3  NAG D   1 "
           pdb=" C4  NAG D   1 "
           pdb=" O4  NAG D   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.45  176.99  118.46     1      3.00e+01 1.11e-03 1.57e+01
  ... (remaining 4515 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.279: 1209
       0.279 -    0.558: 1
       0.558 -    0.837: 1
       0.837 -    1.117: 0
       1.117 -    1.396: 1
  Chirality restraints: 1212
  Sorted by residual:
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.70    0.30 2.00e-02 2.50e+03 2.22e+02
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-02 2.50e+03 1.35e+02
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-02 2.50e+03 9.43e+01
  ... (remaining 1209 not shown)

  Planarity restraints: 1275
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "    0.328 2.00e-02 2.50e+03   2.82e-01 9.96e+02
        pdb=" C7  NAG D   2 "   -0.074 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.026 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "   -0.490 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "    0.211 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.300 2.00e-02 2.50e+03   2.52e-01 7.94e+02
        pdb=" C7  NAG D   1 "    0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.188 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.431 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   1 "   -0.294 2.00e-02 2.50e+03   2.50e-01 7.79e+02
        pdb=" C7  NAG F   1 "    0.076 2.00e-02 2.50e+03
        pdb=" C8  NAG F   1 "   -0.182 2.00e-02 2.50e+03
        pdb=" N2  NAG F   1 "    0.430 2.00e-02 2.50e+03
        pdb=" O7  NAG F   1 "   -0.030 2.00e-02 2.50e+03
  ... (remaining 1272 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 873
        2.75 -     3.28: 7800
        3.28 -     3.82: 12211
        3.82 -     4.36: 13372
        4.36 -     4.90: 22899
  Nonbonded interactions: 57155
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 356 "
            pdb=" OG  SER A 359 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" NH2 ARG B 419 "
            pdb=" O   LYS B 422 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" OD1 ASN A 366 "
            pdb=" C8  NAG D   2 "
     model   vdw
     2.219 3.460
  nonbonded pdb=" O   TYR A 251 "
            pdb=" OG  SER A 254 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   ILE B 268 "
            pdb=" ND2 ASN B 273 "
     model   vdw
     2.256 3.120
  ... (remaining 57150 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.320
  Find NCS groups from input model:        0.110
  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:             0.010
  Load rotamer database and sin/cos tables:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.151   7551  Z= 0.225
  Angle     :  0.824  26.608  10297  Z= 0.384
  Chirality :  0.062   1.396   1212
  Planarity :  0.016   0.282   1271
  Dihedral  : 17.563 126.907   2797
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  0.89 %
    Favored  : 98.22 %
  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:  0.16 (0.29), residues: 928
  helix:  1.32 (0.25), residues: 481
  sheet:  0.09 (0.67), residues: 59
  loop : -1.48 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 184 
 HIS   0.004   0.001   HIS B 319 
 PHE   0.014   0.001   PHE B 402 
 TYR   0.015   0.001   TYR B 289 
 ARG   0.008   0.000   ARG A 614 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.10309 (    4)
  link_NAG-ASN         : angle      12.07163 (   12)
  link_BETA1-4         : bond        0.01903 (    4)
  link_BETA1-4         : angle       4.89330 (   12)
  hydrogen bonds       : bond        0.18774 (  379)
  hydrogen bonds       : angle       6.82108 ( 1095)
  SS BOND              : bond        0.00274 (    1)
  SS BOND              : angle       1.28614 (    2)
  covalent geometry    : bond        0.00376 ( 7542)
  covalent geometry    : angle       0.69449 (10271)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8006 (m-30) cc_final: 0.7689 (m-30)
REVERT: B   84 LEU cc_start: 0.9120 (tp) cc_final: 0.8914 (tt)
REVERT: B  141 ARG cc_start: 0.8992 (mmp80) cc_final: 0.8547 (mmp80)
REVERT: B  259 TYR cc_start: 0.8902 (m-80) cc_final: 0.8506 (m-80)
REVERT: B  383 MET cc_start: 0.8573 (tpp) cc_final: 0.7994 (mpp)
  outliers start: 7
  outliers final: 2
  residues processed: 107
  average time/residue: 0.1772
  time to fit residues: 26.7670
Evaluate side-chains
  66 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 429 ASN
A 561 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.062794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.045830 restraints weight = 38508.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.047296 restraints weight = 20661.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.048252 restraints weight = 14467.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7551  Z= 0.146
  Angle     :  0.746  11.384  10297  Z= 0.341
  Chirality :  0.045   0.332   1212
  Planarity :  0.005   0.048   1271
  Dihedral  : 14.328 103.780   1159
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 10.55 %
    Favored  : 88.69 %
  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:  0.70 (0.28), residues: 928
  helix:  1.76 (0.24), residues: 492
  sheet: -0.30 (0.63), residues: 66
  loop : -1.20 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 325 
 HIS   0.006   0.001   HIS B 367 
 PHE   0.021   0.001   PHE A 190 
 TYR   0.015   0.002   TYR B 103 
 ARG   0.005   0.001   ARG A 614 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00521 (    4)
  link_NAG-ASN         : angle       4.50007 (   12)
  link_BETA1-4         : bond        0.00978 (    4)
  link_BETA1-4         : angle       3.76601 (   12)
  hydrogen bonds       : bond        0.06073 (  379)
  hydrogen bonds       : angle       4.91556 ( 1095)
  SS BOND              : bond        0.00165 (    1)
  SS BOND              : angle       0.63438 (    2)
  covalent geometry    : bond        0.00295 ( 7542)
  covalent geometry    : angle       0.71955 (10271)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9351 (pp)
REVERT: A  471 ASP cc_start: 0.8107 (m-30) cc_final: 0.7701 (m-30)
REVERT: A  508 MET cc_start: 0.9269 (ptp) cc_final: 0.8815 (ptp)
REVERT: B   47 GLN cc_start: 0.8250 (mm110) cc_final: 0.8034 (mm-40)
REVERT: B  120 MET cc_start: 0.9004 (ppp) cc_final: 0.8604 (ppp)
REVERT: B  141 ARG cc_start: 0.9202 (mmp80) cc_final: 0.8885 (mmp80)
REVERT: B  262 PHE cc_start: 0.9487 (m-10) cc_final: 0.9284 (m-80)
REVERT: B  267 MET cc_start: 0.9282 (mpp) cc_final: 0.8956 (pmm)
REVERT: B  365 MET cc_start: 0.8161 (mmm) cc_final: 0.7891 (mmm)
REVERT: B  383 MET cc_start: 0.9211 (tpp) cc_final: 0.8632 (mpp)
  outliers start: 6
  outliers final: 4
  residues processed: 80
  average time/residue: 0.1544
  time to fit residues: 18.3629
Evaluate side-chains
  67 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9980
   chunk 48 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 221 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.063070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.045993 restraints weight = 39337.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.047490 restraints weight = 20965.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.048446 restraints weight = 14646.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7551  Z= 0.126
  Angle     :  0.662  12.537  10297  Z= 0.303
  Chirality :  0.041   0.222   1212
  Planarity :  0.005   0.059   1271
  Dihedral  : 13.195 110.795   1157
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 12.07 %
    Favored  : 87.04 %
  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:  0.88 (0.28), residues: 928
  helix:  1.94 (0.24), residues: 488
  sheet: -0.24 (0.64), residues: 66
  loop : -1.13 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 477 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.019   0.001   PHE B 402 
 TYR   0.013   0.001   TYR B 103 
 ARG   0.006   0.000   ARG A 614 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00546 (    4)
  link_NAG-ASN         : angle       3.83954 (   12)
  link_BETA1-4         : bond        0.01103 (    4)
  link_BETA1-4         : angle       3.30321 (   12)
  hydrogen bonds       : bond        0.05108 (  379)
  hydrogen bonds       : angle       4.44245 ( 1095)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       0.55204 (    2)
  covalent geometry    : bond        0.00255 ( 7542)
  covalent geometry    : angle       0.63942 (10271)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8113 (m-30) cc_final: 0.7696 (m-30)
REVERT: B  120 MET cc_start: 0.9030 (ppp) cc_final: 0.8583 (ppp)
REVERT: B  262 PHE cc_start: 0.9513 (m-10) cc_final: 0.9237 (m-80)
REVERT: B  267 MET cc_start: 0.9318 (mpp) cc_final: 0.8955 (pmm)
REVERT: B  365 MET cc_start: 0.8228 (mmm) cc_final: 0.7864 (mmm)
REVERT: B  383 MET cc_start: 0.9206 (tpp) cc_final: 0.8672 (mpp)
  outliers start: 7
  outliers final: 2
  residues processed: 77
  average time/residue: 0.1535
  time to fit residues: 17.7918
Evaluate side-chains
  67 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 88 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 483 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.061174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.044006 restraints weight = 40412.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.045450 restraints weight = 21738.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.046328 restraints weight = 15334.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   7551  Z= 0.198
  Angle     :  0.697   9.889  10297  Z= 0.324
  Chirality :  0.042   0.250   1212
  Planarity :  0.005   0.100   1271
  Dihedral  : 12.280 111.086   1157
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 14.74 %
    Favored  : 84.12 %
  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:  0.95 (0.29), residues: 928
  helix:  2.02 (0.24), residues: 486
  sheet: -0.46 (0.65), residues: 66
  loop : -1.07 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 134 
 HIS   0.004   0.001   HIS A 266 
 PHE   0.015   0.001   PHE B 402 
 TYR   0.017   0.002   TYR B 472 
 ARG   0.006   0.000   ARG A 614 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00316 (    4)
  link_NAG-ASN         : angle       3.31727 (   12)
  link_BETA1-4         : bond        0.01013 (    4)
  link_BETA1-4         : angle       3.33419 (   12)
  hydrogen bonds       : bond        0.04998 (  379)
  hydrogen bonds       : angle       4.43812 ( 1095)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       0.75685 (    2)
  covalent geometry    : bond        0.00440 ( 7542)
  covalent geometry    : angle       0.67888 (10271)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8091 (m-30) cc_final: 0.7684 (m-30)
REVERT: A  508 MET cc_start: 0.9267 (ptp) cc_final: 0.8861 (ptp)
REVERT: B  120 MET cc_start: 0.9080 (ppp) cc_final: 0.8529 (ppp)
REVERT: B  262 PHE cc_start: 0.9549 (m-80) cc_final: 0.9302 (m-80)
REVERT: B  267 MET cc_start: 0.9260 (mpp) cc_final: 0.8941 (pmm)
REVERT: B  365 MET cc_start: 0.8439 (mmm) cc_final: 0.7966 (mmm)
REVERT: B  383 MET cc_start: 0.9235 (tpp) cc_final: 0.8651 (mpp)
  outliers start: 9
  outliers final: 8
  residues processed: 67
  average time/residue: 0.1807
  time to fit residues: 17.9545
Evaluate side-chains
  64 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 67 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.061355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.044223 restraints weight = 40104.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.045679 restraints weight = 21510.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.046583 restraints weight = 15110.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7551  Z= 0.149
  Angle     :  0.670  16.138  10297  Z= 0.307
  Chirality :  0.041   0.236   1212
  Planarity :  0.005   0.076   1271
  Dihedral  : 11.715 111.595   1157
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 15.25 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.04 (0.29), residues: 928
  helix:  2.15 (0.24), residues: 483
  sheet: -0.53 (0.65), residues: 66
  loop : -1.05 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 134 
 HIS   0.004   0.001   HIS B 319 
 PHE   0.020   0.001   PHE B 402 
 TYR   0.008   0.001   TYR B 248 
 ARG   0.006   0.000   ARG A 614 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00422 (    4)
  link_NAG-ASN         : angle       3.11321 (   12)
  link_BETA1-4         : bond        0.01056 (    4)
  link_BETA1-4         : angle       3.37171 (   12)
  hydrogen bonds       : bond        0.04617 (  379)
  hydrogen bonds       : angle       4.24448 ( 1095)
  SS BOND              : bond        0.00117 (    1)
  SS BOND              : angle       0.64523 (    2)
  covalent geometry    : bond        0.00323 ( 7542)
  covalent geometry    : angle       0.65191 (10271)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8118 (m-30) cc_final: 0.7675 (m-30)
REVERT: B  120 MET cc_start: 0.9094 (ppp) cc_final: 0.8583 (ppp)
REVERT: B  262 PHE cc_start: 0.9505 (m-80) cc_final: 0.9282 (m-80)
REVERT: B  267 MET cc_start: 0.9316 (mpp) cc_final: 0.8925 (pmm)
REVERT: B  365 MET cc_start: 0.8498 (mmm) cc_final: 0.7154 (mmp)
REVERT: B  383 MET cc_start: 0.9239 (tpp) cc_final: 0.8659 (mpp)
  outliers start: 15
  outliers final: 10
  residues processed: 76
  average time/residue: 0.1776
  time to fit residues: 19.4305
Evaluate side-chains
  68 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  385 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.062023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.045221 restraints weight = 39980.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.046639 restraints weight = 22188.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.047537 restraints weight = 15897.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7551  Z= 0.131
  Angle     :  0.678  13.221  10297  Z= 0.307
  Chirality :  0.041   0.232   1212
  Planarity :  0.005   0.083   1271
  Dihedral  : 11.411 111.258   1156
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.90 %
    Favored  : 81.58 %
  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:  1.10 (0.29), residues: 928
  helix:  2.20 (0.24), residues: 483
  sheet: -0.55 (0.64), residues: 66
  loop : -1.02 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 134 
 HIS   0.007   0.001   HIS B 367 
 PHE   0.023   0.001   PHE B 402 
 TYR   0.008   0.001   TYR B 248 
 ARG   0.009   0.000   ARG B 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00390 (    4)
  link_NAG-ASN         : angle       3.08126 (   12)
  link_BETA1-4         : bond        0.00907 (    4)
  link_BETA1-4         : angle       3.35311 (   12)
  hydrogen bonds       : bond        0.04412 (  379)
  hydrogen bonds       : angle       4.18644 ( 1095)
  SS BOND              : bond        0.00125 (    1)
  SS BOND              : angle       0.50777 (    2)
  covalent geometry    : bond        0.00284 ( 7542)
  covalent geometry    : angle       0.66024 (10271)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8132 (m-30) cc_final: 0.7693 (m-30)
REVERT: A  508 MET cc_start: 0.9332 (ptp) cc_final: 0.8948 (ptp)
REVERT: B  120 MET cc_start: 0.9131 (ppp) cc_final: 0.8592 (ppp)
REVERT: B  262 PHE cc_start: 0.9501 (m-80) cc_final: 0.9288 (m-80)
REVERT: B  267 MET cc_start: 0.9307 (mpp) cc_final: 0.8904 (pmm)
REVERT: B  365 MET cc_start: 0.8582 (mmm) cc_final: 0.7263 (mmp)
  outliers start: 12
  outliers final: 10
  residues processed: 73
  average time/residue: 0.1770
  time to fit residues: 18.6670
Evaluate side-chains
  72 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  385 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 65 optimal weight:    0.1980
   chunk 58 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0770
   chunk 3 optimal weight:    0.8980
   chunk 66 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 186 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.063100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.046706 restraints weight = 38721.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.048161 restraints weight = 21093.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.049086 restraints weight = 14946.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7551  Z= 0.114
  Angle     :  0.677  13.379  10297  Z= 0.303
  Chirality :  0.041   0.241   1212
  Planarity :  0.005   0.081   1271
  Dihedral  : 11.034 110.673   1156
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 18.17 %
    Favored  : 80.18 %
  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:  1.18 (0.29), residues: 928
  helix:  2.25 (0.24), residues: 483
  sheet: -0.52 (0.64), residues: 66
  loop : -0.95 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 134 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.024   0.001   PHE B 402 
 TYR   0.008   0.001   TYR B 387 
 ARG   0.007   0.001   ARG B  48 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00467 (    4)
  link_NAG-ASN         : angle       3.06454 (   12)
  link_BETA1-4         : bond        0.00994 (    4)
  link_BETA1-4         : angle       3.41171 (   12)
  hydrogen bonds       : bond        0.04135 (  379)
  hydrogen bonds       : angle       4.02817 ( 1095)
  SS BOND              : bond        0.00176 (    1)
  SS BOND              : angle       0.48226 (    2)
  covalent geometry    : bond        0.00234 ( 7542)
  covalent geometry    : angle       0.65964 (10271)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8175 (m-30) cc_final: 0.7745 (m-30)
REVERT: A  508 MET cc_start: 0.9283 (ptp) cc_final: 0.8894 (ptp)
REVERT: B  120 MET cc_start: 0.9136 (ppp) cc_final: 0.8568 (ppp)
REVERT: B  262 PHE cc_start: 0.9456 (m-80) cc_final: 0.9244 (m-80)
REVERT: B  267 MET cc_start: 0.9232 (mpp) cc_final: 0.8806 (pmm)
REVERT: B  365 MET cc_start: 0.8550 (mmm) cc_final: 0.7941 (mmm)
REVERT: B  383 MET cc_start: 0.9165 (tpp) cc_final: 0.8608 (mpp)
  outliers start: 13
  outliers final: 11
  residues processed: 75
  average time/residue: 0.1680
  time to fit residues: 18.1076
Evaluate side-chains
  73 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 8 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 86 optimal weight:    0.3980
   chunk 67 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0020
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.063351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.046762 restraints weight = 39602.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.048242 restraints weight = 21257.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.049186 restraints weight = 14982.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7551  Z= 0.111
  Angle     :  0.676  11.685  10297  Z= 0.303
  Chirality :  0.042   0.252   1212
  Planarity :  0.004   0.075   1271
  Dihedral  : 10.546 109.882   1156
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 18.81 %
    Favored  : 79.67 %
  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:  1.21 (0.29), residues: 928
  helix:  2.22 (0.24), residues: 486
  sheet: -0.44 (0.65), residues: 66
  loop : -0.90 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.022   0.001   PHE B 402 
 TYR   0.009   0.001   TYR B 103 
 ARG   0.007   0.000   ARG A 614 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00446 (    4)
  link_NAG-ASN         : angle       3.03677 (   12)
  link_BETA1-4         : bond        0.00947 (    4)
  link_BETA1-4         : angle       3.44091 (   12)
  hydrogen bonds       : bond        0.03824 (  379)
  hydrogen bonds       : angle       4.00975 ( 1095)
  SS BOND              : bond        0.00158 (    1)
  SS BOND              : angle       0.45068 (    2)
  covalent geometry    : bond        0.00234 ( 7542)
  covalent geometry    : angle       0.65821 (10271)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8176 (m-30) cc_final: 0.7746 (m-30)
REVERT: A  508 MET cc_start: 0.9262 (ptp) cc_final: 0.8889 (ptp)
REVERT: B  120 MET cc_start: 0.9144 (ppp) cc_final: 0.8593 (ppp)
REVERT: B  145 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.8841 (mp10)
REVERT: B  262 PHE cc_start: 0.9404 (m-80) cc_final: 0.9173 (m-80)
REVERT: B  365 MET cc_start: 0.8523 (mmm) cc_final: 0.6868 (tpp)
REVERT: B  383 MET cc_start: 0.9132 (tpp) cc_final: 0.8619 (mpp)
  outliers start: 12
  outliers final: 9
  residues processed: 79
  average time/residue: 0.1818
  time to fit residues: 20.2432
Evaluate side-chains
  70 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  473 PHE
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 77 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 87 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.063173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.046427 restraints weight = 40363.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.047893 restraints weight = 21765.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.048858 restraints weight = 15382.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7551  Z= 0.117
  Angle     :  0.693  11.357  10297  Z= 0.311
  Chirality :  0.043   0.257   1212
  Planarity :  0.005   0.076   1271
  Dihedral  : 10.234 109.448   1156
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 19.06 %
    Favored  : 79.29 %
  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:  1.16 (0.29), residues: 928
  helix:  2.11 (0.24), residues: 492
  sheet: -0.41 (0.65), residues: 66
  loop : -0.88 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 134 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.024   0.001   PHE B 402 
 TYR   0.007   0.001   TYR B 103 
 ARG   0.008   0.000   ARG A 614 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00402 (    4)
  link_NAG-ASN         : angle       2.97862 (   12)
  link_BETA1-4         : bond        0.01002 (    4)
  link_BETA1-4         : angle       3.46028 (   12)
  hydrogen bonds       : bond        0.03803 (  379)
  hydrogen bonds       : angle       4.05737 ( 1095)
  SS BOND              : bond        0.00146 (    1)
  SS BOND              : angle       0.48475 (    2)
  covalent geometry    : bond        0.00249 ( 7542)
  covalent geometry    : angle       0.67573 (10271)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8163 (m-30) cc_final: 0.7740 (m-30)
REVERT: B  120 MET cc_start: 0.9148 (ppp) cc_final: 0.8592 (ppp)
REVERT: B  262 PHE cc_start: 0.9391 (m-80) cc_final: 0.9172 (m-80)
REVERT: B  267 MET cc_start: 0.9351 (mpp) cc_final: 0.9034 (pmm)
REVERT: B  365 MET cc_start: 0.8611 (mmm) cc_final: 0.6936 (tpp)
REVERT: B  383 MET cc_start: 0.9111 (tpp) cc_final: 0.8596 (mpp)
  outliers start: 13
  outliers final: 11
  residues processed: 69
  average time/residue: 0.1569
  time to fit residues: 16.1793
Evaluate side-chains
  73 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  473 PHE
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0010
   chunk 86 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 85 optimal weight:    0.0270
   overall best weight:    0.5644

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.063755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.047182 restraints weight = 39600.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.048649 restraints weight = 21454.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.049576 restraints weight = 15182.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7551  Z= 0.111
  Angle     :  0.695  11.426  10297  Z= 0.311
  Chirality :  0.042   0.262   1212
  Planarity :  0.004   0.055   1271
  Dihedral  :  9.686 108.773   1156
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 19.70 %
    Favored  : 79.16 %
  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:  1.19 (0.29), residues: 928
  helix:  2.14 (0.24), residues: 492
  sheet: -0.30 (0.66), residues: 66
  loop : -0.89 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 134 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.023   0.001   PHE B 402 
 TYR   0.014   0.001   TYR B 248 
 ARG   0.007   0.000   ARG A 614 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00451 (    4)
  link_NAG-ASN         : angle       2.91108 (   12)
  link_BETA1-4         : bond        0.01029 (    4)
  link_BETA1-4         : angle       3.53548 (   12)
  hydrogen bonds       : bond        0.03634 (  379)
  hydrogen bonds       : angle       3.92243 ( 1095)
  SS BOND              : bond        0.00171 (    1)
  SS BOND              : angle       0.44874 (    2)
  covalent geometry    : bond        0.00233 ( 7542)
  covalent geometry    : angle       0.67779 (10271)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8125 (m-30) cc_final: 0.7715 (m-30)
REVERT: A  508 MET cc_start: 0.9326 (ptp) cc_final: 0.8933 (mpp)
REVERT: B  120 MET cc_start: 0.9151 (ppp) cc_final: 0.8598 (ppp)
REVERT: B  141 ARG cc_start: 0.8898 (mmp80) cc_final: 0.8118 (mmp80)
REVERT: B  145 GLN cc_start: 0.9357 (OUTLIER) cc_final: 0.8827 (mp10)
REVERT: B  267 MET cc_start: 0.9225 (mpp) cc_final: 0.8916 (pmm)
REVERT: B  365 MET cc_start: 0.8356 (mmm) cc_final: 0.7590 (mmm)
REVERT: B  383 MET cc_start: 0.9047 (tpp) cc_final: 0.8596 (mpp)
  outliers start: 9
  outliers final: 7
  residues processed: 72
  average time/residue: 0.1535
  time to fit residues: 16.4700
Evaluate side-chains
  71 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  473 PHE
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 63 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 34 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 50 optimal weight:    8.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 GLN
B 420 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.060814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.044038 restraints weight = 40847.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.045399 restraints weight = 22698.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.046267 restraints weight = 16317.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   7551  Z= 0.239
  Angle     :  0.757  10.639  10297  Z= 0.350
  Chirality :  0.044   0.249   1212
  Planarity :  0.004   0.044   1271
  Dihedral  :  9.570 110.248   1156
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 19.44 %
    Favored  : 78.78 %
  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:  1.18 (0.29), residues: 928
  helix:  2.12 (0.24), residues: 493
  sheet: -0.53 (0.65), residues: 66
  loop : -0.84 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 257 
 HIS   0.004   0.001   HIS A 266 
 PHE   0.024   0.002   PHE B 402 
 TYR   0.015   0.002   TYR B 387 
 ARG   0.007   0.001   ARG A 614 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    4)
  link_NAG-ASN         : angle       2.74459 (   12)
  link_BETA1-4         : bond        0.00884 (    4)
  link_BETA1-4         : angle       3.30644 (   12)
  hydrogen bonds       : bond        0.04427 (  379)
  hydrogen bonds       : angle       4.32082 ( 1095)
  SS BOND              : bond        0.00058 (    1)
  SS BOND              : angle       0.81615 (    2)
  covalent geometry    : bond        0.00523 ( 7542)
  covalent geometry    : angle       0.74363 (10271)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2575.05 seconds
wall clock time: 45 minutes 26.20 seconds (2726.20 seconds total)