Starting phenix.real_space_refine
on Fri Aug 22 19:48:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j8l_36073/08_2025/8j8l_36073_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j8l_36073/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j8l_36073/08_2025/8j8l_36073_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j8l_36073/08_2025/8j8l_36073_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j8l_36073/08_2025/8j8l_36073.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j8l_36073/08_2025/8j8l_36073.map"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.75, per 1000 atoms: 0.24
  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: 0.72
  Conformation dependent library (CDL) restraints added in 359.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.29
  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: 1.10

  Time building geometry restraints manager: 0.90 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:             1.230
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.390
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.130
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (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
 ARG   0.008   0.000   ARG A 614 
 TYR   0.015   0.001   TYR B 289 
 PHE   0.014   0.001   PHE B 402 
 TRP   0.006   0.001   TRP A 184 
 HIS   0.004   0.001   HIS B 319 

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

*********************** 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  : 0.245 
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: 0.0775
  time to fit residues: 11.7455
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  : 0.283 
-------------------------------------------------------------------------------
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 49 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0020
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7794

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.062836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.045810 restraints weight = 38973.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.047291 restraints weight = 20818.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.048225 restraints weight = 14546.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.048788 restraints weight = 11815.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.049170 restraints weight = 10433.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1523

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= 0.150
  Angle     :  0.739  11.365  10297  Z= 0.340
  Chirality :  0.044   0.278   1212
  Planarity :  0.005   0.047   1271
  Dihedral  : 14.662 105.673   1159
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.28), residues: 928
  helix:  1.77 (0.24), residues: 492
  sheet: -0.28 (0.63), residues: 66
  loop : -1.19 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 614 
 TYR   0.013   0.001   TYR B 296 
 PHE   0.021   0.001   PHE A 190 
 TRP   0.007   0.001   TRP B 325 
 HIS   0.006   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 7542)
  covalent geometry    : angle       0.71213 (10271)
  SS BOND              : bond        0.00162 (    1)
  SS BOND              : angle       0.53423 (    2)
  hydrogen bonds       : bond        0.06316 (  379)
  hydrogen bonds       : angle       4.98067 ( 1095)
  link_BETA1-4         : bond        0.00949 (    4)
  link_BETA1-4         : angle       3.64375 (   12)
  link_NAG-ASN         : bond        0.00513 (    4)
  link_NAG-ASN         : angle       4.65764 (   12)

*********************** 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  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8120 (m-30) cc_final: 0.7712 (m-30)
REVERT: B   47 GLN cc_start: 0.8184 (mm110) cc_final: 0.7963 (mm-40)
REVERT: B  141 ARG cc_start: 0.9183 (mmp80) cc_final: 0.8859 (mmp80)
REVERT: B  262 PHE cc_start: 0.9490 (m-10) cc_final: 0.9289 (m-80)
REVERT: B  267 MET cc_start: 0.9253 (mpp) cc_final: 0.8905 (pmm)
REVERT: B  365 MET cc_start: 0.8113 (mmm) cc_final: 0.7839 (mmm)
REVERT: B  383 MET cc_start: 0.9212 (tpp) cc_final: 0.8621 (mpp)
  outliers start: 6
  outliers final: 4
  residues processed: 80
  average time/residue: 0.0702
  time to fit residues: 8.3791
Evaluate side-chains
  67 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 83 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0370
   chunk 43 optimal weight:    4.9990
   chunk 80 optimal weight:    0.3980
   chunk 6 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 63 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    2.0864

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

Flipped N/Q/H residues before XYZ refinement:
A 221 HIS
A 483 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.061461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.044182 restraints weight = 39860.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.045621 restraints weight = 21600.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.046520 restraints weight = 15279.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.047077 restraints weight = 12443.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.047439 restraints weight = 11024.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7551  Z= 0.171
  Angle     :  0.671   8.817  10297  Z= 0.314
  Chirality :  0.042   0.222   1212
  Planarity :  0.004   0.055   1271
  Dihedral  : 13.230 112.403   1157
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.58 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.29), residues: 928
  helix:  2.01 (0.24), residues: 488
  sheet: -0.40 (0.65), residues: 66
  loop : -1.13 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 614 
 TYR   0.015   0.002   TYR B 472 
 PHE   0.018   0.001   PHE B 402 
 TRP   0.012   0.001   TRP B 477 
 HIS   0.004   0.001   HIS A 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 7542)
  covalent geometry    : angle       0.65210 (10271)
  SS BOND              : bond        0.00046 (    1)
  SS BOND              : angle       0.91010 (    2)
  hydrogen bonds       : bond        0.05326 (  379)
  hydrogen bonds       : angle       4.60084 ( 1095)
  link_BETA1-4         : bond        0.00875 (    4)
  link_BETA1-4         : angle       3.12757 (   12)
  link_NAG-ASN         : bond        0.00322 (    4)
  link_NAG-ASN         : angle       3.60172 (   12)

*********************** 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
  76 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8113 (m-30) cc_final: 0.7703 (m-30)
REVERT: A  508 MET cc_start: 0.9258 (ptp) cc_final: 0.8765 (ptp)
REVERT: B  262 PHE cc_start: 0.9544 (m-10) cc_final: 0.9280 (m-80)
REVERT: B  267 MET cc_start: 0.9302 (mpp) cc_final: 0.8948 (pmm)
REVERT: B  365 MET cc_start: 0.8397 (mmm) cc_final: 0.7918 (mmm)
REVERT: B  383 MET cc_start: 0.9240 (tpp) cc_final: 0.8667 (mpp)
  outliers start: 9
  outliers final: 6
  residues processed: 72
  average time/residue: 0.0655
  time to fit residues: 7.1267
Evaluate side-chains
  63 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain B residue  120 MET
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  431 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 87 optimal weight:    7.9990
   chunk 46 optimal weight:    7.9990
   chunk 91 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 64 optimal weight:   30.0000
   chunk 63 optimal weight:    5.9990
   overall best weight:    3.9588

-------------------------------------------------------------------------------
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**
A 429 ASN
B 218 GLN
B 420 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.059151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.041911 restraints weight = 40988.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.043283 restraints weight = 22207.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.044159 restraints weight = 15786.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.044709 restraints weight = 12888.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.045028 restraints weight = 11404.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.090   7551  Z= 0.270
  Angle     :  0.762  10.854  10297  Z= 0.359
  Chirality :  0.044   0.263   1212
  Planarity :  0.005   0.073   1271
  Dihedral  : 12.386 111.955   1157
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.99 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.28), residues: 928
  helix:  1.61 (0.23), residues: 494
  sheet: -0.72 (0.65), residues: 66
  loop : -1.07 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 614 
 TYR   0.025   0.002   TYR B 472 
 PHE   0.020   0.002   PHE B 402 
 TRP   0.010   0.001   TRP B 477 
 HIS   0.005   0.001   HIS A 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 ( 7542)
  covalent geometry    : angle       0.74741 (10271)
  SS BOND              : bond        0.00027 (    1)
  SS BOND              : angle       0.95213 (    2)
  hydrogen bonds       : bond        0.05520 (  379)
  hydrogen bonds       : angle       4.74725 ( 1095)
  link_BETA1-4         : bond        0.00968 (    4)
  link_BETA1-4         : angle       3.24834 (   12)
  link_NAG-ASN         : bond        0.00371 (    4)
  link_NAG-ASN         : angle       3.08603 (   12)

*********************** 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
  69 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8186 (m-30) cc_final: 0.7786 (m-30)
REVERT: A  508 MET cc_start: 0.9226 (ptp) cc_final: 0.8981 (ptp)
REVERT: B  262 PHE cc_start: 0.9532 (m-80) cc_final: 0.9292 (m-80)
REVERT: B  267 MET cc_start: 0.9337 (mpp) cc_final: 0.8960 (pmm)
REVERT: B  365 MET cc_start: 0.8638 (mmm) cc_final: 0.7368 (mmp)
  outliers start: 15
  outliers final: 11
  residues processed: 63
  average time/residue: 0.0722
  time to fit residues: 6.8004
Evaluate side-chains
  59 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain B residue  120 MET
Chi-restraints excluded: chain B residue  137 LEU
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  431 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0980
   chunk 34 optimal weight:    0.0030
   chunk 79 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0670
   chunk 80 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0050
   chunk 11 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 49 optimal weight:   20.0000
   overall best weight:    0.1942

-------------------------------------------------------------------------------
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 = 0.3348 r_free = 0.3348 target = 0.062184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.045018 restraints weight = 39439.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.046511 restraints weight = 21204.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.047459 restraints weight = 14888.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.048055 restraints weight = 12032.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.048400 restraints weight = 10607.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7551  Z= 0.120
  Angle     :  0.687  15.647  10297  Z= 0.308
  Chirality :  0.041   0.238   1212
  Planarity :  0.005   0.074   1271
  Dihedral  : 11.808 111.766   1157
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.52 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.28), residues: 928
  helix:  2.07 (0.24), residues: 486
  sheet: -0.55 (0.64), residues: 66
  loop : -1.06 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 614 
 TYR   0.008   0.001   TYR A 554 
 PHE   0.023   0.001   PHE B 402 
 TRP   0.004   0.001   TRP B 134 
 HIS   0.003   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 7542)
  covalent geometry    : angle       0.66917 (10271)
  SS BOND              : bond        0.00252 (    1)
  SS BOND              : angle       0.53676 (    2)
  hydrogen bonds       : bond        0.04569 (  379)
  hydrogen bonds       : angle       4.18488 ( 1095)
  link_BETA1-4         : bond        0.01062 (    4)
  link_BETA1-4         : angle       3.43691 (   12)
  link_NAG-ASN         : bond        0.00614 (    4)
  link_NAG-ASN         : angle       3.10891 (   12)

*********************** 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
  83 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8188 (m-30) cc_final: 0.7733 (m-30)
REVERT: B  262 PHE cc_start: 0.9466 (m-80) cc_final: 0.9266 (m-80)
REVERT: B  267 MET cc_start: 0.9271 (mpp) cc_final: 0.8948 (pmm)
REVERT: B  348 ARG cc_start: 0.9434 (mmt-90) cc_final: 0.8817 (mmt-90)
REVERT: B  365 MET cc_start: 0.8495 (mmm) cc_final: 0.7144 (mmp)
REVERT: B  383 MET cc_start: 0.9219 (tpp) cc_final: 0.8640 (mpp)
  outliers start: 11
  outliers final: 8
  residues processed: 78
  average time/residue: 0.0816
  time to fit residues: 8.9227
Evaluate side-chains
  66 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
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  120 MET
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  386 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 61 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 72 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 6 optimal weight:    9.9990
   chunk 62 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 89 optimal weight:   10.0000
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3371 r_free = 0.3371 target = 0.062067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.045263 restraints weight = 40219.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.046704 restraints weight = 21936.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.047617 restraints weight = 15591.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.048172 restraints weight = 12767.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.048424 restraints weight = 11330.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7551  Z= 0.131
  Angle     :  0.673  12.101  10297  Z= 0.308
  Chirality :  0.041   0.233   1212
  Planarity :  0.005   0.078   1271
  Dihedral  : 11.427 111.191   1156
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 17.92 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.29), residues: 928
  helix:  2.10 (0.24), residues: 485
  sheet: -0.60 (0.64), residues: 66
  loop : -0.98 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 355 
 TYR   0.009   0.001   TYR A 554 
 PHE   0.029   0.001   PHE B 297 
 TRP   0.011   0.001   TRP B 134 
 HIS   0.005   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7542)
  covalent geometry    : angle       0.65567 (10271)
  SS BOND              : bond        0.00115 (    1)
  SS BOND              : angle       0.51259 (    2)
  hydrogen bonds       : bond        0.04395 (  379)
  hydrogen bonds       : angle       4.17160 ( 1095)
  link_BETA1-4         : bond        0.00883 (    4)
  link_BETA1-4         : angle       3.33670 (   12)
  link_NAG-ASN         : bond        0.00343 (    4)
  link_NAG-ASN         : angle       3.05161 (   12)

*********************** 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
  80 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8188 (m-30) cc_final: 0.7778 (m-30)
REVERT: A  508 MET cc_start: 0.9345 (ptp) cc_final: 0.8994 (ptp)
REVERT: B  267 MET cc_start: 0.9255 (mpp) cc_final: 0.8856 (pmm)
REVERT: B  365 MET cc_start: 0.8648 (mmm) cc_final: 0.7885 (mmm)
  outliers start: 14
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0756
  time to fit residues: 8.1530
Evaluate side-chains
  70 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  120 MET
Chi-restraints excluded: chain B residue  137 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 58 optimal weight:   10.0000
   chunk 72 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 32 optimal weight:    8.9990
   chunk 68 optimal weight:    7.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.3347 r_free = 0.3347 target = 0.061005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.044183 restraints weight = 40567.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.045567 restraints weight = 22559.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.046455 restraints weight = 16191.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.046972 restraints weight = 13327.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.047266 restraints weight = 11894.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7551  Z= 0.165
  Angle     :  0.700  14.188  10297  Z= 0.320
  Chirality :  0.042   0.241   1212
  Planarity :  0.005   0.075   1271
  Dihedral  : 11.045 110.997   1156
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 18.81 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.29), residues: 928
  helix:  2.11 (0.24), residues: 488
  sheet: -0.64 (0.64), residues: 66
  loop : -0.91 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 614 
 TYR   0.010   0.001   TYR A 554 
 PHE   0.025   0.001   PHE B 402 
 TRP   0.010   0.001   TRP B 134 
 HIS   0.004   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7542)
  covalent geometry    : angle       0.68436 (10271)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       0.66045 (    2)
  hydrogen bonds       : bond        0.04567 (  379)
  hydrogen bonds       : angle       4.27464 ( 1095)
  link_BETA1-4         : bond        0.00953 (    4)
  link_BETA1-4         : angle       3.29593 (   12)
  link_NAG-ASN         : bond        0.00253 (    4)
  link_NAG-ASN         : angle       2.94427 (   12)

*********************** 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
  76 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  471 ASP cc_start: 0.8157 (m-30) cc_final: 0.7751 (m-30)
REVERT: B  262 PHE cc_start: 0.9412 (m-80) cc_final: 0.9141 (m-80)
REVERT: B  267 MET cc_start: 0.9232 (mpp) cc_final: 0.8802 (pmm)
REVERT: B  297 PHE cc_start: 0.8463 (t80) cc_final: 0.8215 (t80)
REVERT: B  365 MET cc_start: 0.8718 (mmm) cc_final: 0.7053 (tpp)
  outliers start: 15
  outliers final: 10
  residues processed: 69
  average time/residue: 0.0692
  time to fit residues: 7.1586
Evaluate side-chains
  66 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue  120 MET
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:   10.0000
   chunk 68 optimal weight:    7.9990
   chunk 50 optimal weight:    9.9990
   chunk 65 optimal weight:   40.0000
   chunk 4 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3398 r_free = 0.3398 target = 0.062131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.045678 restraints weight = 40337.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.047116 restraints weight = 21825.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.048018 restraints weight = 15445.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.048594 restraints weight = 12663.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.048897 restraints weight = 11201.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2971

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= 0.116
  Angle     :  0.676  11.109  10297  Z= 0.305
  Chirality :  0.041   0.257   1212
  Planarity :  0.004   0.068   1271
  Dihedral  : 10.600 110.463   1156
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 18.81 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.29), residues: 928
  helix:  2.14 (0.24), residues: 489
  sheet: -0.59 (0.63), residues: 66
  loop : -0.93 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 614 
 TYR   0.009   0.001   TYR A 554 
 PHE   0.022   0.001   PHE B 402 
 TRP   0.011   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 7542)
  covalent geometry    : angle       0.65910 (10271)
  SS BOND              : bond        0.00209 (    1)
  SS BOND              : angle       0.52975 (    2)
  hydrogen bonds       : bond        0.04096 (  379)
  hydrogen bonds       : angle       4.06362 ( 1095)
  link_BETA1-4         : bond        0.00935 (    4)
  link_BETA1-4         : angle       3.40738 (   12)
  link_NAG-ASN         : bond        0.00396 (    4)
  link_NAG-ASN         : angle       2.93246 (   12)

*********************** 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
  79 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8173 (m-30) cc_final: 0.7798 (m-30)
REVERT: A  508 MET cc_start: 0.9348 (ptp) cc_final: 0.8928 (mpp)
REVERT: B  145 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.8809 (mp10)
REVERT: B  297 PHE cc_start: 0.8480 (t80) cc_final: 0.8178 (t80)
REVERT: B  365 MET cc_start: 0.8672 (mmm) cc_final: 0.7001 (tpp)
  outliers start: 15
  outliers final: 10
  residues processed: 74
  average time/residue: 0.0752
  time to fit residues: 8.1505
Evaluate side-chains
  72 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   49 ASN
Chi-restraints excluded: chain B residue  120 MET
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  196 VAL
Chi-restraints excluded: chain B residue  265 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.3357 r_free = 0.3357 target = 0.061470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.044697 restraints weight = 40289.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.046069 restraints weight = 22407.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.046946 restraints weight = 16095.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.047476 restraints weight = 13253.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.047780 restraints weight = 11826.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7551  Z= 0.148
  Angle     :  0.703  13.468  10297  Z= 0.318
  Chirality :  0.042   0.256   1212
  Planarity :  0.004   0.055   1271
  Dihedral  : 10.292 110.221   1156
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 19.44 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.29), residues: 928
  helix:  2.20 (0.24), residues: 488
  sheet: -0.55 (0.65), residues: 66
  loop : -0.79 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 614 
 TYR   0.010   0.001   TYR A 554 
 PHE   0.024   0.001   PHE B 402 
 TRP   0.011   0.001   TRP B 134 
 HIS   0.003   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7542)
  covalent geometry    : angle       0.68784 (10271)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       0.62819 (    2)
  hydrogen bonds       : bond        0.04208 (  379)
  hydrogen bonds       : angle       4.18100 ( 1095)
  link_BETA1-4         : bond        0.00900 (    4)
  link_BETA1-4         : angle       3.34388 (   12)
  link_NAG-ASN         : bond        0.00234 (    4)
  link_NAG-ASN         : angle       2.80110 (   12)

*********************** 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: 11
    poor density    : 62
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8137 (m-30) cc_final: 0.7736 (m-30)
REVERT: A  508 MET cc_start: 0.9333 (ptp) cc_final: 0.8913 (mpp)
REVERT: B  262 PHE cc_start: 0.9373 (m-80) cc_final: 0.9135 (m-80)
REVERT: B  365 MET cc_start: 0.8705 (mmm) cc_final: 0.7060 (tpp)
REVERT: B  383 MET cc_start: 0.9170 (tpp) cc_final: 0.8445 (mpp)
  outliers start: 11
  outliers final: 10
  residues processed: 68
  average time/residue: 0.0697
  time to fit residues: 6.9406
Evaluate side-chains
  67 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue  120 MET
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  294 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 45 optimal weight:    0.1980
   chunk 63 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3370 r_free = 0.3370 target = 0.062014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.045238 restraints weight = 39710.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.046637 restraints weight = 22023.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.047532 restraints weight = 15800.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.048036 restraints weight = 13004.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.048332 restraints weight = 11651.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.3133

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= 0.123
  Angle     :  0.709  12.659  10297  Z= 0.318
  Chirality :  0.043   0.264   1212
  Planarity :  0.004   0.050   1271
  Dihedral  : 10.038 110.035   1156
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 19.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.29), residues: 928
  helix:  2.10 (0.24), residues: 494
  sheet: -0.47 (0.65), residues: 66
  loop : -0.83 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 614 
 TYR   0.011   0.001   TYR B 387 
 PHE   0.024   0.001   PHE B 402 
 TRP   0.010   0.001   TRP B 134 
 HIS   0.003   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7542)
  covalent geometry    : angle       0.69356 (10271)
  SS BOND              : bond        0.00190 (    1)
  SS BOND              : angle       0.56292 (    2)
  hydrogen bonds       : bond        0.04051 (  379)
  hydrogen bonds       : angle       4.15384 ( 1095)
  link_BETA1-4         : bond        0.00943 (    4)
  link_BETA1-4         : angle       3.41010 (   12)
  link_NAG-ASN         : bond        0.00313 (    4)
  link_NAG-ASN         : angle       2.74564 (   12)

********************** 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
  73 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8127 (m-30) cc_final: 0.7770 (m-30)
REVERT: A  508 MET cc_start: 0.9308 (ptp) cc_final: 0.8901 (mpp)
REVERT: B  262 PHE cc_start: 0.9358 (m-80) cc_final: 0.9125 (m-80)
REVERT: B  365 MET cc_start: 0.8671 (mmm) cc_final: 0.7058 (tpp)
REVERT: B  383 MET cc_start: 0.9188 (tpp) cc_final: 0.8451 (mpp)
  outliers start: 12
  outliers final: 10
  residues processed: 69
  average time/residue: 0.0650
  time to fit residues: 6.6390
Evaluate side-chains
  71 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   49 ASN
Chi-restraints excluded: chain B residue  120 MET
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 73 optimal weight:   10.0000
   chunk 69 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0970
   chunk 56 optimal weight:    0.7980
   chunk 11 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 = 0.3411 r_free = 0.3411 target = 0.062693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.046436 restraints weight = 39683.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.047868 restraints weight = 21525.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.048788 restraints weight = 15217.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.049283 restraints weight = 12405.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.049649 restraints weight = 11073.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7551  Z= 0.114
  Angle     :  0.703  12.523  10297  Z= 0.314
  Chirality :  0.042   0.262   1212
  Planarity :  0.004   0.055   1271
  Dihedral  :  9.500 109.364   1156
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 20.08 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.29), residues: 928
  helix:  2.08 (0.24), residues: 494
  sheet: -0.43 (0.65), residues: 66
  loop : -0.82 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 614 
 TYR   0.012   0.001   TYR B 248 
 PHE   0.024   0.001   PHE B 402 
 TRP   0.010   0.001   TRP B 134 
 HIS   0.003   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7542)
  covalent geometry    : angle       0.68797 (10271)
  SS BOND              : bond        0.00184 (    1)
  SS BOND              : angle       0.51090 (    2)
  hydrogen bonds       : bond        0.03798 (  379)
  hydrogen bonds       : angle       4.01558 ( 1095)
  link_BETA1-4         : bond        0.01039 (    4)
  link_BETA1-4         : angle       3.48696 (   12)
  link_NAG-ASN         : bond        0.00368 (    4)
  link_NAG-ASN         : angle       2.62786 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1310.61 seconds
wall clock time: 23 minutes 20.35 seconds (1400.35 seconds total)