Starting phenix.real_space_refine
on Fri Aug 22 19:44:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ida_35361/08_2025/8ida_35361_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ida_35361/08_2025/8ida_35361.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ida_35361/08_2025/8ida_35361_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ida_35361/08_2025/8ida_35361_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ida_35361/08_2025/8ida_35361.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ida_35361/08_2025/8ida_35361.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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    4816      2.51       5
     N    1189      2.21       5
     O    1340      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 7372
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 470, 3661
          Classifications: {'peptide': 470}
          Link IDs: {'PTRANS': 22, 'TRANS': 447}
    Chain: "B"
      Number of atoms: 3586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 464, 3586
          Classifications: {'peptide': 464}
          Link IDs: {'PTRANS': 24, 'TRANS': 439}
    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: "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: "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: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 1.63, per 1000 atoms: 0.22
  Number of scatterers: 7372
  At special positions: 0
  Unit cell: (97.83, 81.525, 129.353, 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    1340      8.00
     N    1189      7.00
     C    4816      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: 0.47
  Conformation dependent library (CDL) restraints added in 353.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1722

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 5 sheets defined
      60.4% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 175
      removed outlier: 3.704A  pdb=" N   GLY A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 207
      removed outlier: 4.101A  pdb=" N   ARG A 183 " --> pdb=" O   TRP A 179 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TRP A 184 " --> pdb=" O   VAL A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 235
      removed outlier: 3.689A  pdb=" N   PHE A 234 " --> pdb=" O   ASP A 230 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 230 through 235'
    Processing helix  chain 'A' and resid 241 through 243
      No H-bonds generated for 'chain 'A' and resid 241 through 243'
    Processing helix  chain 'A' and resid 244 through 256
      removed outlier: 3.624A  pdb=" N   ARG A 248 " --> pdb=" O   GLY A 244 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   ASP A 250 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   TYR A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU A 252 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 276
      removed outlier: 3.575A  pdb=" N   GLN A 275 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 301
    Processing helix  chain 'A' and resid 323 through 342
      removed outlier: 4.196A  pdb=" N   VAL A 327 " --> pdb=" O   GLN A 323 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 354
      removed outlier: 3.565A  pdb=" N   ASN A 353 " --> pdb=" O   ASP A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 370
      removed outlier: 3.765A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
      removed outlier: 3.547A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A 393 " --> pdb=" O   ILE A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 428
    Processing helix  chain 'A' and resid 441 through 445
    Processing helix  chain 'A' and resid 450 through 459
    Processing helix  chain 'A' and resid 509 through 516
      removed outlier: 3.790A  pdb=" N   GLU A 515 " --> pdb=" O   LYS A 511 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASP A 516 " --> pdb=" O   GLY A 512 " (cutoff:3.500A)
    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
      removed outlier: 3.765A  pdb=" N   SER A 589 " --> pdb=" O   ALA A 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 80
      removed outlier: 3.536A  pdb=" N   VAL B  70 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      Proline residue:  B  72  - end of helix
    Processing helix  chain 'B' and resid 81 through 110
    Processing helix  chain 'B' and resid 117 through 124
    Processing helix  chain 'B' and resid 125 through 139
      removed outlier: 4.004A  pdb=" N   ALA B 129 " --> pdb=" O   GLY B 125 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ILE B 135 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 157
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 4.042A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 221
      removed outlier: 3.522A  pdb=" N   LYS B 221 " --> pdb=" O   VAL B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 254
      removed outlier: 5.336A  pdb=" N   LEU B 245 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   PHE B 252 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ALA B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   TYR B 254 " --> pdb=" O   GLY B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 264
      removed outlier: 3.708A  pdb=" N   THR B 264 " --> pdb=" O   ASN B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 298
      Proline residue:  B 275  - end of helix
      removed outlier: 3.664A  pdb=" N   ILE B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 301 through 307
    Processing helix  chain 'B' and resid 310 through 320
    Processing helix  chain 'B' and resid 325 through 356
      removed outlier: 4.042A  pdb=" N   THR B 345 " --> pdb=" O   GLY B 341 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLU B 356 " --> pdb=" O   VAL B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 386
    Processing helix  chain 'B' and resid 387 through 390
    Processing helix  chain 'B' and resid 392 through 400
      removed outlier: 4.250A  pdb=" N   VAL B 396 " --> pdb=" O   ASP B 392 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   ILE B 397 " --> pdb=" O   ILE B 393 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   ASN B 398 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 422
    Processing helix  chain 'B' and resid 434 through 454
      removed outlier: 3.708A  pdb=" N   PHE B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   THR B 454 " --> pdb=" O   SER B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 467
      removed outlier: 3.757A  pdb=" N   CYS B 458 " --> pdb=" O   THR B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 476
      removed outlier: 3.633A  pdb=" N   TYR B 472 " --> pdb=" O   GLY B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 501
      removed outlier: 3.599A  pdb=" N   LEU B 486 " --> pdb=" O   PRO B 482 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLN B 487 " --> pdb=" O   LYS B 483 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLY B 488 " --> pdb=" O   TRP B 484 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402
      removed outlier: 6.857A  pdb=" N   LEU A 377 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   THR A 402 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   ALA A 379 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   TYR A 226 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   LEU A 225 " --> pdb=" O   PHE A 467 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   CYS A 432 " --> pdb=" O   THR A 464 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   VAL A 466 " --> pdb=" O   CYS A 432 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   TRP A 434 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   SER A 468 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 541 through 545
      removed outlier: 4.327A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLU A 621 " --> pdb=" O   ASN A 569 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 575 through 576
    Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 594
    Processing sheet with id=AA5, first strand: chain 'B' and resid 365 through 366

    393 hydrogen bonds defined for protein.
    1143 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: 0.83

  Time building geometry restraints manager: 0.61 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: 2250
        1.34 -     1.46: 1279
        1.46 -     1.58: 3984
        1.58 -     1.70: 0
        1.70 -     1.82: 40
  Bond restraints: 7553
  Sorted by residual:
  bond pdb=" CA  TYR B 601 "
       pdb=" C   TYR B 601 "
    ideal  model  delta    sigma   weight residual
    1.525  1.489  0.036 2.10e-02 2.27e+03 2.87e+00
  bond pdb=" CA  TYR B 601 "
       pdb=" CB  TYR B 601 "
    ideal  model  delta    sigma   weight residual
    1.530  1.497  0.033 2.00e-02 2.50e+03 2.70e+00
  bond pdb=" N   TYR B 601 "
       pdb=" CA  TYR B 601 "
    ideal  model  delta    sigma   weight residual
    1.458  1.427  0.031 1.90e-02 2.77e+03 2.67e+00
  bond pdb=" C4  NAG F   1 "
       pdb=" O4  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.409  1.440 -0.031 2.00e-02 2.50e+03 2.47e+00
  bond pdb=" C3  NAG D   1 "
       pdb=" O3  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.403  1.432 -0.029 2.00e-02 2.50e+03 2.07e+00
  ... (remaining 7548 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 10072
        1.86 -     3.72: 169
        3.72 -     5.58: 36
        5.58 -     7.44: 5
        7.44 -     9.31: 4
  Bond angle restraints: 10286
  Sorted by residual:
  angle pdb=" CA  TYR B 601 "
        pdb=" CB  TYR B 601 "
        pdb=" CG  TYR B 601 "
      ideal   model   delta    sigma   weight residual
     113.90  105.26    8.64 1.80e+00 3.09e-01 2.31e+01
  angle pdb=" C   ASP B 228 "
        pdb=" N   PRO B 229 "
        pdb=" CA  PRO B 229 "
      ideal   model   delta    sigma   weight residual
     121.65  117.26    4.39 1.01e+00 9.80e-01 1.89e+01
  angle pdb=" N   GLY B 222 "
        pdb=" CA  GLY B 222 "
        pdb=" C   GLY B 222 "
      ideal   model   delta    sigma   weight residual
     110.20  115.03   -4.83 1.32e+00 5.74e-01 1.34e+01
  angle pdb=" N   ARG B 421 "
        pdb=" CA  ARG B 421 "
        pdb=" C   ARG B 421 "
      ideal   model   delta    sigma   weight residual
     112.23  116.66   -4.43 1.26e+00 6.30e-01 1.23e+01
  angle pdb=" CA  PRO A 602 "
        pdb=" N   PRO A 602 "
        pdb=" CD  PRO A 602 "
      ideal   model   delta    sigma   weight residual
     112.00  107.43    4.57 1.40e+00 5.10e-01 1.07e+01
  ... (remaining 10281 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.68: 4197
       25.68 -    51.37: 240
       51.37 -    77.05: 40
       77.05 -   102.74: 25
      102.74 -   128.42: 26
  Dihedral angle restraints: 4528
    sinusoidal: 1848
      harmonic: 2680
  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   65.46 -128.42     1      3.00e+01 1.11e-03 1.73e+01
  dihedral pdb=" C2  NAG E   1 "
           pdb=" C3  NAG E   1 "
           pdb=" C4  NAG E   1 "
           pdb=" O4  NAG E   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   58.60  116.51     1      3.00e+01 1.11e-03 1.54e+01
  dihedral pdb=" O3  NAG E   1 "
           pdb=" C3  NAG E   1 "
           pdb=" C4  NAG E   1 "
           pdb=" O4  NAG E   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.45  178.97  116.48     1      3.00e+01 1.11e-03 1.54e+01
  ... (remaining 4525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.263: 1211
       0.263 -    0.525: 2
       0.525 -    0.788: 1
       0.788 -    1.050: 0
       1.050 -    1.313: 1
  Chirality restraints: 1215
  Sorted by residual:
  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   -2.16   -0.24 2.00e-02 2.50e+03 1.39e+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   -2.22   -0.18 2.00e-02 2.50e+03 8.02e+01
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 507 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.09   -1.31 2.00e-01 2.50e+01 4.31e+01
  ... (remaining 1212 not shown)

  Planarity restraints: 1277
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   1 "    0.358 2.00e-02 2.50e+03   3.06e-01 1.17e+03
        pdb=" C7  NAG E   1 "   -0.086 2.00e-02 2.50e+03
        pdb=" C8  NAG E   1 "    0.041 2.00e-02 2.50e+03
        pdb=" N2  NAG E   1 "   -0.531 2.00e-02 2.50e+03
        pdb=" O7  NAG E   1 "    0.218 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.344 2.00e-02 2.50e+03   2.96e-01 1.09e+03
        pdb=" C7  NAG D   2 "    0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "   -0.038 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.515 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.213 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   2 "   -0.336 2.00e-02 2.50e+03   2.88e-01 1.04e+03
        pdb=" C7  NAG F   2 "    0.081 2.00e-02 2.50e+03
        pdb=" C8  NAG F   2 "   -0.160 2.00e-02 2.50e+03
        pdb=" N2  NAG F   2 "    0.511 2.00e-02 2.50e+03
        pdb=" O7  NAG F   2 "   -0.095 2.00e-02 2.50e+03
  ... (remaining 1274 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1230
        2.76 -     3.30: 7173
        3.30 -     3.83: 12087
        3.83 -     4.37: 13466
        4.37 -     4.90: 23897
  Nonbonded interactions: 57853
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  81 "
            pdb=" O   ASN B 230 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OH  TYR A 469 "
            pdb=" O   PRO A 488 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" NH2 ARG A 604 "
            pdb=" O   LYS A 616 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" O   VAL B 224 "
            pdb=" ND2 ASN B 226 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" OG1 THR A 460 "
            pdb=" OH  TYR A 554 "
     model   vdw
     2.302 3.040
  ... (remaining 57848 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.540
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.680
  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:             0.020
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
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   0.104   7562  Z= 0.182
  Angle     :  0.867  30.289  10312  Z= 0.369
  Chirality :  0.060   1.313   1215
  Planarity :  0.021   0.306   1273
  Dihedral  : 20.753 128.423   2803
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  0.25 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.28), residues: 930
  helix:  1.94 (0.23), residues: 491
  sheet:  0.17 (0.65), residues: 64
  loop : -1.14 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 440 
 TYR   0.007   0.001   TYR B 259 
 PHE   0.016   0.001   PHE B 233 
 TRP   0.007   0.001   TRP A 338 
 HIS   0.001   0.000   HIS B 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 7553)
  covalent geometry    : angle       0.61689 (10286)
  SS BOND              : bond        0.00035 (    1)
  SS BOND              : angle       1.41780 (    2)
  hydrogen bonds       : bond        0.13808 (  393)
  hydrogen bonds       : angle       5.41843 ( 1143)
  link_BETA1-4         : bond        0.00561 (    4)
  link_BETA1-4         : angle       2.00956 (   12)
  link_NAG-ASN         : bond        0.08018 (    4)
  link_NAG-ASN         : angle      17.76843 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A  319 TRP cc_start: 0.6455 (m100) cc_final: 0.5888 (m100)
REVERT: B   78 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7936 (tp30)
REVERT: B  158 LYS cc_start: 0.8849 (tppt) cc_final: 0.8635 (tptt)
  outliers start: 3
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0637
  time to fit residues: 8.2003
Evaluate side-chains
  66 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.2980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.127465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.096512 restraints weight = 11645.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 2.74
r_work: 0.2999 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.0924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7562  Z= 0.139
  Angle     :  0.699  12.085  10312  Z= 0.309
  Chirality :  0.044   0.425   1215
  Planarity :  0.004   0.034   1273
  Dihedral  : 20.138 106.111   1159
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  7.22 %
    Favored  : 91.38 %
  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:  1.26 (0.28), residues: 930
  helix:  2.23 (0.23), residues: 501
  sheet:  0.12 (0.63), residues: 64
  loop : -1.07 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 141 
 TYR   0.009   0.001   TYR A 454 
 PHE   0.012   0.001   PHE B 200 
 TRP   0.007   0.001   TRP A 220 
 HIS   0.002   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7553)
  covalent geometry    : angle       0.62642 (10286)
  SS BOND              : bond        0.01183 (    1)
  SS BOND              : angle       3.11630 (    2)
  hydrogen bonds       : bond        0.05149 (  393)
  hydrogen bonds       : angle       4.00194 ( 1143)
  link_BETA1-4         : bond        0.00973 (    4)
  link_BETA1-4         : angle       3.86457 (   12)
  link_NAG-ASN         : bond        0.00550 (    4)
  link_NAG-ASN         : angle       8.14997 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  249 LEU cc_start: 0.7772 (tt) cc_final: 0.7510 (tt)
REVERT: A  319 TRP cc_start: 0.6792 (m100) cc_final: 0.6158 (m100)
REVERT: B   78 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8348 (tp30)
REVERT: B  233 PHE cc_start: 0.7445 (t80) cc_final: 0.6841 (t80)
REVERT: B  432 ASN cc_start: 0.7433 (m-40) cc_final: 0.6854 (t0)
  outliers start: 11
  outliers final: 10
  residues processed: 82
  average time/residue: 0.0498
  time to fit residues: 6.2867
Evaluate side-chains
  78 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  228 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 46 optimal weight:    0.3980
   chunk 82 optimal weight:    0.7980
   chunk 80 optimal weight:    0.2980
   chunk 56 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 68 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 83 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.125228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.093494 restraints weight = 11475.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 2.83
r_work: 0.2969 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7562  Z= 0.118
  Angle     :  0.618   7.436  10312  Z= 0.279
  Chirality :  0.042   0.306   1215
  Planarity :  0.003   0.034   1273
  Dihedral  : 15.647 104.815   1159
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  :  8.49 %
    Favored  : 89.23 %
  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:  1.42 (0.28), residues: 930
  helix:  2.41 (0.23), residues: 498
  sheet:  0.21 (0.64), residues: 64
  loop : -1.06 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 440 
 TYR   0.007   0.001   TYR A 554 
 PHE   0.015   0.001   PHE B 216 
 TRP   0.008   0.001   TRP A 220 
 HIS   0.002   0.001   HIS A 557 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7553)
  covalent geometry    : angle       0.59123 (10286)
  SS BOND              : bond        0.00491 (    1)
  SS BOND              : angle       3.37181 (    2)
  hydrogen bonds       : bond        0.04290 (  393)
  hydrogen bonds       : angle       3.67738 ( 1143)
  link_BETA1-4         : bond        0.00702 (    4)
  link_BETA1-4         : angle       3.22927 (   12)
  link_NAG-ASN         : bond        0.00523 (    4)
  link_NAG-ASN         : angle       3.99042 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.207 
Fit side-chains
REVERT: A  319 TRP cc_start: 0.6523 (m100) cc_final: 0.5969 (m100)
REVERT: B   78 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8207 (tp30)
REVERT: B  432 ASN cc_start: 0.7410 (m-40) cc_final: 0.6851 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 91
  average time/residue: 0.0528
  time to fit residues: 7.0926
Evaluate side-chains
  81 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  228 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 91 optimal weight:    0.4980
   chunk 63 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 46 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 235 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.122420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.090501 restraints weight = 11612.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 2.83
r_work: 0.2924 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7562  Z= 0.152
  Angle     :  0.653  10.389  10312  Z= 0.294
  Chirality :  0.044   0.270   1215
  Planarity :  0.003   0.030   1273
  Dihedral  : 13.356 104.588   1159
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 10.65 %
    Favored  : 86.82 %
  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:  1.32 (0.28), residues: 930
  helix:  2.36 (0.23), residues: 501
  sheet:  0.13 (0.64), residues: 66
  loop : -1.17 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 440 
 TYR   0.009   0.001   TYR A 454 
 PHE   0.014   0.001   PHE B 200 
 TRP   0.008   0.001   TRP A 220 
 HIS   0.002   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 7553)
  covalent geometry    : angle       0.62147 (10286)
  SS BOND              : bond        0.00493 (    1)
  SS BOND              : angle       3.55758 (    2)
  hydrogen bonds       : bond        0.04834 (  393)
  hydrogen bonds       : angle       3.71476 ( 1143)
  link_BETA1-4         : bond        0.00603 (    4)
  link_BETA1-4         : angle       3.97839 (   12)
  link_NAG-ASN         : bond        0.00538 (    4)
  link_NAG-ASN         : angle       4.23191 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.184 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8379 (tp30)
REVERT: B  432 ASN cc_start: 0.7387 (m-40) cc_final: 0.6847 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 85
  average time/residue: 0.0583
  time to fit residues: 7.2064
Evaluate side-chains
  81 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 12 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0980
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.124535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.092670 restraints weight = 11445.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 2.83
r_work: 0.2955 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7562  Z= 0.117
  Angle     :  0.629  10.458  10312  Z= 0.280
  Chirality :  0.042   0.253   1215
  Planarity :  0.003   0.032   1273
  Dihedral  : 11.663 107.272   1159
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.79 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.28), residues: 930
  helix:  2.47 (0.24), residues: 498
  sheet:  0.23 (0.65), residues: 64
  loop : -1.07 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 440 
 TYR   0.007   0.001   TYR B 155 
 PHE   0.015   0.001   PHE B 216 
 TRP   0.008   0.001   TRP A 220 
 HIS   0.002   0.001   HIS A 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7553)
  covalent geometry    : angle       0.59598 (10286)
  SS BOND              : bond        0.00438 (    1)
  SS BOND              : angle       3.33228 (    2)
  hydrogen bonds       : bond        0.04130 (  393)
  hydrogen bonds       : angle       3.54079 ( 1143)
  link_BETA1-4         : bond        0.00678 (    4)
  link_BETA1-4         : angle       4.13963 (   12)
  link_NAG-ASN         : bond        0.00496 (    4)
  link_NAG-ASN         : angle       4.05811 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
REVERT: B   78 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8323 (tp30)
REVERT: B  432 ASN cc_start: 0.7374 (m-40) cc_final: 0.6828 (t0)
  outliers start: 17
  outliers final: 15
  residues processed: 81
  average time/residue: 0.0535
  time to fit residues: 6.5394
Evaluate side-chains
  82 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  228 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 5 optimal weight:    0.0870
   chunk 20 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.0162

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.122462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.091506 restraints weight = 11469.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 2.75
r_work: 0.2917 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7562  Z= 0.149
  Angle     :  0.642   8.489  10312  Z= 0.291
  Chirality :  0.043   0.240   1215
  Planarity :  0.003   0.031   1273
  Dihedral  : 10.481 106.686   1159
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.80 %
    Favored  : 85.17 %
  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:  1.33 (0.28), residues: 930
  helix:  2.36 (0.23), residues: 501
  sheet:  0.17 (0.64), residues: 66
  loop : -1.16 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 440 
 TYR   0.010   0.001   TYR B 146 
 PHE   0.014   0.001   PHE B 200 
 TRP   0.008   0.001   TRP B  89 
 HIS   0.002   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 7553)
  covalent geometry    : angle       0.60925 (10286)
  SS BOND              : bond        0.00473 (    1)
  SS BOND              : angle       3.47436 (    2)
  hydrogen bonds       : bond        0.04849 (  393)
  hydrogen bonds       : angle       3.65746 ( 1143)
  link_BETA1-4         : bond        0.00670 (    4)
  link_BETA1-4         : angle       4.22620 (   12)
  link_NAG-ASN         : bond        0.00510 (    4)
  link_NAG-ASN         : angle       3.98321 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: B   78 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8315 (tp30)
REVERT: B  432 ASN cc_start: 0.7378 (m-40) cc_final: 0.6805 (t0)
  outliers start: 16
  outliers final: 16
  residues processed: 80
  average time/residue: 0.0617
  time to fit residues: 7.2832
Evaluate side-chains
  82 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  228 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0170
   chunk 50 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.7018

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.122901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.091589 restraints weight = 11466.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 2.78
r_work: 0.2940 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7562  Z= 0.122
  Angle     :  0.611   8.600  10312  Z= 0.277
  Chirality :  0.041   0.235   1215
  Planarity :  0.003   0.031   1273
  Dihedral  :  9.801 107.205   1159
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.31 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.29), residues: 930
  helix:  2.45 (0.24), residues: 498
  sheet:  0.22 (0.64), residues: 66
  loop : -1.03 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 440 
 TYR   0.007   0.001   TYR A 454 
 PHE   0.012   0.001   PHE A 542 
 TRP   0.010   0.001   TRP A 319 
 HIS   0.002   0.001   HIS A 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7553)
  covalent geometry    : angle       0.57844 (10286)
  SS BOND              : bond        0.00433 (    1)
  SS BOND              : angle       3.34617 (    2)
  hydrogen bonds       : bond        0.04297 (  393)
  hydrogen bonds       : angle       3.54956 ( 1143)
  link_BETA1-4         : bond        0.00625 (    4)
  link_BETA1-4         : angle       4.22662 (   12)
  link_NAG-ASN         : bond        0.00493 (    4)
  link_NAG-ASN         : angle       3.81090 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: B   78 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8325 (tp30)
REVERT: B  432 ASN cc_start: 0.7371 (m-40) cc_final: 0.6812 (t0)
  outliers start: 16
  outliers final: 15
  residues processed: 80
  average time/residue: 0.0489
  time to fit residues: 5.7823
Evaluate side-chains
  81 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  228 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0040
   chunk 0 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 56 optimal weight:    0.3980
   overall best weight:    0.4992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.124398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.092542 restraints weight = 11633.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 2.84
r_work: 0.2952 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7562  Z= 0.111
  Angle     :  0.593   8.727  10312  Z= 0.269
  Chirality :  0.040   0.228   1215
  Planarity :  0.003   0.031   1273
  Dihedral  :  9.215 107.163   1159
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.69 %
    Favored  : 84.28 %
  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:  1.55 (0.29), residues: 930
  helix:  2.54 (0.24), residues: 496
  sheet:  0.24 (0.64), residues: 66
  loop : -1.00 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 440 
 TYR   0.006   0.001   TYR B 146 
 PHE   0.011   0.001   PHE A 542 
 TRP   0.011   0.001   TRP A 319 
 HIS   0.001   0.001   HIS B 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7553)
  covalent geometry    : angle       0.56070 (10286)
  SS BOND              : bond        0.00420 (    1)
  SS BOND              : angle       3.25493 (    2)
  hydrogen bonds       : bond        0.03960 (  393)
  hydrogen bonds       : angle       3.48690 ( 1143)
  link_BETA1-4         : bond        0.00664 (    4)
  link_BETA1-4         : angle       4.24223 (   12)
  link_NAG-ASN         : bond        0.00491 (    4)
  link_NAG-ASN         : angle       3.60661 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  580 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7334 (pp30)
REVERT: B   78 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8308 (tp30)
REVERT: B  432 ASN cc_start: 0.7421 (m-40) cc_final: 0.6859 (t0)
  outliers start: 16
  outliers final: 15
  residues processed: 80
  average time/residue: 0.0481
  time to fit residues: 5.7037
Evaluate side-chains
  80 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  228 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 30 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 45 optimal weight:    0.3980
   chunk 43 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.123254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.091415 restraints weight = 11397.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 2.81
r_work: 0.2941 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7562  Z= 0.126
  Angle     :  0.606   9.049  10312  Z= 0.277
  Chirality :  0.041   0.242   1215
  Planarity :  0.003   0.031   1273
  Dihedral  :  8.798 106.921   1159
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.32 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.53 (0.29), residues: 930
  helix:  2.47 (0.24), residues: 498
  sheet:  0.23 (0.64), residues: 66
  loop : -0.96 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 440 
 TYR   0.008   0.001   TYR B 146 
 PHE   0.012   0.001   PHE B 200 
 TRP   0.012   0.001   TRP A 319 
 HIS   0.001   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7553)
  covalent geometry    : angle       0.57490 (10286)
  SS BOND              : bond        0.00435 (    1)
  SS BOND              : angle       3.30147 (    2)
  hydrogen bonds       : bond        0.04269 (  393)
  hydrogen bonds       : angle       3.53672 ( 1143)
  link_BETA1-4         : bond        0.00674 (    4)
  link_BETA1-4         : angle       4.22856 (   12)
  link_NAG-ASN         : bond        0.00465 (    4)
  link_NAG-ASN         : angle       3.50616 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A  580 GLN cc_start: 0.7567 (tm-30) cc_final: 0.7333 (pp30)
REVERT: B   78 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8319 (tp30)
REVERT: B  432 ASN cc_start: 0.7407 (m-40) cc_final: 0.6854 (t0)
  outliers start: 15
  outliers final: 15
  residues processed: 79
  average time/residue: 0.0530
  time to fit residues: 6.2636
Evaluate side-chains
  81 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  228 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 92 optimal weight:    0.0970
   chunk 11 optimal weight:    0.0870
   chunk 54 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 90 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 72 optimal weight:    0.5980
   overall best weight:    0.4756

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.124802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.093068 restraints weight = 11428.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 2.82
r_work: 0.2972 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7562  Z= 0.110
  Angle     :  0.584   9.112  10312  Z= 0.267
  Chirality :  0.040   0.242   1215
  Planarity :  0.003   0.031   1273
  Dihedral  :  8.479 107.095   1159
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.07 %
    Favored  : 83.90 %
  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:  1.62 (0.29), residues: 930
  helix:  2.55 (0.24), residues: 498
  sheet:  0.28 (0.64), residues: 66
  loop : -0.91 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 440 
 TYR   0.006   0.001   TYR B 155 
 PHE   0.021   0.001   PHE B 216 
 TRP   0.012   0.001   TRP A 319 
 HIS   0.002   0.001   HIS A 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7553)
  covalent geometry    : angle       0.55376 (10286)
  SS BOND              : bond        0.00424 (    1)
  SS BOND              : angle       3.22648 (    2)
  hydrogen bonds       : bond        0.03849 (  393)
  hydrogen bonds       : angle       3.46166 ( 1143)
  link_BETA1-4         : bond        0.00699 (    4)
  link_BETA1-4         : angle       4.18413 (   12)
  link_NAG-ASN         : bond        0.00481 (    4)
  link_NAG-ASN         : angle       3.36066 (   12)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: B   78 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8280 (tp30)
REVERT: B  432 ASN cc_start: 0.7416 (m-40) cc_final: 0.6855 (t0)
  outliers start: 16
  outliers final: 14
  residues processed: 79
  average time/residue: 0.0429
  time to fit residues: 5.3002
Evaluate side-chains
  80 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  228 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0980
   chunk 2 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.123859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.092135 restraints weight = 11456.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 2.82
r_work: 0.2947 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7562  Z= 0.119
  Angle     :  0.595   9.287  10312  Z= 0.274
  Chirality :  0.040   0.254   1215
  Planarity :  0.003   0.031   1273
  Dihedral  :  8.285 106.790   1159
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.32 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.61 (0.28), residues: 930
  helix:  2.53 (0.24), residues: 498
  sheet:  0.27 (0.64), residues: 66
  loop : -0.91 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 440 
 TYR   0.007   0.001   TYR B 146 
 PHE   0.019   0.001   PHE B 216 
 TRP   0.013   0.001   TRP A 319 
 HIS   0.002   0.001   HIS A 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7553)
  covalent geometry    : angle       0.56651 (10286)
  SS BOND              : bond        0.00422 (    1)
  SS BOND              : angle       3.24147 (    2)
  hydrogen bonds       : bond        0.04059 (  393)
  hydrogen bonds       : angle       3.48525 ( 1143)
  link_BETA1-4         : bond        0.00716 (    4)
  link_BETA1-4         : angle       4.14613 (   12)
  link_NAG-ASN         : bond        0.00431 (    4)
  link_NAG-ASN         : angle       3.18992 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1203.06 seconds
wall clock time: 21 minutes 15.81 seconds (1275.81 seconds total)