Starting phenix.real_space_refine
on Sat May 10 15:23:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fdk_31546/05_2025/7fdk_31546.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fdk_31546/05_2025/7fdk_31546.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fdk_31546/05_2025/7fdk_31546.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fdk_31546/05_2025/7fdk_31546.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fdk_31546/05_2025/7fdk_31546.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fdk_31546/05_2025/7fdk_31546.cif"
  }
  resolution = 3.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      37      5.16       5
     C    4113      2.51       5
     N    1076      2.21       5
     O    1223      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6449
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4867
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 597, 4860
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 26, 'TRANS': 570}
      Conformer: "B"
        Number of residues, atoms: 597, 4860
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 26, 'TRANS': 570}
          bond proxies already assigned to first conformer: 4986
    Chain: "E"
      Number of atoms: 1540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1540
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "A"
      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: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.62, per 1000 atoms: 0.87
  Number of scatterers: 6449
  At special positions: 0
  Unit cell: (118.56, 83.2, 80.08, 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      37     16.00
     O    1223      8.00
     N    1076      7.00
     C    4113      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " 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
    NAG-ASN
      " NAG A 701 " - " ASN A 546 "
      " NAG A 702 " - " ASN A  53 "
      " NAG E 601 " - " ASN E 343 "
  Time building additional restraints: 1.42
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 6 sheets defined
      50.8% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.883A  pdb=" N   ASN A  24 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   ASP A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 79
      removed outlier: 4.058A  pdb=" N   SER A  63 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   GLU A  64 " --> pdb=" O   GLN A  60 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ALA A  65 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA A  66 " --> pdb=" O   MET A  62 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   THR A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 144 through 148
    Processing helix  chain 'A' and resid 150 through 155
      removed outlier: 3.614A  pdb=" N   THR A 154 " --> pdb=" O   GLU A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 194
      Proline residue:  A 178  - end of helix
      removed outlier: 3.962A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 220 through 231
      removed outlier: 4.171A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 252
      removed outlier: 3.540A  pdb=" N   LYS A 247 " --> pdb=" O   TYR A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 3.561A  pdb=" N   THR A 282 " --> pdb=" O   TYR A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 299
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.526A  pdb=" N   ALA A 311 " --> pdb=" O   ILE A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.808A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ALA A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 383
      removed outlier: 4.248A  pdb=" N   ALA A 372 " --> pdb=" O   ASN A 368 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 411
      removed outlier: 4.328A  pdb=" N   GLU A 406 " --> pdb=" O   GLU A 402 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 465
      removed outlier: 4.036A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   GLY A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   LEU A 450 " --> pdb=" O   ILE A 446 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
      removed outlier: 3.549A  pdb=" N   ARG A 465 " --> pdb=" O   TRP A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 485
    Processing helix  chain 'A' and resid 499 through 503
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 4.439A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 559
      removed outlier: 4.528A  pdb=" N   LEU A 554 " --> pdb=" O   ALA A 550 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.529A  pdb=" N   ALA A 569 " --> pdb=" O   PRO A 565 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'E' and resid 337 through 343
    Processing helix  chain 'E' and resid 365 through 370
    Processing helix  chain 'E' and resid 383 through 390
    Processing helix  chain 'E' and resid 403 through 407
      removed outlier: 3.638A  pdb=" N   GLU E 406 " --> pdb=" O   ARG E 403 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 438 through 443
      removed outlier: 3.524A  pdb=" N   ASP E 442 " --> pdb=" O   SER E 438 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.405A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.426A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 355
      removed outlier: 4.005A  pdb=" N   ASN E 354 " --> pdb=" O   SER E 399 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   SER E 399 " --> pdb=" O   ASN E 354 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ASN E 394 " --> pdb=" O   GLU E 516 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU E 516 " --> pdb=" O   ASN E 394 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ILE E 402 " --> pdb=" O   TYR E 508 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474

    270 hydrogen bonds defined for protein.
    788 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: 1.69

  Time building geometry restraints manager: 1.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2071
        1.34 -     1.46: 1721
        1.46 -     1.58: 2781
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6631
  Sorted by residual:
  bond pdb=" C   LYS A 359 "
       pdb=" N   MET A 360 "
    ideal  model  delta    sigma   weight residual
    1.330  1.535 -0.205 1.23e-02 6.61e+03 2.79e+02
  bond pdb=" C   ILE A 358 "
       pdb=" N   LYS A 359 "
    ideal  model  delta    sigma   weight residual
    1.331  1.551 -0.221 1.66e-02 3.63e+03 1.77e+02
  bond pdb=" C   ALA E 397 "
       pdb=" N   ASP E 398 "
    ideal  model  delta    sigma   weight residual
    1.328  1.432 -0.104 1.42e-02 4.96e+03 5.37e+01
  bond pdb=" C   ASP E 398 "
       pdb=" N   SER E 399 "
    ideal  model  delta    sigma   weight residual
    1.332  1.392 -0.060 1.25e-02 6.40e+03 2.34e+01
  bond pdb=" C   SER A 563 "
       pdb=" N   GLU A 564 "
    ideal  model  delta    sigma   weight residual
    1.335  1.231  0.104 3.04e-02 1.08e+03 1.16e+01
  ... (remaining 6626 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 8756
        2.24 -     4.47: 219
        4.47 -     6.71: 29
        6.71 -     8.95: 2
        8.95 -    11.18: 4
  Bond angle restraints: 9010
  Sorted by residual:
  angle pdb=" O   ILE A 358 "
        pdb=" C   ILE A 358 "
        pdb=" N   LYS A 359 "
      ideal   model   delta    sigma   weight residual
     123.26  134.44  -11.18 1.08e+00 8.57e-01 1.07e+02
  angle pdb=" CA  ILE A 358 "
        pdb=" C   ILE A 358 "
        pdb=" N   LYS A 359 "
      ideal   model   delta    sigma   weight residual
     116.31  105.62   10.69 1.14e+00 7.69e-01 8.79e+01
  angle pdb=" N   GLN A  86 "
        pdb=" CA  GLN A  86 "
        pdb=" C   GLN A  86 "
      ideal   model   delta    sigma   weight residual
     114.56  108.10    6.46 1.27e+00 6.20e-01 2.59e+01
  angle pdb=" O   ALA E 397 "
        pdb=" C   ALA E 397 "
        pdb=" N   ASP E 398 "
      ideal   model   delta    sigma   weight residual
     123.27  129.19   -5.92 1.17e+00 7.31e-01 2.56e+01
  angle pdb=" CA  ALA E 397 "
        pdb=" C   ALA E 397 "
        pdb=" N   ASP E 398 "
      ideal   model   delta    sigma   weight residual
     116.45  110.39    6.06 1.23e+00 6.61e-01 2.43e+01
  ... (remaining 9005 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 3478
       17.73 -    35.45: 361
       35.45 -    53.18: 74
       53.18 -    70.91: 18
       70.91 -    88.64: 10
  Dihedral angle restraints: 3941
    sinusoidal: 1615
      harmonic: 2326
  Sorted by residual:
  dihedral pdb=" CA  GLU A 145 "
           pdb=" C   GLU A 145 "
           pdb=" N   PRO A 146 "
           pdb=" CA  PRO A 146 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -130.48  -49.52     0      5.00e+00 4.00e-02 9.81e+01
  dihedral pdb=" CA  VAL A 581 "
           pdb=" C   VAL A 581 "
           pdb=" N   LYS A 582 "
           pdb=" CA  LYS A 582 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.16   29.84     0      5.00e+00 4.00e-02 3.56e+01
  dihedral pdb=" CA  CYS E 361 "
           pdb=" C   CYS E 361 "
           pdb=" N   VAL E 362 "
           pdb=" CA  VAL E 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.67   28.33     0      5.00e+00 4.00e-02 3.21e+01
  ... (remaining 3938 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 523
       0.036 -    0.072: 311
       0.072 -    0.108: 84
       0.108 -    0.144: 22
       0.144 -    0.180: 4
  Chirality restraints: 944
  Sorted by residual:
  chirality pdb=" C1  NAG E 601 "
            pdb=" ND2 ASN E 343 "
            pdb=" C2  NAG E 601 "
            pdb=" O5  NAG E 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-01 2.50e+01 8.11e-01
  chirality pdb=" CA  PRO E 337 "
            pdb=" N   PRO E 337 "
            pdb=" C   PRO E 337 "
            pdb=" CB  PRO E 337 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.60e-01
  chirality pdb=" CA  ILE E 434 "
            pdb=" N   ILE E 434 "
            pdb=" C   ILE E 434 "
            pdb=" CB  ILE E 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.57e-01
  ... (remaining 941 not shown)

  Planarity restraints: 1170
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 145 "   -0.046 5.00e-02 4.00e+02   6.91e-02 7.64e+00
        pdb=" N   PRO A 146 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO A 146 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 146 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 453 "    0.021 2.00e-02 2.50e+03   1.68e-02 5.68e+00
        pdb=" CG  TYR E 453 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 453 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 453 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 453 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 453 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 453 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR E 453 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 388 "   -0.039 5.00e-02 4.00e+02   5.78e-02 5.35e+00
        pdb=" N   PRO A 389 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 389 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 389 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1167 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 138
        2.64 -     3.21: 6520
        3.21 -     3.77: 9963
        3.77 -     4.34: 13424
        4.34 -     4.90: 21531
  Nonbonded interactions: 51576
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  41 "
            pdb=" O   THR E 500 "
     model   vdw
     2.080 3.040
  nonbonded pdb=" OH  TYR A 237 "
            pdb=" O   VAL A 485 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" OH  TYR A 535 "
            pdb=" O   SER A 538 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" O   ILE E 418 "
            pdb=" N   ASP E 420 "
     model   vdw
     2.122 3.120
  nonbonded pdb=" OH  TYR A 535 "
            pdb=" O   LYS A 541 "
     model   vdw
     2.156 3.040
  ... (remaining 51571 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.50 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:             0.440
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.880
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.221   6637  Z= 0.439
  Angle     :  0.889  11.185   9025  Z= 0.523
  Chirality :  0.048   0.180    944
  Planarity :  0.006   0.069   1167
  Dihedral  : 15.522  88.637   2442
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 18.21
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 13.21 %
    Favored  : 86.66 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  6.83 %
    Favored  : 92.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.54 (0.24), residues: 788
  helix: -2.30 (0.21), residues: 373
  sheet: -3.02 (0.68), residues: 44
  loop : -3.82 (0.27), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 302 
 HIS   0.006   0.002   HIS A 378 
 PHE   0.028   0.003   PHE A 390 
 TYR   0.041   0.002   TYR E 453 
 ARG   0.003   0.000   ARG E 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00919 (    3)
  link_NAG-ASN         : angle       3.36865 (    9)
  hydrogen bonds       : bond        0.16363 (  270)
  hydrogen bonds       : angle       7.44417 (  788)
  SS BOND              : bond        0.00350 (    3)
  SS BOND              : angle       2.12552 (    6)
  covalent geometry    : bond        0.00848 ( 6631)
  covalent geometry    : angle       0.88154 ( 9010)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 HIS cc_start: 0.8167 (p-80) cc_final: 0.7876 (p90)
REVERT: A  297 MET cc_start: 0.6037 (ptt) cc_final: 0.5796 (ptp)
REVERT: A  454 TYR cc_start: 0.7576 (t80) cc_final: 0.7248 (t80)
REVERT: E  346 ARG cc_start: 0.7135 (ttm110) cc_final: 0.5726 (ptt180)
REVERT: E  356 LYS cc_start: 0.8944 (tttm) cc_final: 0.8680 (ttmt)
REVERT: E  357 ARG cc_start: 0.8591 (ttt90) cc_final: 0.6566 (mtt180)
REVERT: E  424 LYS cc_start: 0.8907 (tptp) cc_final: 0.8506 (tttp)
REVERT: E  451 TYR cc_start: 0.8044 (m-80) cc_final: 0.7096 (m-80)
REVERT: E  462 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8407 (mtpp)
REVERT: E  465 GLU cc_start: 0.6060 (tp30) cc_final: 0.5740 (tp30)
REVERT: E  466 ARG cc_start: 0.8504 (ttm110) cc_final: 0.8212 (ttm110)
REVERT: E  467 ASP cc_start: 0.7996 (t0) cc_final: 0.7492 (t70)
REVERT: E  508 TYR cc_start: 0.8344 (m-80) cc_final: 0.7998 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 99
  average time/residue: 0.2374
  time to fit residues: 29.7798
Evaluate side-chains
  77 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  24 ASN
A  33 ASN
A  34 GLN
A 134 ASN
A 195 ASN
A 388 GLN
A 522 GLN
A 599 ASN
E 460 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.141136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.111691 restraints weight = 19853.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.113934 restraints weight = 10495.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.114242 restraints weight = 9184.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3548
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3547 r_free = 0.3547    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3547
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6637  Z= 0.162
  Angle     :  0.681   8.228   9025  Z= 0.347
  Chirality :  0.044   0.217    944
  Planarity :  0.006   0.062   1167
  Dihedral  :  7.028  58.281    932
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.53 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.19 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.92 (0.27), residues: 788
  helix: -0.68 (0.25), residues: 370
  sheet: -2.75 (0.64), residues: 50
  loop : -3.23 (0.28), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 163 
 HIS   0.004   0.001   HIS A 373 
 PHE   0.017   0.002   PHE A 390 
 TYR   0.016   0.002   TYR E 495 
 ARG   0.006   0.001   ARG E 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00592 (    3)
  link_NAG-ASN         : angle       2.52121 (    9)
  hydrogen bonds       : bond        0.04865 (  270)
  hydrogen bonds       : angle       5.36414 (  788)
  SS BOND              : bond        0.00139 (    3)
  SS BOND              : angle       1.88268 (    6)
  covalent geometry    : bond        0.00374 ( 6631)
  covalent geometry    : angle       0.67496 ( 9010)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 GLN cc_start: 0.6638 (mm-40) cc_final: 0.6170 (pp30)
REVERT: A  152 MET cc_start: 0.6774 (mtp) cc_final: 0.6477 (ttm)
REVERT: A  265 HIS cc_start: 0.8110 (p-80) cc_final: 0.7661 (p90)
REVERT: A  383 MET cc_start: 0.8693 (ttt) cc_final: 0.8384 (ttt)
REVERT: A  557 MET cc_start: 0.8861 (tmm) cc_final: 0.8622 (tmm)
REVERT: E  347 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6294 (m-80)
REVERT: E  357 ARG cc_start: 0.8546 (ttt90) cc_final: 0.6465 (mtt180)
REVERT: E  424 LYS cc_start: 0.8848 (tptp) cc_final: 0.8401 (tttp)
REVERT: E  451 TYR cc_start: 0.8006 (m-80) cc_final: 0.6886 (m-80)
REVERT: E  462 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8387 (mtpp)
REVERT: E  467 ASP cc_start: 0.7804 (t0) cc_final: 0.7312 (t70)
REVERT: E  495 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.8115 (p90)
REVERT: E  508 TYR cc_start: 0.8363 (m-80) cc_final: 0.7953 (m-80)
  outliers start: 9
  outliers final: 5
  residues processed: 101
  average time/residue: 0.2169
  time to fit residues: 28.2555
Evaluate side-chains
  87 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  495 TYR
Chi-restraints excluded: chain E residue  501 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    1.1782

-------------------------------------------------------------------------------
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 = 0.3946 r_free = 0.3946 target = 0.143661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.114491 restraints weight = 20213.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.117510 restraints weight = 13387.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.117995 restraints weight = 9213.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3600
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3600 r_free = 0.3600    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3600 r_free = 0.3600    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3600
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6637  Z= 0.140
  Angle     :  0.633   7.411   9025  Z= 0.321
  Chirality :  0.043   0.204    944
  Planarity :  0.005   0.059   1167
  Dihedral  :  6.378  56.402    932
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.64 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.08 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.29), residues: 788
  helix:  0.02 (0.27), residues: 369
  sheet: -2.22 (0.66), residues: 46
  loop : -2.74 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.016   0.002   PHE A 390 
 TYR   0.019   0.001   TYR A 252 
 ARG   0.005   0.001   ARG E 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00515 (    3)
  link_NAG-ASN         : angle       2.44586 (    9)
  hydrogen bonds       : bond        0.04466 (  270)
  hydrogen bonds       : angle       4.99084 (  788)
  SS BOND              : bond        0.00117 (    3)
  SS BOND              : angle       1.56127 (    6)
  covalent geometry    : bond        0.00318 ( 6631)
  covalent geometry    : angle       0.62774 ( 9010)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 GLN cc_start: 0.6610 (mm-40) cc_final: 0.6262 (pp30)
REVERT: A  265 HIS cc_start: 0.7940 (p-80) cc_final: 0.7482 (p90)
REVERT: A  402 GLU cc_start: 0.6962 (tp30) cc_final: 0.6477 (mp0)
REVERT: E  347 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6192 (m-80)
REVERT: E  356 LYS cc_start: 0.8713 (tttt) cc_final: 0.7738 (mmtt)
REVERT: E  357 ARG cc_start: 0.8563 (ttt90) cc_final: 0.6452 (mtt180)
REVERT: E  424 LYS cc_start: 0.8816 (tptp) cc_final: 0.8314 (tttm)
REVERT: E  451 TYR cc_start: 0.7984 (m-80) cc_final: 0.6842 (m-80)
REVERT: E  462 LYS cc_start: 0.8596 (mtpt) cc_final: 0.8338 (mtpp)
REVERT: E  467 ASP cc_start: 0.7688 (t0) cc_final: 0.7178 (t70)
REVERT: E  495 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.8008 (p90)
REVERT: E  508 TYR cc_start: 0.8227 (m-80) cc_final: 0.7817 (m-80)
  outliers start: 12
  outliers final: 7
  residues processed: 108
  average time/residue: 0.1988
  time to fit residues: 28.2526
Evaluate side-chains
  95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  398 ASP
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  495 TYR
Chi-restraints excluded: chain E residue  501 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 8 optimal weight:    0.0000
   chunk 17 optimal weight:    0.0970
   chunk 35 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.9386

-------------------------------------------------------------------------------
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 = 0.3975 r_free = 0.3975 target = 0.145752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.116365 restraints weight = 26341.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.122915 restraints weight = 16889.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.123016 restraints weight = 7166.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3673
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3673 r_free = 0.3673    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3673 r_free = 0.3673    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3673
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6637  Z= 0.129
  Angle     :  0.632   7.040   9025  Z= 0.314
  Chirality :  0.042   0.196    944
  Planarity :  0.005   0.056   1167
  Dihedral  :  5.735  56.153    932
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.02 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 14.83 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.29), residues: 788
  helix:  0.23 (0.27), residues: 380
  sheet: -1.96 (0.68), residues: 46
  loop : -2.45 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.016   0.002   PHE A 512 
 TYR   0.015   0.001   TYR A 255 
 ARG   0.004   0.000   ARG E 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00411 (    3)
  link_NAG-ASN         : angle       2.16516 (    9)
  hydrogen bonds       : bond        0.04052 (  270)
  hydrogen bonds       : angle       4.84932 (  788)
  SS BOND              : bond        0.00098 (    3)
  SS BOND              : angle       1.72181 (    6)
  covalent geometry    : bond        0.00297 ( 6631)
  covalent geometry    : angle       0.62750 ( 9010)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 HIS cc_start: 0.7917 (p-80) cc_final: 0.7591 (p90)
REVERT: A  402 GLU cc_start: 0.7086 (tp30) cc_final: 0.5943 (mp0)
REVERT: A  518 ARG cc_start: 0.8371 (ptt-90) cc_final: 0.7864 (ttp-170)
REVERT: A  591 LEU cc_start: 0.8214 (tt) cc_final: 0.7878 (tt)
REVERT: E  356 LYS cc_start: 0.8628 (tttt) cc_final: 0.7774 (mmtt)
REVERT: E  357 ARG cc_start: 0.8544 (ttt90) cc_final: 0.6395 (mtt180)
REVERT: E  424 LYS cc_start: 0.8818 (tptp) cc_final: 0.8342 (tttm)
REVERT: E  451 TYR cc_start: 0.7936 (m-80) cc_final: 0.6804 (m-80)
REVERT: E  462 LYS cc_start: 0.8506 (mtpt) cc_final: 0.8249 (mtpp)
REVERT: E  495 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7973 (p90)
REVERT: E  508 TYR cc_start: 0.8220 (m-80) cc_final: 0.7864 (m-80)
REVERT: E  516 GLU cc_start: 0.6788 (pm20) cc_final: 0.6457 (pm20)
  outliers start: 11
  outliers final: 7
  residues processed: 100
  average time/residue: 0.2197
  time to fit residues: 28.4501
Evaluate side-chains
  95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  478 THR
Chi-restraints excluded: chain E residue  495 TYR
Chi-restraints excluded: chain E residue  501 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 59 optimal weight:    0.4980
   chunk 60 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 3 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   chunk 70 optimal weight:    0.0870
   chunk 27 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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 = 0.4041 r_free = 0.4041 target = 0.149825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.119420 restraints weight = 20662.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.122700 restraints weight = 13476.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.122913 restraints weight = 11061.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3677
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3677 r_free = 0.3677    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3677 r_free = 0.3677    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3677
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6637  Z= 0.118
  Angle     :  0.618   6.949   9025  Z= 0.306
  Chirality :  0.042   0.192    944
  Planarity :  0.005   0.054   1167
  Dihedral  :  5.333  55.331    932
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.88 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.26 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.30), residues: 788
  helix:  0.52 (0.27), residues: 382
  sheet: -1.55 (0.71), residues: 46
  loop : -2.32 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.014   0.001   PHE A 512 
 TYR   0.017   0.001   TYR A  50 
 ARG   0.005   0.000   ARG E 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00386 (    3)
  link_NAG-ASN         : angle       2.01540 (    9)
  hydrogen bonds       : bond        0.03821 (  270)
  hydrogen bonds       : angle       4.73317 (  788)
  SS BOND              : bond        0.00113 (    3)
  SS BOND              : angle       1.48024 (    6)
  covalent geometry    : bond        0.00266 ( 6631)
  covalent geometry    : angle       0.61362 ( 9010)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 TRP cc_start: 0.7479 (t-100) cc_final: 0.6958 (t-100)
REVERT: A  265 HIS cc_start: 0.7965 (p-80) cc_final: 0.7739 (p90)
REVERT: A  267 LEU cc_start: 0.8276 (mt) cc_final: 0.7672 (mt)
REVERT: A  401 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.6641 (m-70)
REVERT: A  402 GLU cc_start: 0.7037 (tp30) cc_final: 0.6735 (mp0)
REVERT: A  480 MET cc_start: 0.7839 (mtp) cc_final: 0.7510 (mtm)
REVERT: E  347 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.6136 (m-80)
REVERT: E  356 LYS cc_start: 0.8496 (tttt) cc_final: 0.7869 (mmtt)
REVERT: E  357 ARG cc_start: 0.8533 (ttt90) cc_final: 0.6383 (mtt180)
REVERT: E  424 LYS cc_start: 0.8746 (tptp) cc_final: 0.8403 (tttm)
REVERT: E  451 TYR cc_start: 0.7846 (m-80) cc_final: 0.6817 (m-80)
REVERT: E  462 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8171 (mtpp)
REVERT: E  495 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7924 (p90)
REVERT: E  508 TYR cc_start: 0.8264 (m-80) cc_final: 0.7934 (m-80)
  outliers start: 16
  outliers final: 8
  residues processed: 113
  average time/residue: 0.2258
  time to fit residues: 33.0680
Evaluate side-chains
  97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  398 ASP
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  478 THR
Chi-restraints excluded: chain E residue  495 TYR
Chi-restraints excluded: chain E residue  501 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 7 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   chunk 25 optimal weight:    4.9990
   chunk 34 optimal weight:    9.9990
   chunk 69 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 586 ASN
E 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.149220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.118348 restraints weight = 22540.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.122810 restraints weight = 13903.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.122747 restraints weight = 11134.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3668
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3668 r_free = 0.3668    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3668 r_free = 0.3668    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3668
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6637  Z= 0.127
  Angle     :  0.625   7.607   9025  Z= 0.308
  Chirality :  0.042   0.190    944
  Planarity :  0.005   0.052   1167
  Dihedral  :  5.225  55.336    932
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.01 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.72 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.30), residues: 788
  helix:  0.58 (0.27), residues: 379
  sheet: -1.24 (0.73), residues: 46
  loop : -2.21 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.013   0.001   PHE A 390 
 TYR   0.015   0.001   TYR A 385 
 ARG   0.005   0.000   ARG E 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00391 (    3)
  link_NAG-ASN         : angle       1.99749 (    9)
  hydrogen bonds       : bond        0.03841 (  270)
  hydrogen bonds       : angle       4.65875 (  788)
  SS BOND              : bond        0.00099 (    3)
  SS BOND              : angle       1.64584 (    6)
  covalent geometry    : bond        0.00294 ( 6631)
  covalent geometry    : angle       0.62047 ( 9010)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.660 
Fit side-chains
REVERT: A  161 ARG cc_start: 0.7105 (mtp180) cc_final: 0.6521 (ttm170)
REVERT: A  168 TRP cc_start: 0.7493 (t-100) cc_final: 0.6807 (t-100)
REVERT: A  249 MET cc_start: 0.7966 (tpp) cc_final: 0.7666 (tpp)
REVERT: A  265 HIS cc_start: 0.7996 (p-80) cc_final: 0.7177 (p90)
REVERT: A  267 LEU cc_start: 0.8228 (mt) cc_final: 0.7581 (mt)
REVERT: A  402 GLU cc_start: 0.6960 (tp30) cc_final: 0.6632 (mp0)
REVERT: A  480 MET cc_start: 0.7890 (mtp) cc_final: 0.7502 (mtm)
REVERT: A  557 MET cc_start: 0.8746 (tmm) cc_final: 0.8502 (tmm)
REVERT: A  591 LEU cc_start: 0.8243 (tt) cc_final: 0.7878 (tt)
REVERT: E  347 PHE cc_start: 0.6857 (OUTLIER) cc_final: 0.6090 (m-80)
REVERT: E  356 LYS cc_start: 0.8521 (tttt) cc_final: 0.7796 (mmtt)
REVERT: E  357 ARG cc_start: 0.8584 (ttt90) cc_final: 0.6395 (mtt180)
REVERT: E  424 LYS cc_start: 0.8801 (tptp) cc_final: 0.8484 (tttm)
REVERT: E  451 TYR cc_start: 0.7920 (m-80) cc_final: 0.6805 (m-80)
REVERT: E  462 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8165 (mtpp)
REVERT: E  508 TYR cc_start: 0.8285 (m-80) cc_final: 0.7914 (m-80)
REVERT: E  516 GLU cc_start: 0.6798 (pm20) cc_final: 0.6496 (pm20)
  outliers start: 14
  outliers final: 10
  residues processed: 97
  average time/residue: 0.2149
  time to fit residues: 27.0096
Evaluate side-chains
  97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  398 ASP
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  478 THR
Chi-restraints excluded: chain E residue  501 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
E 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.150003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.119494 restraints weight = 26915.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.125333 restraints weight = 18635.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.127019 restraints weight = 7493.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3710
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3710 r_free = 0.3710    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3710 r_free = 0.3710    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3710
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.3589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6637  Z= 0.124
  Angle     :  0.620   7.226   9025  Z= 0.307
  Chirality :  0.042   0.189    944
  Planarity :  0.005   0.051   1167
  Dihedral  :  5.154  55.090    932
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.44 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.30), residues: 788
  helix:  0.59 (0.27), residues: 379
  sheet: -1.07 (0.75), residues: 46
  loop : -2.10 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 477 
 HIS   0.006   0.001   HIS E 493 
 PHE   0.014   0.001   PHE A 390 
 TYR   0.015   0.001   TYR A 385 
 ARG   0.005   0.000   ARG E 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00385 (    3)
  link_NAG-ASN         : angle       1.93509 (    9)
  hydrogen bonds       : bond        0.03765 (  270)
  hydrogen bonds       : angle       4.65219 (  788)
  SS BOND              : bond        0.00091 (    3)
  SS BOND              : angle       1.61110 (    6)
  covalent geometry    : bond        0.00283 ( 6631)
  covalent geometry    : angle       0.61612 ( 9010)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ARG cc_start: 0.7122 (mtp180) cc_final: 0.6518 (ttt180)
REVERT: A  265 HIS cc_start: 0.7967 (p-80) cc_final: 0.7235 (p90)
REVERT: A  270 MET cc_start: 0.5994 (tpp) cc_final: 0.5573 (tpp)
REVERT: A  480 MET cc_start: 0.7839 (mtp) cc_final: 0.7474 (mtm)
REVERT: A  557 MET cc_start: 0.8717 (tmm) cc_final: 0.8488 (tmm)
REVERT: A  591 LEU cc_start: 0.8168 (tt) cc_final: 0.7777 (tt)
REVERT: E  347 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.5982 (m-80)
REVERT: E  356 LYS cc_start: 0.8396 (tttt) cc_final: 0.7684 (mptt)
REVERT: E  357 ARG cc_start: 0.8596 (ttt90) cc_final: 0.6422 (mtt180)
REVERT: E  424 LYS cc_start: 0.8792 (tptp) cc_final: 0.8502 (tttm)
REVERT: E  451 TYR cc_start: 0.7889 (m-80) cc_final: 0.6769 (m-80)
REVERT: E  462 LYS cc_start: 0.8315 (mtpt) cc_final: 0.8048 (mtpp)
REVERT: E  495 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.8010 (p90)
REVERT: E  508 TYR cc_start: 0.8380 (m-80) cc_final: 0.7974 (m-80)
REVERT: E  516 GLU cc_start: 0.6672 (pm20) cc_final: 0.6427 (pm20)
  outliers start: 15
  outliers final: 8
  residues processed: 93
  average time/residue: 0.2422
  time to fit residues: 28.9193
Evaluate side-chains
  89 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  398 ASP
Chi-restraints excluded: chain E residue  478 THR
Chi-restraints excluded: chain E residue  495 TYR
Chi-restraints excluded: chain E residue  501 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 57.1399 > 50:
  distance: 1 - 18:  13.500
  distance: 5 - 32:  15.687
  distance: 11 - 40:  17.381
  distance: 14 - 18:  12.563
  distance: 15 - 52:  19.706
  distance: 18 - 19:  10.242
  distance: 19 - 20:  10.245
  distance: 19 - 22:   9.118
  distance: 20 - 21:  14.218
  distance: 20 - 32:  23.330
  distance: 21 - 60:  25.537
  distance: 22 - 23:   8.801
  distance: 23 - 24:  13.093
  distance: 23 - 25:   9.117
  distance: 24 - 26:   3.585
  distance: 25 - 27:   9.138
  distance: 25 - 28:   9.116
  distance: 26 - 27:   7.512
  distance: 27 - 29:   5.853
  distance: 28 - 30:   8.101
  distance: 29 - 31:  10.351
  distance: 30 - 31:  12.204
  distance: 32 - 33:  10.424
  distance: 33 - 34:  11.690
  distance: 33 - 36:   4.251
  distance: 34 - 35:  10.471
  distance: 34 - 40:  22.138
  distance: 35 - 67:   7.086
  distance: 36 - 37:   5.582
  distance: 37 - 38:  12.458
  distance: 37 - 39:  16.013
  distance: 40 - 41:  18.676
  distance: 41 - 42:  34.480
  distance: 41 - 44:  24.762
  distance: 42 - 43:  30.686
  distance: 42 - 52:  31.258
  distance: 44 - 45:  14.109
  distance: 45 - 46:   5.394
  distance: 45 - 47:  15.274
  distance: 46 - 48:   9.315
  distance: 47 - 49:  18.010
  distance: 48 - 50:   7.642
  distance: 49 - 50:  14.427
  distance: 50 - 51:   3.738
  distance: 52 - 53:  33.949
  distance: 53 - 54:  43.410
  distance: 53 - 56:  20.180
  distance: 54 - 55:  22.119
  distance: 54 - 60:  35.925
  distance: 56 - 57:  18.374
  distance: 57 - 58:  15.105
  distance: 57 - 59:  27.471
  distance: 60 - 61:  14.306
  distance: 61 - 62:  21.838
  distance: 61 - 64:   6.149
  distance: 62 - 63:  19.168
  distance: 62 - 67:  19.176
  distance: 64 - 65:  23.782
  distance: 64 - 66:  21.265
  distance: 67 - 68:  11.732
  distance: 68 - 69:  34.808
  distance: 68 - 71:  24.095
  distance: 69 - 70:  28.821
  distance: 69 - 75:  45.544
  distance: 71 - 72:  12.058
  distance: 72 - 73:   4.574
  distance: 72 - 74:   4.854
  distance: 75 - 76:  22.117
  distance: 76 - 77:   6.804
  distance: 76 - 79:  12.013
  distance: 77 - 78:  34.652
  distance: 77 - 83:  11.679
  distance: 79 - 80:   5.835
  distance: 79 - 81:   9.152
  distance: 80 - 82:  12.330
  distance: 83 - 84:  12.800
  distance: 84 - 85:  20.623
  distance: 84 - 87:   5.255
  distance: 85 - 86:  13.554
  distance: 85 - 90:  34.146
  distance: 87 - 88:   3.584
  distance: 87 - 89:  11.568
  distance: 90 - 91:   9.949
  distance: 91 - 92:  11.281
  distance: 91 - 94:   9.363
  distance: 92 - 93:  10.952
  distance: 92 - 99:  14.215
  distance: 93 - 121:   6.937
  distance: 94 - 95:  16.065
  distance: 95 - 96:   6.492
  distance: 96 - 97:   6.235
  distance: 99 - 100:  11.519
  distance: 100 - 103:   5.744
  distance: 101 - 102:  10.594
  distance: 101 - 108:   6.193
  distance: 102 - 129:  18.188
  distance: 103 - 104:   5.820
  distance: 104 - 105:   3.446
  distance: 105 - 106:   4.100
  distance: 105 - 107:   7.481