Starting phenix.real_space_refine
on Tue Mar  3 12:26:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ukn_20807/03_2026/6ukn_20807.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ukn_20807/03_2026/6ukn_20807.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ukn_20807/03_2026/6ukn_20807.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ukn_20807/03_2026/6ukn_20807.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ukn_20807/03_2026/6ukn_20807.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ukn_20807/03_2026/6ukn_20807.map"
  }
  resolution = 3.65
  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=   1.000
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: 6
    Type Number    sf(0)   Gaussians
     K       1      8.98       5
     S      40      5.16       5
     Cl      1      4.86       5
     C    2689      2.51       5
     N     639      2.21       5
     O     739      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4109
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4029
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 536, 4029
          Classifications: {'peptide': 536}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 514}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {'  K': 1, ' CL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.14, per 1000 atoms: 0.28
  Number of scatterers: 4109
  At special positions: 0
  Unit cell: (93.234, 68.22, 94.371, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     K       1     19.00
     Cl      1     17.00
     S      40     16.00
     O     739      8.00
     N     639      7.00
     C    2689      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 163 " - pdb=" SG  CYS A 626 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 343 " - pdb=" SG  CYS A 352 " 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 B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 312 "
      " NAG C   1 " - " ASN A 360 "
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 154.7 milliseconds
  

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  970

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 1 sheets defined
      66.8% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 124 through 133
      removed outlier: 3.599A  pdb=" N   LEU A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 140
      removed outlier: 4.286A  pdb=" N   PHE A 138 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 148
    Processing helix  chain 'A' and resid 149 through 177
      removed outlier: 3.852A  pdb=" N   THR A 164 " --> pdb=" O   CYS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 193
      removed outlier: 3.629A  pdb=" N   MET A 188 " --> pdb=" O   GLY A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 227
    Processing helix  chain 'A' and resid 239 through 269
      removed outlier: 4.421A  pdb=" N   ALA A 244 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   LEU A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ASN A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 298
      removed outlier: 3.579A  pdb=" N   VAL A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ASN A 274 " --> pdb=" O   VAL A 270 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   LYS A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   LEU A 278 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   VAL A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 343
    Processing helix  chain 'A' and resid 353 through 359
    Processing helix  chain 'A' and resid 421 through 428
      removed outlier: 4.156A  pdb=" N   GLY A 425 " --> pdb=" O   THR A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 431
      No H-bonds generated for 'chain 'A' and resid 429 through 431'
    Processing helix  chain 'A' and resid 440 through 444
      removed outlier: 3.752A  pdb=" N   LEU A 444 " --> pdb=" O   SER A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 477
      Proline residue:  A 452  - end of helix
      removed outlier: 3.942A  pdb=" N   ILE A 456 " --> pdb=" O   PRO A 452 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA A 475 " --> pdb=" O   VAL A 471 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE A 477 " --> pdb=" O   PHE A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 483
      removed outlier: 3.783A  pdb=" N   ARG A 483 " --> pdb=" O   GLY A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 499
    Processing helix  chain 'A' and resid 504 through 536
      removed outlier: 3.952A  pdb=" N   ILE A 509 " --> pdb=" O   TRP A 505 " (cutoff:3.500A)
      Proline residue:  A 527  - end of helix
      removed outlier: 3.870A  pdb=" N   ASP A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 543
      removed outlier: 4.038A  pdb=" N   GLN A 543 " --> pdb=" O   PRO A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 570
      removed outlier: 3.842A  pdb=" N   LEU A 559 " --> pdb=" O   THR A 555 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LEU A 560 " --> pdb=" O   TRP A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 602
      removed outlier: 3.696A  pdb=" N   ALA A 578 " --> pdb=" O   LEU A 574 " (cutoff:3.500A)
      Proline residue:  A 579  - end of helix
    Processing helix  chain 'A' and resid 615 through 634
      removed outlier: 4.425A  pdb=" N   SER A 619 " --> pdb=" O   HIS A 615 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   PHE A 620 " --> pdb=" O   TRP A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 652
      removed outlier: 4.034A  pdb=" N   PHE A 640 " --> pdb=" O   TYR A 636 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   TYR A 651 " --> pdb=" O   CYS A 647 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ILE A 652 " --> pdb=" O   ILE A 648 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 309
      removed outlier: 4.046A  pdb=" N   ILE A 305 " --> pdb=" O   GLY A 366 " (cutoff:3.500A)

    240 hydrogen bonds defined for protein.
    711 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: 0.63

  Time building geometry restraints manager: 0.41 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1233
        1.35 -     1.47: 1103
        1.47 -     1.59: 1805
        1.59 -     1.71: 0
        1.71 -     1.84: 60
  Bond restraints: 4201
  Sorted by residual:
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.50e+00
  bond pdb=" C1  BMA B   3 "
       pdb=" C2  BMA B   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.550 -0.031 2.00e-02 2.50e+03 2.47e+00
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.32e+00
  bond pdb=" CG1 ILE A 221 "
       pdb=" CD1 ILE A 221 "
    ideal  model  delta    sigma   weight residual
    1.513  1.466  0.047 3.90e-02 6.57e+02 1.46e+00
  bond pdb=" C   PHE A 428 "
       pdb=" N   PRO A 429 "
    ideal  model  delta    sigma   weight residual
    1.336  1.349 -0.013 1.08e-02 8.57e+03 1.39e+00
  ... (remaining 4196 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 5477
        1.84 -     3.67: 201
        3.67 -     5.51: 33
        5.51 -     7.34: 11
        7.34 -     9.18: 1
  Bond angle restraints: 5723
  Sorted by residual:
  angle pdb=" C   ASP A 484 "
        pdb=" N   LYS A 485 "
        pdb=" CA  LYS A 485 "
      ideal   model   delta    sigma   weight residual
     121.54  130.72   -9.18 1.91e+00 2.74e-01 2.31e+01
  angle pdb=" C   LYS A 325 "
        pdb=" N   MET A 326 "
        pdb=" CA  MET A 326 "
      ideal   model   delta    sigma   weight residual
     120.82  127.52   -6.70 1.50e+00 4.44e-01 2.00e+01
  angle pdb=" C   PHE A 420 "
        pdb=" N   THR A 421 "
        pdb=" CA  THR A 421 "
      ideal   model   delta    sigma   weight residual
     121.54  127.50   -5.96 1.91e+00 2.74e-01 9.75e+00
  angle pdb=" C   VAL A 400 "
        pdb=" N   SER A 401 "
        pdb=" CA  SER A 401 "
      ideal   model   delta    sigma   weight residual
     122.35  126.42   -4.07 1.46e+00 4.69e-01 7.79e+00
  angle pdb=" C   ALA A 350 "
        pdb=" N   THR A 351 "
        pdb=" CA  THR A 351 "
      ideal   model   delta    sigma   weight residual
     122.46  126.36   -3.90 1.41e+00 5.03e-01 7.64e+00
  ... (remaining 5718 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.88: 2316
       22.88 -    45.75: 147
       45.75 -    68.63: 10
       68.63 -    91.51: 28
       91.51 -   114.38: 16
  Dihedral angle restraints: 2517
    sinusoidal: 991
      harmonic: 1526
  Sorted by residual:
  dihedral pdb=" CA  LYS A 325 "
           pdb=" C   LYS A 325 "
           pdb=" N   MET A 326 "
           pdb=" CA  MET A 326 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.93  -25.07     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  CYS A 626 "
           pdb=" C   CYS A 626 "
           pdb=" N   LEU A 627 "
           pdb=" CA  LEU A 627 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.73   21.27     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  GLN A 327 "
           pdb=" C   GLN A 327 "
           pdb=" N   VAL A 328 "
           pdb=" CA  VAL A 328 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.14   20.86     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 2514 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 671
       0.113 -    0.226: 26
       0.226 -    0.339: 3
       0.339 -    0.452: 0
       0.452 -    0.564: 1
  Chirality restraints: 701
  Sorted by residual:
  chirality pdb=" C1  BMA C   3 "
            pdb=" O4  NAG C   2 "
            pdb=" C2  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-02 2.50e+03 1.46e+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   -2.56    0.16 2.00e-02 2.50e+03 6.27e+01
  chirality pdb=" C1  BMA B   3 "
            pdb=" O4  NAG B   2 "
            pdb=" C2  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-02 2.50e+03 4.13e+01
  ... (remaining 698 not shown)

  Planarity restraints: 696
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 604 "    0.044 5.00e-02 4.00e+02   6.64e-02 7.06e+00
        pdb=" N   PRO A 605 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 605 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 605 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 626 "    0.012 2.00e-02 2.50e+03   2.29e-02 5.25e+00
        pdb=" C   CYS A 626 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   CYS A 626 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A 627 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 428 "   -0.036 5.00e-02 4.00e+02   5.40e-02 4.67e+00
        pdb=" N   PRO A 429 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 429 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 429 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 693 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.85: 1459
        2.85 -     3.42: 4729
        3.42 -     4.00: 7005
        4.00 -     4.57: 10048
        4.57 -     5.14: 14405
  Nonbonded interactions: 37646
  Sorted by model distance:
  nonbonded pdb=" O   SER A 438 "
            pdb=" OG  SER A 438 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   SER A 511 "
            pdb=" OG1 THR A 515 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O4  BMA B   3 "
            pdb=" O6  BMA B   3 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" OD2 ASP A 415 "
            pdb=" NZ  LYS A 485 "
     model   vdw
     2.386 3.120
  nonbonded pdb=" O   SER A 231 "
            pdb=" OG  SER A 231 "
     model   vdw
     2.407 3.040
  ... (remaining 37641 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 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.820
  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:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.020
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
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      :  0.006   0.066   4210  Z= 0.259
  Angle     :  1.138  26.037   5747  Z= 0.517
  Chirality :  0.055   0.564    701
  Planarity :  0.006   0.066    694
  Dihedral  : 20.626 114.383   1538
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  9.53 %
    Favored  : 90.00 %
  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 are not related in a simple way.
  whole: -2.59 (0.33), residues: 534
  helix: -0.93 (0.25), residues: 333
  sheet: -2.49 (1.44), residues: 10
  loop : -3.02 (0.43), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 528 
 TYR   0.011   0.001   TYR A 186 
 PHE   0.016   0.002   PHE A 428 
 TRP   0.009   0.001   TRP A 505 
 HIS   0.004   0.002   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 ( 4201)
  covalent geometry    : angle       0.83135 ( 5723)
  SS BOND              : bond        0.00630 (    3)
  SS BOND              : angle       1.91657 (    6)
  hydrogen bonds       : bond        0.14098 (  240)
  hydrogen bonds       : angle       5.36859 (  711)
  link_BETA1-4         : bond        0.06482 (    4)
  link_BETA1-4         : angle      15.15885 (   12)
  link_NAG-ASN         : bond        0.02339 (    2)
  link_NAG-ASN         : angle      10.86311 (    6)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 MET cc_start: 0.7574 (ttm) cc_final: 0.6959 (ttm)
REVERT: A  279 VAL cc_start: 0.9342 (t) cc_final: 0.8915 (p)
REVERT: A  435 MET cc_start: 0.8319 (mmt) cc_final: 0.7700 (mmt)
REVERT: A  521 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8676 (tm-30)
REVERT: A  547 HIS cc_start: 0.7428 (m170) cc_final: 0.7073 (m170)
REVERT: A  559 LEU cc_start: 0.8698 (tp) cc_final: 0.8481 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0592
  time to fit residues: 9.5560
Evaluate side-chains
  85 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 130 GLN
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 359 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.122270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.102774 restraints weight = 8302.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.105999 restraints weight = 4191.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.108168 restraints weight = 2634.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.109664 restraints weight = 1924.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.110445 restraints weight = 1552.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   4210  Z= 0.177
  Angle     :  0.813  17.907   5747  Z= 0.381
  Chirality :  0.048   0.452    701
  Planarity :  0.005   0.058    694
  Dihedral  : 18.901 102.608    693
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.91 %
    Favored  : 78.60 %
  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 are not related in a simple way.
  whole: -1.23 (0.36), residues: 534
  helix:  0.31 (0.28), residues: 332
  sheet: -2.04 (1.65), residues: 10
  loop : -2.81 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 117 
 TYR   0.010   0.001   TYR A 186 
 PHE   0.013   0.001   PHE A 428 
 TRP   0.012   0.001   TRP A 505 
 HIS   0.003   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 4201)
  covalent geometry    : angle       0.74043 ( 5723)
  SS BOND              : bond        0.00219 (    3)
  SS BOND              : angle       1.74029 (    6)
  hydrogen bonds       : bond        0.05172 (  240)
  hydrogen bonds       : angle       4.38510 (  711)
  link_BETA1-4         : bond        0.00800 (    4)
  link_BETA1-4         : angle       3.26443 (   12)
  link_NAG-ASN         : bond        0.01680 (    2)
  link_NAG-ASN         : angle       9.27144 (    6)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.8429 (t80) cc_final: 0.8226 (t80)
REVERT: A  262 MET cc_start: 0.8831 (mmm) cc_final: 0.8566 (mmm)
REVERT: A  385 ASP cc_start: 0.8564 (t0) cc_final: 0.8361 (t0)
REVERT: A  521 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8557 (tm-30)
REVERT: A  547 HIS cc_start: 0.7459 (m170) cc_final: 0.7105 (m170)
REVERT: A  583 MET cc_start: 0.7787 (tmm) cc_final: 0.7522 (tmm)
  outliers start: 15
  outliers final: 9
  residues processed: 109
  average time/residue: 0.0393
  time to fit residues: 6.1391
Evaluate side-chains
  93 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  636 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0470
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 11 optimal weight:    0.3980
   chunk 52 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
A 250 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.123961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.104413 restraints weight = 8212.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.107602 restraints weight = 4142.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.109853 restraints weight = 2600.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.111301 restraints weight = 1885.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.112361 restraints weight = 1524.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4210  Z= 0.133
  Angle     :  0.757  17.451   5747  Z= 0.345
  Chirality :  0.047   0.476    701
  Planarity :  0.004   0.052    694
  Dihedral  : 15.930  96.111    693
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 20.23 %
    Favored  : 74.42 %
  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 are not related in a simple way.
  whole: -0.51 (0.37), residues: 534
  helix:  1.06 (0.29), residues: 325
  sheet: -1.52 (1.69), residues: 10
  loop : -2.76 (0.42), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 603 
 TYR   0.010   0.001   TYR A 614 
 PHE   0.013   0.001   PHE A 154 
 TRP   0.016   0.001   TRP A 635 
 HIS   0.001   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4201)
  covalent geometry    : angle       0.68401 ( 5723)
  SS BOND              : bond        0.00505 (    3)
  SS BOND              : angle       1.51184 (    6)
  hydrogen bonds       : bond        0.04618 (  240)
  hydrogen bonds       : angle       3.98564 (  711)
  link_BETA1-4         : bond        0.00652 (    4)
  link_BETA1-4         : angle       3.14376 (   12)
  link_NAG-ASN         : bond        0.01771 (    2)
  link_NAG-ASN         : angle       8.95850 (    6)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  171 MET cc_start: 0.8138 (ttp) cc_final: 0.6910 (ttm)
REVERT: A  521 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8590 (tm-30)
REVERT: A  547 HIS cc_start: 0.7447 (m170) cc_final: 0.6964 (m90)
  outliers start: 23
  outliers final: 12
  residues processed: 114
  average time/residue: 0.0445
  time to fit residues: 7.0890
Evaluate side-chains
  104 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 27 optimal weight:    0.3980
   chunk 24 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.126010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.106996 restraints weight = 8206.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.109994 restraints weight = 4405.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.111849 restraints weight = 2874.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.113321 restraints weight = 2191.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.113991 restraints weight = 1800.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4210  Z= 0.144
  Angle     :  0.766  17.324   5747  Z= 0.352
  Chirality :  0.048   0.483    701
  Planarity :  0.004   0.052    694
  Dihedral  : 14.436  92.055    693
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 21.86 %
    Favored  : 74.19 %
  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 are not related in a simple way.
  whole: -0.22 (0.38), residues: 534
  helix:  1.33 (0.30), residues: 328
  sheet: -1.37 (1.75), residues: 10
  loop : -2.78 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 340 
 TYR   0.010   0.001   TYR A 186 
 PHE   0.011   0.001   PHE A 428 
 TRP   0.015   0.001   TRP A 635 
 HIS   0.001   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4201)
  covalent geometry    : angle       0.69657 ( 5723)
  SS BOND              : bond        0.00789 (    3)
  SS BOND              : angle       1.91068 (    6)
  hydrogen bonds       : bond        0.04554 (  240)
  hydrogen bonds       : angle       3.92121 (  711)
  link_BETA1-4         : bond        0.00710 (    4)
  link_BETA1-4         : angle       2.85436 (   12)
  link_NAG-ASN         : bond        0.01716 (    2)
  link_NAG-ASN         : angle       8.91918 (    6)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A  385 ASP cc_start: 0.8421 (t0) cc_final: 0.8047 (t0)
REVERT: A  521 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8537 (tm-30)
REVERT: A  547 HIS cc_start: 0.7408 (m170) cc_final: 0.6966 (m90)
REVERT: A  587 MET cc_start: 0.7790 (ttp) cc_final: 0.7524 (ttm)
  outliers start: 17
  outliers final: 12
  residues processed: 106
  average time/residue: 0.0500
  time to fit residues: 7.2569
Evaluate side-chains
  99 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0060
   chunk 19 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0170
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.5434

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.127078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.108100 restraints weight = 7967.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.111224 restraints weight = 4080.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.113169 restraints weight = 2593.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.114691 restraints weight = 1939.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.115605 restraints weight = 1580.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4210  Z= 0.127
  Angle     :  0.721  17.109   5747  Z= 0.331
  Chirality :  0.047   0.492    701
  Planarity :  0.004   0.051    694
  Dihedral  : 13.172  87.684    693
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 24.19 %
    Favored  : 72.33 %
  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 are not related in a simple way.
  whole:  0.08 (0.38), residues: 534
  helix:  1.60 (0.30), residues: 326
  sheet: -1.28 (1.75), residues: 10
  loop : -2.68 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 603 
 TYR   0.010   0.001   TYR A 272 
 PHE   0.011   0.001   PHE A 154 
 TRP   0.017   0.001   TRP A 635 
 HIS   0.001   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4201)
  covalent geometry    : angle       0.65128 ( 5723)
  SS BOND              : bond        0.00674 (    3)
  SS BOND              : angle       1.79788 (    6)
  hydrogen bonds       : bond        0.04263 (  240)
  hydrogen bonds       : angle       3.75297 (  711)
  link_BETA1-4         : bond        0.00655 (    4)
  link_BETA1-4         : angle       2.45622 (   12)
  link_NAG-ASN         : bond        0.01737 (    2)
  link_NAG-ASN         : angle       8.81196 (    6)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A  262 MET cc_start: 0.8886 (tpp) cc_final: 0.8386 (mmm)
REVERT: A  521 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8558 (tm-30)
REVERT: A  547 HIS cc_start: 0.7449 (m170) cc_final: 0.6987 (m90)
REVERT: A  587 MET cc_start: 0.7870 (ttp) cc_final: 0.7550 (ttm)
  outliers start: 15
  outliers final: 11
  residues processed: 111
  average time/residue: 0.0416
  time to fit residues: 6.6000
Evaluate side-chains
  103 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 11 optimal weight:    0.1980
   chunk 33 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.126133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.107391 restraints weight = 8379.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.110302 restraints weight = 4500.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.112152 restraints weight = 2956.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.113570 restraints weight = 2251.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.114091 restraints weight = 1858.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4210  Z= 0.133
  Angle     :  0.728  17.002   5747  Z= 0.333
  Chirality :  0.047   0.503    701
  Planarity :  0.004   0.050    694
  Dihedral  : 12.339  83.149    693
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 24.42 %
    Favored  : 70.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.39), residues: 534
  helix:  1.74 (0.30), residues: 327
  sheet: -1.06 (1.80), residues: 10
  loop : -2.60 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 117 
 TYR   0.009   0.001   TYR A 272 
 PHE   0.011   0.001   PHE A 428 
 TRP   0.017   0.001   TRP A 635 
 HIS   0.001   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4201)
  covalent geometry    : angle       0.66167 ( 5723)
  SS BOND              : bond        0.00594 (    3)
  SS BOND              : angle       1.63363 (    6)
  hydrogen bonds       : bond        0.04201 (  240)
  hydrogen bonds       : angle       3.71387 (  711)
  link_BETA1-4         : bond        0.00705 (    4)
  link_BETA1-4         : angle       2.26329 (   12)
  link_NAG-ASN         : bond        0.01670 (    2)
  link_NAG-ASN         : angle       8.80146 (    6)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: A  262 MET cc_start: 0.8878 (tpp) cc_final: 0.8467 (mmm)
REVERT: A  297 LYS cc_start: 0.8395 (mptt) cc_final: 0.7805 (tmtt)
REVERT: A  385 ASP cc_start: 0.8386 (t0) cc_final: 0.8095 (t0)
REVERT: A  435 MET cc_start: 0.8702 (mmt) cc_final: 0.8489 (mmm)
REVERT: A  520 LEU cc_start: 0.9139 (mt) cc_final: 0.8774 (mt)
REVERT: A  521 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8592 (tm-30)
REVERT: A  547 HIS cc_start: 0.7543 (m170) cc_final: 0.7026 (m90)
  outliers start: 20
  outliers final: 15
  residues processed: 107
  average time/residue: 0.0434
  time to fit residues: 6.4164
Evaluate side-chains
  108 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  292 TYR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  636 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0570
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.127093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.108549 restraints weight = 8125.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.111407 restraints weight = 4319.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.113429 restraints weight = 2831.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.114715 restraints weight = 2113.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.115586 restraints weight = 1751.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4210  Z= 0.130
  Angle     :  0.727  16.825   5747  Z= 0.330
  Chirality :  0.047   0.522    701
  Planarity :  0.004   0.048    694
  Dihedral  : 11.454  78.646    693
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 24.65 %
    Favored  : 70.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.39), residues: 534
  helix:  1.78 (0.30), residues: 327
  sheet: -1.02 (1.78), residues: 10
  loop : -2.55 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 117 
 TYR   0.008   0.001   TYR A 186 
 PHE   0.010   0.001   PHE A 154 
 TRP   0.017   0.001   TRP A 635 
 HIS   0.000   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4201)
  covalent geometry    : angle       0.66087 ( 5723)
  SS BOND              : bond        0.00512 (    3)
  SS BOND              : angle       1.55313 (    6)
  hydrogen bonds       : bond        0.04131 (  240)
  hydrogen bonds       : angle       3.69621 (  711)
  link_BETA1-4         : bond        0.00677 (    4)
  link_BETA1-4         : angle       2.23607 (   12)
  link_NAG-ASN         : bond        0.01663 (    2)
  link_NAG-ASN         : angle       8.77022 (    6)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A  262 MET cc_start: 0.8851 (tpp) cc_final: 0.8471 (mmm)
REVERT: A  520 LEU cc_start: 0.9151 (mt) cc_final: 0.8794 (mt)
REVERT: A  521 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8580 (tm-30)
REVERT: A  547 HIS cc_start: 0.7528 (m170) cc_final: 0.7005 (m90)
  outliers start: 19
  outliers final: 13
  residues processed: 111
  average time/residue: 0.0404
  time to fit residues: 6.4551
Evaluate side-chains
  107 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  636 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 37 optimal weight:    0.3980
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 GLN
A 493 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.127167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.108176 restraints weight = 8144.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.111145 restraints weight = 4338.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.113180 restraints weight = 2837.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.114429 restraints weight = 2123.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.114758 restraints weight = 1766.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4210  Z= 0.132
  Angle     :  0.762  17.008   5747  Z= 0.342
  Chirality :  0.048   0.548    701
  Planarity :  0.004   0.049    694
  Dihedral  : 10.892  75.487    693
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 25.35 %
    Favored  : 70.47 %
  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 are not related in a simple way.
  whole:  0.35 (0.39), residues: 534
  helix:  1.77 (0.30), residues: 327
  sheet: -0.90 (1.81), residues: 10
  loop : -2.54 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 483 
 TYR   0.008   0.001   TYR A 186 
 PHE   0.011   0.001   PHE A 428 
 TRP   0.018   0.001   TRP A 635 
 HIS   0.001   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4201)
  covalent geometry    : angle       0.69831 ( 5723)
  SS BOND              : bond        0.00682 (    3)
  SS BOND              : angle       1.62549 (    6)
  hydrogen bonds       : bond        0.04076 (  240)
  hydrogen bonds       : angle       3.73251 (  711)
  link_BETA1-4         : bond        0.00695 (    4)
  link_BETA1-4         : angle       2.23374 (   12)
  link_NAG-ASN         : bond        0.01559 (    2)
  link_NAG-ASN         : angle       8.82619 (    6)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A  262 MET cc_start: 0.8876 (tpp) cc_final: 0.8456 (mmm)
REVERT: A  358 GLN cc_start: 0.7378 (tt0) cc_final: 0.7057 (tt0)
REVERT: A  520 LEU cc_start: 0.9142 (mt) cc_final: 0.8776 (mt)
REVERT: A  521 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8615 (tm-30)
  outliers start: 18
  outliers final: 15
  residues processed: 109
  average time/residue: 0.0447
  time to fit residues: 6.8364
Evaluate side-chains
  107 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  292 TYR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  636 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.126499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.107423 restraints weight = 8222.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.110404 restraints weight = 4392.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.112435 restraints weight = 2865.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.113640 restraints weight = 2134.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.114672 restraints weight = 1780.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4210  Z= 0.141
  Angle     :  0.796  16.900   5747  Z= 0.354
  Chirality :  0.049   0.572    701
  Planarity :  0.004   0.051    694
  Dihedral  : 10.185  70.880    693
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 26.74 %
    Favored  : 69.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.39), residues: 534
  helix:  1.72 (0.30), residues: 327
  sheet: -0.77 (1.84), residues: 10
  loop : -2.53 (0.44), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 483 
 TYR   0.009   0.001   TYR A 186 
 PHE   0.012   0.001   PHE A 428 
 TRP   0.018   0.001   TRP A 635 
 HIS   0.000   0.000   HIS A 547 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 4201)
  covalent geometry    : angle       0.73487 ( 5723)
  SS BOND              : bond        0.00654 (    3)
  SS BOND              : angle       1.68043 (    6)
  hydrogen bonds       : bond        0.04159 (  240)
  hydrogen bonds       : angle       3.80612 (  711)
  link_BETA1-4         : bond        0.00722 (    4)
  link_BETA1-4         : angle       2.25139 (   12)
  link_NAG-ASN         : bond        0.01509 (    2)
  link_NAG-ASN         : angle       8.90474 (    6)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A  262 MET cc_start: 0.8888 (tpp) cc_final: 0.8491 (mmm)
REVERT: A  358 GLN cc_start: 0.7404 (tt0) cc_final: 0.7106 (tt0)
REVERT: A  520 LEU cc_start: 0.9160 (mt) cc_final: 0.8778 (mt)
REVERT: A  521 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8592 (tm-30)
  outliers start: 17
  outliers final: 15
  residues processed: 104
  average time/residue: 0.0472
  time to fit residues: 6.7865
Evaluate side-chains
  107 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  292 TYR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  636 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 51 optimal weight:    0.4980
   chunk 15 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0980
   chunk 25 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.127511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.108793 restraints weight = 7848.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.111752 restraints weight = 4299.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.113732 restraints weight = 2831.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.114467 restraints weight = 2124.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.115701 restraints weight = 1840.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.3087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4210  Z= 0.133
  Angle     :  0.810  16.834   5747  Z= 0.357
  Chirality :  0.048   0.573    701
  Planarity :  0.004   0.051    694
  Dihedral  :  9.721  68.065    693
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 27.21 %
    Favored  : 69.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.39), residues: 534
  helix:  1.72 (0.30), residues: 327
  sheet: -0.91 (1.75), residues: 10
  loop : -2.48 (0.44), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 117 
 TYR   0.007   0.001   TYR A 186 
 PHE   0.011   0.001   PHE A 428 
 TRP   0.019   0.001   TRP A 635 
 HIS   0.001   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4201)
  covalent geometry    : angle       0.75000 ( 5723)
  SS BOND              : bond        0.00480 (    3)
  SS BOND              : angle       1.57856 (    6)
  hydrogen bonds       : bond        0.04035 (  240)
  hydrogen bonds       : angle       3.77840 (  711)
  link_BETA1-4         : bond        0.00709 (    4)
  link_BETA1-4         : angle       2.27497 (   12)
  link_NAG-ASN         : bond        0.01543 (    2)
  link_NAG-ASN         : angle       8.89296 (    6)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A  262 MET cc_start: 0.8844 (tpp) cc_final: 0.8452 (mmm)
REVERT: A  358 GLN cc_start: 0.7459 (tt0) cc_final: 0.7136 (tt0)
REVERT: A  520 LEU cc_start: 0.9164 (mt) cc_final: 0.8781 (mt)
REVERT: A  521 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8576 (tm-30)
  outliers start: 15
  outliers final: 14
  residues processed: 101
  average time/residue: 0.0397
  time to fit residues: 5.8844
Evaluate side-chains
  104 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  292 TYR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  636 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.125159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.106408 restraints weight = 7916.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.109273 restraints weight = 4351.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.111274 restraints weight = 2876.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.112500 restraints weight = 2159.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.113467 restraints weight = 1793.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   4210  Z= 0.164
  Angle     :  0.837  17.057   5747  Z= 0.371
  Chirality :  0.050   0.617    701
  Planarity :  0.004   0.051    694
  Dihedral  :  9.077  62.040    693
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 27.91 %
    Favored  : 68.84 %
  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 are not related in a simple way.
  whole:  0.30 (0.39), residues: 534
  helix:  1.66 (0.30), residues: 327
  sheet: -0.96 (1.73), residues: 10
  loop : -2.42 (0.45), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 117 
 TYR   0.011   0.001   TYR A 186 
 PHE   0.014   0.001   PHE A 428 
 TRP   0.018   0.001   TRP A 635 
 HIS   0.001   0.000   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 4201)
  covalent geometry    : angle       0.77698 ( 5723)
  SS BOND              : bond        0.00462 (    3)
  SS BOND              : angle       1.81886 (    6)
  hydrogen bonds       : bond        0.04329 (  240)
  hydrogen bonds       : angle       3.91032 (  711)
  link_BETA1-4         : bond        0.00726 (    4)
  link_BETA1-4         : angle       2.25975 (   12)
  link_NAG-ASN         : bond        0.01486 (    2)
  link_NAG-ASN         : angle       9.02141 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 806.31 seconds
wall clock time: 14 minutes 35.70 seconds (875.70 seconds total)