Starting phenix.real_space_refine
on Tue Mar  3 14:58:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wrq_32735/03_2026/7wrq_32735_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wrq_32735/03_2026/7wrq_32735.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wrq_32735/03_2026/7wrq_32735.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wrq_32735/03_2026/7wrq_32735.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wrq_32735/03_2026/7wrq_32735_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wrq_32735/03_2026/7wrq_32735_neut.cif"
  }
  resolution = 3.6
  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=  -0.001 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    3930      2.51       5
     N    1125      2.21       5
     O    1151      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Residue "B ARG   36": not complete - not flipped  Time to flip 8 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: 6247
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 566, 4384
          Classifications: {'peptide': 566}
          Link IDs: {'PTRANS': 32, 'TRANS': 533}
    Chain: "B"
      Number of atoms: 1269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 1269
          Classifications: {'peptide': 167}
          Link IDs: {'PTRANS': 16, 'TRANS': 150}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 499
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 499
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 4, 'TRANS': 60}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      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: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 1.45, per 1000 atoms: 0.23
  Number of scatterers: 6247
  At special positions: 0
  Unit cell: (63.576, 98.896, 123.62, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      41     16.00
     O    1151      8.00
     N    1125      7.00
     C    3930      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  41 " - pdb=" SG  CYS A  47 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  45 " - pdb=" SG  CYS A  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 373 " - pdb=" SG  CYS A 397 " distance=1.73
    Simple disulfide: pdb=" SG  CYS A 540 " - pdb=" SG  CYS A 583 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 542 " - pdb=" SG  CYS A 605 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 566 " - pdb=" SG  CYS A 571 " distance=2.09
    Simple disulfide: pdb=" SG  CYS B  13 " - pdb=" SG  CYS B  40 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  16 " - pdb=" SG  CYS B  42 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  43 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B  31 " - pdb=" SG  CYS B  46 " distance=2.10
    Simple disulfide: pdb=" SG  CYS B  54 " - pdb=" SG  CYS B  67 " distance=2.19
    Simple disulfide: pdb=" SG  CYS B  61 " - pdb=" SG  CYS B  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 186 " - pdb=" SG  CYS B 213 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 224 " - pdb=" SG  CYS B 235 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 237 " - pdb=" SG  CYS B 258 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   6 " - pdb=" SG  CYS C  48 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  18 " - pdb=" SG  CYS C  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  47 " - pdb=" SG  CYS C  52 " 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 D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    NAG-ASN
      " NAG A 701 " - " ASN A  64 "
      " NAG A 702 " - " ASN A  96 "
      " NAG A 703 " - " ASN A 515 "
      " NAG A 704 " - " ASN A 580 "
      " NAG D   1 " - " ASN A 368 "
  Time building additional restraints: 0.55
  Conformation dependent library (CDL) restraints added in 205.5 milliseconds
  

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1450

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 9 sheets defined
      8.6% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 498 through 502
      removed outlier: 3.754A  pdb=" N   LEU A 502 " --> pdb=" O   ASN A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 554
    Processing helix  chain 'B' and resid 17 through 24
    Processing helix  chain 'B' and resid 75 through 82
    Processing helix  chain 'B' and resid 186 through 195
      removed outlier: 3.883A  pdb=" N   ASP B 192 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 19
    Processing helix  chain 'C' and resid 42 through 50
    Processing helix  chain 'C' and resid 53 through 59
      removed outlier: 3.567A  pdb=" N   LEU C  57 " --> pdb=" O   ASP C  53 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47
      removed outlier: 6.722A  pdb=" N   VAL A  58 " --> pdb=" O   TRP A  80 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   LEU A  79 " --> pdb=" O   ASN A 104 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 200
      removed outlier: 3.523A  pdb=" N   LEU A 199 " --> pdb=" O   GLU A 222 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASP A 224 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU A 223 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   TYR A 248 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 367
      removed outlier: 3.666A  pdb=" N   MET A 367 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 464
      removed outlier: 7.082A  pdb=" N   LEU A 463 " --> pdb=" O   ASP A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 563
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11
      removed outlier: 6.300A  pdb=" N   VAL B  10 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 36
    Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54
    Processing sheet with id=AA9, first strand: chain 'B' and resid 222 through 223

    50 hydrogen bonds defined for protein.
    132 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: 0.62

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1181
        1.32 -     1.45: 1573
        1.45 -     1.58: 3579
        1.58 -     1.70: 0
        1.70 -     1.83: 44
  Bond restraints: 6377
  Sorted by residual:
  bond pdb=" C   GLU A 567 "
       pdb=" N   GLY A 568 "
    ideal  model  delta    sigma   weight residual
    1.331  1.574 -0.244 1.46e-02 4.69e+03 2.79e+02
  bond pdb=" C   VAL B  30 "
       pdb=" N   CYS B  31 "
    ideal  model  delta    sigma   weight residual
    1.332  1.525 -0.192 1.40e-02 5.10e+03 1.89e+02
  bond pdb=" C   ILE A 565 "
       pdb=" N   CYS A 566 "
    ideal  model  delta    sigma   weight residual
    1.331  1.206  0.125 1.24e-02 6.50e+03 1.01e+02
  bond pdb=" C   LEU C  64 "
       pdb=" N   LYS C  65 "
    ideal  model  delta    sigma   weight residual
    1.329  1.463 -0.134 1.40e-02 5.10e+03 9.10e+01
  bond pdb=" C   GLU A 394 "
       pdb=" N   GLY A 395 "
    ideal  model  delta    sigma   weight residual
    1.333  1.460 -0.127 1.41e-02 5.03e+03 8.09e+01
  ... (remaining 6372 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.68: 8503
        3.68 -     7.35: 113
        7.35 -    11.03: 16
       11.03 -    14.70: 9
       14.70 -    18.38: 4
  Bond angle restraints: 8645
  Sorted by residual:
  angle pdb=" O   ILE A 565 "
        pdb=" C   ILE A 565 "
        pdb=" N   CYS A 566 "
      ideal   model   delta    sigma   weight residual
     122.57  106.94   15.63 1.25e+00 6.40e-01 1.56e+02
  angle pdb=" O   GLU A 394 "
        pdb=" C   GLU A 394 "
        pdb=" N   GLY A 395 "
      ideal   model   delta    sigma   weight residual
     122.85  135.51  -12.66 1.14e+00 7.69e-01 1.23e+02
  angle pdb=" C   ALA B  32 "
        pdb=" N   GLU B  33 "
        pdb=" CA  GLU B  33 "
      ideal   model   delta    sigma   weight residual
     122.68  138.10  -15.42 1.47e+00 4.63e-01 1.10e+02
  angle pdb=" C   SER A  62 "
        pdb=" N   ARG A  63 "
        pdb=" CA  ARG A  63 "
      ideal   model   delta    sigma   weight residual
     121.69  140.07  -18.38 1.85e+00 2.92e-01 9.87e+01
  angle pdb=" O   ALA A 603 "
        pdb=" C   ALA A 603 "
        pdb=" N   PRO A 604 "
      ideal   model   delta    sigma   weight residual
     121.32  109.96   11.36 1.15e+00 7.56e-01 9.75e+01
  ... (remaining 8640 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.98: 3901
       35.98 -    71.97: 88
       71.97 -   107.95: 13
      107.95 -   143.93: 0
      143.93 -   179.91: 1
  Dihedral angle restraints: 4003
    sinusoidal: 1743
      harmonic: 2260
  Sorted by residual:
  dihedral pdb=" CD  ARG B  36 "
           pdb=" NE  ARG B  36 "
           pdb=" CZ  ARG B  36 "
           pdb=" NH1 ARG B  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00 -179.91  179.91     1      1.00e+01 1.00e-02 1.92e+02
  dihedral pdb=" CD  ARG A 160 "
           pdb=" NE  ARG A 160 "
           pdb=" CZ  ARG A 160 "
           pdb=" NH1 ARG A 160 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -79.75   79.75     1      1.00e+01 1.00e-02 7.89e+01
  dihedral pdb=" CB  CYS B  24 "
           pdb=" SG  CYS B  24 "
           pdb=" SG  CYS B  43 "
           pdb=" CB  CYS B  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.98  -74.98     1      1.00e+01 1.00e-02 7.11e+01
  ... (remaining 4000 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 831
       0.096 -    0.193: 116
       0.193 -    0.289: 21
       0.289 -    0.386: 4
       0.386 -    0.482: 3
  Chirality restraints: 975
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-02 2.50e+03 1.30e+02
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 368 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.92   -0.48 2.00e-01 2.50e+01 5.81e+00
  chirality pdb=" CA  LEU A 398 "
            pdb=" N   LEU A 398 "
            pdb=" C   LEU A 398 "
            pdb=" CB  LEU A 398 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.60e+00
  ... (remaining 972 not shown)

  Planarity restraints: 1142
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "    0.345 2.00e-02 2.50e+03   2.93e-01 1.07e+03
        pdb=" C7  NAG D   2 "   -0.087 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.176 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "   -0.514 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "    0.080 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 702 "   -0.286 2.00e-02 2.50e+03   2.45e-01 7.53e+02
        pdb=" C7  NAG A 702 "    0.068 2.00e-02 2.50e+03
        pdb=" C8  NAG A 702 "   -0.169 2.00e-02 2.50e+03
        pdb=" N2  NAG A 702 "    0.429 2.00e-02 2.50e+03
        pdb=" O7  NAG A 702 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 704 "    0.212 2.00e-02 2.50e+03   1.76e-01 3.89e+02
        pdb=" C7  NAG A 704 "   -0.058 2.00e-02 2.50e+03
        pdb=" C8  NAG A 704 "    0.151 2.00e-02 2.50e+03
        pdb=" N2  NAG A 704 "   -0.290 2.00e-02 2.50e+03
        pdb=" O7  NAG A 704 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1139 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 2230
        2.87 -     3.37: 4769
        3.37 -     3.88: 8412
        3.88 -     4.39: 9122
        4.39 -     4.90: 16849
  Nonbonded interactions: 41382
  Sorted by model distance:
  nonbonded pdb=" O   SER A 195 "
            pdb=" OG  SER A 195 "
     model   vdw
     2.357 3.040
  nonbonded pdb=" O   GLU B 189 "
            pdb=" OG1 THR B 193 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" O   SER C  34 "
            pdb=" OG  SER C  34 "
     model   vdw
     2.386 3.040
  nonbonded pdb=" N   GLN A  95 "
            pdb=" O   GLN A  95 "
     model   vdw
     2.398 2.496
  nonbonded pdb=" NH1 ARG A 269 "
            pdb=" OH  TYR B 183 "
     model   vdw
     2.417 3.120
  ... (remaining 41377 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.370
  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:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
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      :  0.012   0.303   6402  Z= 0.696
  Angle     :  1.380  25.271   8702  Z= 0.845
  Chirality :  0.076   0.482    975
  Planarity :  0.024   0.484   1137
  Dihedral  : 15.483 179.913   2499
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 1.04
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  : 19.87 %
    Favored  : 79.62 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  6.65 %
    Favored  : 92.30 %
  Cbeta Deviations :  0.14 %
  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: -5.87 (0.21), residues: 790
  helix: -2.24 (0.61), residues: 60
  sheet: -4.22 (0.40), residues: 100
  loop : -4.45 (0.17), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  56 
 TYR   0.012   0.002   TYR B 183 
 PHE   0.017   0.002   PHE A 262 
 TRP   0.011   0.001   TRP A 179 
 HIS   0.014   0.002   HIS A 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.01074 ( 6377)
  covalent geometry    : angle       1.29142 ( 8645)
  SS BOND              : bond        0.08369 (   18)
  SS BOND              : angle       6.62618 (   36)
  hydrogen bonds       : bond        0.25345 (   50)
  hydrogen bonds       : angle       9.05070 (  132)
  link_BETA1-4         : bond        0.00146 (    2)
  link_BETA1-4         : angle       2.58030 (    6)
  link_NAG-ASN         : bond        0.02790 (    5)
  link_NAG-ASN         : angle       5.98642 (   15)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 LYS cc_start: 0.9073 (tttp) cc_final: 0.8872 (tptp)
REVERT: B   37 GLU cc_start: 0.9295 (pt0) cc_final: 0.8467 (pm20)
REVERT: B   49 SER cc_start: 0.9460 (t) cc_final: 0.9195 (p)
REVERT: B   68 GLN cc_start: 0.9127 (mt0) cc_final: 0.8816 (mt0)
REVERT: B   72 ASP cc_start: 0.8863 (p0) cc_final: 0.8576 (p0)
REVERT: B  209 HIS cc_start: 0.8327 (m170) cc_final: 0.8090 (m170)
REVERT: B  243 GLN cc_start: 0.8755 (mp10) cc_final: 0.8243 (mp10)
REVERT: B  259 TYR cc_start: 0.8094 (m-80) cc_final: 0.7892 (m-10)
REVERT: C    5 LEU cc_start: 0.8986 (tp) cc_final: 0.8707 (tt)
  outliers start: 7
  outliers final: 3
  residues processed: 89
  average time/residue: 0.0987
  time to fit residues: 11.0543
Evaluate side-chains
  55 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 CYS
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain A residue  571 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0070
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6000

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

Flipped N/Q/H residues before XYZ refinement:
A 601 HIS
B 196 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.089043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.062087 restraints weight = 15140.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.064642 restraints weight = 8401.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.066319 restraints weight = 5863.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.067474 restraints weight = 4676.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.068244 restraints weight = 4044.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   6402  Z= 0.131
  Angle     :  0.705   6.802   8702  Z= 0.352
  Chirality :  0.043   0.157    975
  Planarity :  0.005   0.050   1137
  Dihedral  : 10.496 179.999   1019
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 11.01 %
    Favored  : 88.73 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 10.42 %
    Favored  : 87.46 %
  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: -5.22 (0.23), residues: 790
  helix: -1.68 (0.58), residues: 68
  sheet: -4.01 (0.37), residues: 113
  loop : -3.93 (0.19), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C  55 
 TYR   0.017   0.001   TYR A 208 
 PHE   0.012   0.001   PHE A 416 
 TRP   0.020   0.001   TRP A 173 
 HIS   0.014   0.001   HIS A 601 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6377)
  covalent geometry    : angle       0.69171 ( 8645)
  SS BOND              : bond        0.00814 (   18)
  SS BOND              : angle       1.29764 (   36)
  hydrogen bonds       : bond        0.04387 (   50)
  hydrogen bonds       : angle       6.43663 (  132)
  link_BETA1-4         : bond        0.00092 (    2)
  link_BETA1-4         : angle       2.57668 (    6)
  link_NAG-ASN         : bond        0.00265 (    5)
  link_NAG-ASN         : angle       2.34653 (   15)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 LYS cc_start: 0.9132 (tttp) cc_final: 0.8820 (tptp)
REVERT: B   37 GLU cc_start: 0.9267 (pt0) cc_final: 0.8428 (pm20)
REVERT: B   49 SER cc_start: 0.9447 (t) cc_final: 0.9163 (p)
REVERT: B  209 HIS cc_start: 0.8346 (m170) cc_final: 0.8110 (m170)
REVERT: B  243 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8458 (mp10)
REVERT: B  259 TYR cc_start: 0.8164 (m-80) cc_final: 0.7937 (m-10)
  outliers start: 14
  outliers final: 6
  residues processed: 65
  average time/residue: 0.0873
  time to fit residues: 7.4227
Evaluate side-chains
  54 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain A residue  571 CYS
Chi-restraints excluded: chain B residue  243 GLN
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   33 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 39 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.084546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.057668 restraints weight = 15282.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.060004 restraints weight = 8506.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.061612 restraints weight = 5991.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.062604 restraints weight = 4803.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.063285 restraints weight = 4192.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   6402  Z= 0.231
  Angle     :  0.780   9.344   8702  Z= 0.387
  Chirality :  0.047   0.171    975
  Planarity :  0.005   0.053   1137
  Dihedral  :  8.992 179.238   1018
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 15.70 %
    Favored  : 84.18 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.75 %
    Favored  : 84.59 %
  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: -4.86 (0.24), residues: 790
  helix: -1.33 (0.57), residues: 69
  sheet: -3.49 (0.59), residues: 52
  loop : -3.82 (0.19), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  50 
 TYR   0.024   0.002   TYR A  49 
 PHE   0.012   0.002   PHE A 382 
 TRP   0.009   0.001   TRP A 173 
 HIS   0.004   0.001   HIS A 601 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 6377)
  covalent geometry    : angle       0.77047 ( 8645)
  SS BOND              : bond        0.00371 (   18)
  SS BOND              : angle       1.28305 (   36)
  hydrogen bonds       : bond        0.04898 (   50)
  hydrogen bonds       : angle       6.25616 (  132)
  link_BETA1-4         : bond        0.00585 (    2)
  link_BETA1-4         : angle       2.42219 (    6)
  link_NAG-ASN         : bond        0.00345 (    5)
  link_NAG-ASN         : angle       2.15625 (   15)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 GLU cc_start: 0.9201 (pt0) cc_final: 0.8329 (pm20)
REVERT: B   49 SER cc_start: 0.9472 (t) cc_final: 0.9191 (p)
REVERT: B  259 TYR cc_start: 0.8209 (m-80) cc_final: 0.7996 (m-10)
  outliers start: 11
  outliers final: 9
  residues processed: 58
  average time/residue: 0.0912
  time to fit residues: 6.9285
Evaluate side-chains
  53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  347 HIS
Chi-restraints excluded: chain A residue  376 ASN
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain C residue   29 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 72 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.0988

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS
B 209 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.085480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.058868 restraints weight = 15458.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.061261 restraints weight = 8803.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.062838 restraints weight = 6195.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.063864 restraints weight = 4981.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.064564 restraints weight = 4342.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6402  Z= 0.132
  Angle     :  0.647   9.361   8702  Z= 0.325
  Chirality :  0.042   0.156    975
  Planarity :  0.005   0.049   1137
  Dihedral  :  8.357 179.488   1017
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.27 %
    Favored  : 88.61 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.20 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.49 (0.25), residues: 790
  helix: -1.10 (0.58), residues: 69
  sheet: -3.13 (0.60), residues: 52
  loop : -3.55 (0.20), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG C  55 
 TYR   0.008   0.001   TYR B 183 
 PHE   0.010   0.001   PHE A 416 
 TRP   0.006   0.001   TRP A 173 
 HIS   0.005   0.001   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6377)
  covalent geometry    : angle       0.63985 ( 8645)
  SS BOND              : bond        0.00232 (   18)
  SS BOND              : angle       0.83022 (   36)
  hydrogen bonds       : bond        0.03450 (   50)
  hydrogen bonds       : angle       5.96514 (  132)
  link_BETA1-4         : bond        0.00281 (    2)
  link_BETA1-4         : angle       1.87590 (    6)
  link_NAG-ASN         : bond        0.00153 (    5)
  link_NAG-ASN         : angle       1.93523 (   15)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 TYR cc_start: 0.7723 (t80) cc_final: 0.7442 (t80)
REVERT: A  208 TYR cc_start: 0.8336 (t80) cc_final: 0.8115 (t80)
REVERT: A  545 LYS cc_start: 0.9159 (tttp) cc_final: 0.8876 (tptp)
REVERT: B   37 GLU cc_start: 0.9165 (pt0) cc_final: 0.8278 (pm20)
REVERT: B   49 SER cc_start: 0.9504 (t) cc_final: 0.9210 (p)
REVERT: B  259 TYR cc_start: 0.8214 (m-80) cc_final: 0.7960 (m-10)
REVERT: C   40 GLN cc_start: 0.7283 (pm20) cc_final: 0.6989 (pm20)
REVERT: C   46 GLU cc_start: 0.9025 (tt0) cc_final: 0.8755 (tt0)
  outliers start: 14
  outliers final: 6
  residues processed: 61
  average time/residue: 0.0996
  time to fit residues: 7.7905
Evaluate side-chains
  51 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain A residue  601 HIS
Chi-restraints excluded: chain B residue  250 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 10 optimal weight:    0.1980
   chunk 7 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0770
   chunk 75 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.9942

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

Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS
B 196 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.086127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.058955 restraints weight = 15719.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.061346 restraints weight = 8779.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.062995 restraints weight = 6195.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.064141 restraints weight = 4972.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.064847 restraints weight = 4292.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6402  Z= 0.127
  Angle     :  0.638   8.516   8702  Z= 0.321
  Chirality :  0.042   0.166    975
  Planarity :  0.004   0.049   1137
  Dihedral  :  8.128 179.225   1017
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 12.41 %
    Favored  : 87.47 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.56 %
    Favored  : 82.33 %
  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: -4.31 (0.25), residues: 790
  helix: -0.80 (0.59), residues: 69
  sheet: -3.45 (0.51), residues: 70
  loop : -3.37 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  66 
 TYR   0.011   0.001   TYR A  49 
 PHE   0.009   0.001   PHE A 416 
 TRP   0.006   0.001   TRP A 173 
 HIS   0.010   0.001   HIS A 601 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6377)
  covalent geometry    : angle       0.63131 ( 8645)
  SS BOND              : bond        0.00227 (   18)
  SS BOND              : angle       0.91985 (   36)
  hydrogen bonds       : bond        0.03354 (   50)
  hydrogen bonds       : angle       5.77019 (  132)
  link_BETA1-4         : bond        0.00349 (    2)
  link_BETA1-4         : angle       1.57818 (    6)
  link_NAG-ASN         : bond        0.00161 (    5)
  link_NAG-ASN         : angle       1.75028 (   15)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 TYR cc_start: 0.7689 (t80) cc_final: 0.7375 (t80)
REVERT: A  208 TYR cc_start: 0.8336 (t80) cc_final: 0.8054 (t80)
REVERT: A  545 LYS cc_start: 0.9156 (tttp) cc_final: 0.8865 (tptp)
REVERT: B   37 GLU cc_start: 0.9140 (pt0) cc_final: 0.8286 (pm20)
REVERT: B   49 SER cc_start: 0.9510 (t) cc_final: 0.9207 (p)
REVERT: B   59 GLU cc_start: 0.8629 (mp0) cc_final: 0.8426 (mp0)
REVERT: B  259 TYR cc_start: 0.8193 (m-80) cc_final: 0.7972 (m-10)
  outliers start: 14
  outliers final: 10
  residues processed: 60
  average time/residue: 0.0879
  time to fit residues: 6.9901
Evaluate side-chains
  55 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  516 ASN
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   33 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0980
   chunk 66 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0030
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.7792

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.086376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.059319 restraints weight = 15319.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.061712 restraints weight = 8646.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.063321 restraints weight = 6090.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.064357 restraints weight = 4867.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.064907 restraints weight = 4236.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6402  Z= 0.115
  Angle     :  0.627   9.428   8702  Z= 0.313
  Chirality :  0.041   0.152    975
  Planarity :  0.004   0.048   1137
  Dihedral  :  8.033 179.648   1017
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.89 %
    Favored  : 88.99 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.56 %
    Favored  : 82.02 %
  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: -4.15 (0.26), residues: 790
  helix: -0.56 (0.62), residues: 69
  sheet: -3.38 (0.51), residues: 70
  loop : -3.26 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  55 
 TYR   0.008   0.001   TYR A  49 
 PHE   0.008   0.001   PHE A 416 
 TRP   0.008   0.001   TRP A 173 
 HIS   0.006   0.001   HIS A 601 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6377)
  covalent geometry    : angle       0.62148 ( 8645)
  SS BOND              : bond        0.00187 (   18)
  SS BOND              : angle       0.74356 (   36)
  hydrogen bonds       : bond        0.03067 (   50)
  hydrogen bonds       : angle       5.67443 (  132)
  link_BETA1-4         : bond        0.00327 (    2)
  link_BETA1-4         : angle       1.40378 (    6)
  link_NAG-ASN         : bond        0.00369 (    5)
  link_NAG-ASN         : angle       1.88274 (   15)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 46
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 TYR cc_start: 0.7711 (t80) cc_final: 0.7334 (t80)
REVERT: A  208 TYR cc_start: 0.8340 (t80) cc_final: 0.8067 (t80)
REVERT: A  545 LYS cc_start: 0.9149 (tttp) cc_final: 0.8858 (tptp)
REVERT: B   37 GLU cc_start: 0.9112 (pt0) cc_final: 0.8263 (pm20)
REVERT: B   49 SER cc_start: 0.9508 (t) cc_final: 0.9186 (p)
REVERT: B  259 TYR cc_start: 0.8210 (m-80) cc_final: 0.7977 (m-10)
REVERT: C   36 ARG cc_start: 0.8262 (tpp-160) cc_final: 0.7786 (tpp80)
  outliers start: 16
  outliers final: 9
  residues processed: 59
  average time/residue: 0.0903
  time to fit residues: 7.1397
Evaluate side-chains
  54 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   41 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 61 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0040
   chunk 16 optimal weight:    0.0050
   chunk 41 optimal weight:    3.9990
   chunk 27 optimal weight:    0.4980
   chunk 77 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.1010

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS
B 196 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.085822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.058679 restraints weight = 15439.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.061006 restraints weight = 8789.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.062631 restraints weight = 6224.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.063674 restraints weight = 4982.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.064361 restraints weight = 4325.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6402  Z= 0.133
  Angle     :  0.632   9.413   8702  Z= 0.317
  Chirality :  0.042   0.149    975
  Planarity :  0.004   0.049   1137
  Dihedral  :  7.931 179.242   1017
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 12.66 %
    Favored  : 87.22 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.37 %
    Favored  : 80.97 %
  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: -4.08 (0.26), residues: 790
  helix: -0.34 (0.67), residues: 63
  sheet: -3.45 (0.56), residues: 60
  loop : -3.21 (0.21), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  37 
 TYR   0.007   0.001   TYR A  49 
 PHE   0.010   0.001   PHE A 416 
 TRP   0.011   0.001   TRP A 173 
 HIS   0.007   0.001   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6377)
  covalent geometry    : angle       0.62825 ( 8645)
  SS BOND              : bond        0.00197 (   18)
  SS BOND              : angle       0.71893 (   36)
  hydrogen bonds       : bond        0.03091 (   50)
  hydrogen bonds       : angle       5.52415 (  132)
  link_BETA1-4         : bond        0.00253 (    2)
  link_BETA1-4         : angle       1.37919 (    6)
  link_NAG-ASN         : bond        0.00167 (    5)
  link_NAG-ASN         : angle       1.60710 (   15)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 TYR cc_start: 0.8359 (t80) cc_final: 0.8069 (t80)
REVERT: B   37 GLU cc_start: 0.9073 (pt0) cc_final: 0.8243 (pm20)
REVERT: B   49 SER cc_start: 0.9509 (t) cc_final: 0.9184 (p)
REVERT: B  259 TYR cc_start: 0.8181 (m-80) cc_final: 0.7966 (m-10)
REVERT: C   36 ARG cc_start: 0.8251 (tpp-160) cc_final: 0.7738 (tpp80)
  outliers start: 11
  outliers final: 10
  residues processed: 50
  average time/residue: 0.0895
  time to fit residues: 5.8759
Evaluate side-chains
  53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain A residue  601 HIS
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   33 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 47 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.084872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.057865 restraints weight = 15627.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.060162 restraints weight = 8881.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.061757 restraints weight = 6310.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.062750 restraints weight = 5057.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.063368 restraints weight = 4409.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.3208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6402  Z= 0.171
  Angle     :  0.662   9.209   8702  Z= 0.331
  Chirality :  0.043   0.148    975
  Planarity :  0.005   0.049   1137
  Dihedral  :  7.996 179.567   1017
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 13.04 %
    Favored  : 86.84 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 17.22 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.06 (0.26), residues: 790
  helix: -0.29 (0.66), residues: 63
  sheet: -3.32 (0.51), residues: 70
  loop : -3.19 (0.21), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  55 
 TYR   0.008   0.001   TYR C  24 
 PHE   0.010   0.001   PHE A 416 
 TRP   0.009   0.001   TRP A 173 
 HIS   0.010   0.001   HIS A 601 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 6377)
  covalent geometry    : angle       0.65772 ( 8645)
  SS BOND              : bond        0.00237 (   18)
  SS BOND              : angle       0.79751 (   36)
  hydrogen bonds       : bond        0.03377 (   50)
  hydrogen bonds       : angle       5.56703 (  132)
  link_BETA1-4         : bond        0.00130 (    2)
  link_BETA1-4         : angle       1.35585 (    6)
  link_NAG-ASN         : bond        0.00165 (    5)
  link_NAG-ASN         : angle       1.61400 (   15)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 TYR cc_start: 0.7701 (t80) cc_final: 0.7356 (t80)
REVERT: A  208 TYR cc_start: 0.8394 (t80) cc_final: 0.8119 (t80)
REVERT: A  578 TYR cc_start: 0.8988 (m-80) cc_final: 0.8391 (m-10)
REVERT: B   37 GLU cc_start: 0.9062 (pt0) cc_final: 0.8212 (pm20)
REVERT: B   49 SER cc_start: 0.9516 (t) cc_final: 0.9188 (p)
REVERT: B  259 TYR cc_start: 0.8181 (m-80) cc_final: 0.7974 (m-10)
  outliers start: 14
  outliers final: 10
  residues processed: 56
  average time/residue: 0.0879
  time to fit residues: 6.4432
Evaluate side-chains
  53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   33 SER
Chi-restraints excluded: chain C residue   41 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 57 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 67 optimal weight:    0.4980
   chunk 24 optimal weight:    0.0870
   chunk 27 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.8562

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

Flipped N/Q/H residues before XYZ refinement:
** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS
** B  68 GLN ** 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 = 0.3358 r_free = 0.3358 target = 0.086045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.059155 restraints weight = 15584.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.061533 restraints weight = 8795.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.063132 restraints weight = 6190.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.064195 restraints weight = 4943.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.064925 restraints weight = 4274.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.3334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6402  Z= 0.119
  Angle     :  0.642   9.460   8702  Z= 0.320
  Chirality :  0.041   0.152    975
  Planarity :  0.004   0.048   1137
  Dihedral  :  7.871 179.570   1017
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.89 %
    Favored  : 88.99 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 18.13 %
    Favored  : 80.36 %
  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: -3.85 (0.26), residues: 790
  helix: -0.07 (0.67), residues: 63
  sheet: -3.44 (0.54), residues: 60
  loop : -3.04 (0.21), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  66 
 TYR   0.006   0.001   TYR B 183 
 PHE   0.008   0.001   PHE A 416 
 TRP   0.005   0.001   TRP B 236 
 HIS   0.002   0.000   HIS A 601 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6377)
  covalent geometry    : angle       0.63912 ( 8645)
  SS BOND              : bond        0.00167 (   18)
  SS BOND              : angle       0.65891 (   36)
  hydrogen bonds       : bond        0.02914 (   50)
  hydrogen bonds       : angle       5.33839 (  132)
  link_BETA1-4         : bond        0.00190 (    2)
  link_BETA1-4         : angle       1.25861 (    6)
  link_NAG-ASN         : bond        0.00136 (    5)
  link_NAG-ASN         : angle       1.47801 (   15)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 TYR cc_start: 0.8362 (t80) cc_final: 0.8095 (t80)
REVERT: A  578 TYR cc_start: 0.8980 (m-80) cc_final: 0.8376 (m-10)
REVERT: B   37 GLU cc_start: 0.9036 (pt0) cc_final: 0.8200 (pm20)
REVERT: B   49 SER cc_start: 0.9510 (t) cc_final: 0.9175 (p)
REVERT: B   68 GLN cc_start: 0.8606 (mm-40) cc_final: 0.7837 (mp10)
REVERT: B  259 TYR cc_start: 0.8175 (m-80) cc_final: 0.7952 (m-10)
  outliers start: 10
  outliers final: 8
  residues processed: 51
  average time/residue: 0.0800
  time to fit residues: 5.5164
Evaluate side-chains
  52 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   41 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 67 optimal weight:    0.5980
   chunk 10 optimal weight:    0.2980
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS
** B  68 GLN ** 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 = 0.3348 r_free = 0.3348 target = 0.085389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.058528 restraints weight = 15462.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.060837 restraints weight = 8809.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.062441 restraints weight = 6247.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.063504 restraints weight = 5000.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.064176 restraints weight = 4336.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6402  Z= 0.141
  Angle     :  0.659   9.439   8702  Z= 0.329
  Chirality :  0.042   0.149    975
  Planarity :  0.004   0.049   1137
  Dihedral  :  7.877 179.698   1017
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 13.16 %
    Favored  : 86.71 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 18.13 %
    Favored  : 80.51 %
  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: -3.80 (0.27), residues: 790
  helix:  0.13 (0.66), residues: 63
  sheet: -3.40 (0.55), residues: 60
  loop : -3.02 (0.21), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  66 
 TYR   0.007   0.001   TYR C  24 
 PHE   0.010   0.001   PHE A 416 
 TRP   0.004   0.001   TRP B 236 
 HIS   0.002   0.001   HIS A 601 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6377)
  covalent geometry    : angle       0.65599 ( 8645)
  SS BOND              : bond        0.00196 (   18)
  SS BOND              : angle       0.71325 (   36)
  hydrogen bonds       : bond        0.03174 (   50)
  hydrogen bonds       : angle       5.52715 (  132)
  link_BETA1-4         : bond        0.00272 (    2)
  link_BETA1-4         : angle       1.31845 (    6)
  link_NAG-ASN         : bond        0.00143 (    5)
  link_NAG-ASN         : angle       1.52822 (   15)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 TYR cc_start: 0.8381 (t80) cc_final: 0.8113 (t80)
REVERT: A  578 TYR cc_start: 0.8990 (m-80) cc_final: 0.8355 (m-10)
REVERT: B   37 GLU cc_start: 0.9018 (pt0) cc_final: 0.8210 (pm20)
REVERT: B   49 SER cc_start: 0.9520 (t) cc_final: 0.9186 (p)
REVERT: B   68 GLN cc_start: 0.8503 (mm-40) cc_final: 0.7707 (mp10)
REVERT: B  259 TYR cc_start: 0.8159 (m-80) cc_final: 0.7949 (m-10)
  outliers start: 9
  outliers final: 7
  residues processed: 50
  average time/residue: 0.0816
  time to fit residues: 5.5706
Evaluate side-chains
  50 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   29 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 10 optimal weight:    0.1980
   chunk 36 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 43 optimal weight:    0.2980
   chunk 0 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS
** B  68 GLN ** 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 = 0.3354 r_free = 0.3354 target = 0.085573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.058622 restraints weight = 15545.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.060939 restraints weight = 8833.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.062547 restraints weight = 6245.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.063579 restraints weight = 4999.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.064187 restraints weight = 4341.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6402  Z= 0.134
  Angle     :  0.655   9.413   8702  Z= 0.327
  Chirality :  0.041   0.150    975
  Planarity :  0.004   0.048   1137
  Dihedral  :  7.844 179.769   1017
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.52 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.82 %
    Favored  : 80.51 %
  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: -3.72 (0.27), residues: 790
  helix:  0.35 (0.69), residues: 63
  sheet: -3.41 (0.54), residues: 60
  loop : -2.97 (0.22), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  55 
 TYR   0.006   0.001   TYR C  24 
 PHE   0.009   0.001   PHE A 416 
 TRP   0.005   0.001   TRP B 236 
 HIS   0.002   0.000   HIS A 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6377)
  covalent geometry    : angle       0.65194 ( 8645)
  SS BOND              : bond        0.00181 (   18)
  SS BOND              : angle       0.69535 (   36)
  hydrogen bonds       : bond        0.03062 (   50)
  hydrogen bonds       : angle       5.33922 (  132)
  link_BETA1-4         : bond        0.00275 (    2)
  link_BETA1-4         : angle       1.28023 (    6)
  link_NAG-ASN         : bond        0.00139 (    5)
  link_NAG-ASN         : angle       1.45607 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1073.70 seconds
wall clock time: 19 minutes 2.14 seconds (1142.14 seconds total)