Starting phenix.real_space_refine
on Sun Apr 27 00:12:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bj2_44627/04_2025/9bj2_44627.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bj2_44627/04_2025/9bj2_44627.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bj2_44627/04_2025/9bj2_44627.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bj2_44627/04_2025/9bj2_44627.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bj2_44627/04_2025/9bj2_44627.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bj2_44627/04_2025/9bj2_44627.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.044
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      13      5.16       5
     C    2498      2.51       5
     N     651      2.21       5
     O     758      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3920
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2107
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 13, 'TRANS': 250}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "H"
      Number of atoms: 991
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 991
          Classifications: {'peptide': 129}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 124}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "L"
      Number of atoms: 780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 780
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 7, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          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
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   SER H 131 " occ=0.58
      ... (4 atoms not shown)
      pdb=" OG  SER H 131 " occ=0.58
  Time building chain proxies: 3.91, per 1000 atoms: 1.00
  Number of scatterers: 3920
  At special positions: 0
  Unit cell: (76.689, 83.5058, 105.66, 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      13     16.00
     O     758      8.00
     N     651      7.00
     C    2498      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 165 "
      " NAG A1302 " - " ASN A 234 "
      " NAG A1303 " - " ASN A 122 "
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 444.8 milliseconds
  

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  918

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 11 sheets defined
      7.0% alpha, 45.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 254 through 256
      No H-bonds generated for 'chain 'A' and resid 254 through 256'
    Processing helix  chain 'A' and resid 294 through 303
    Processing helix  chain 'H' and resid 25 through 31
      removed outlier: 3.528A  pdb=" N   PHE H  29 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 65
      removed outlier: 4.009A  pdb=" N   GLN H  65 " --> pdb=" O   GLN H  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 65'
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'H' and resid 102 through 109
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30
    Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 30
      removed outlier: 8.216A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ALA A 263 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55
      removed outlier: 4.051A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.579A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ALA A 243 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   ARG A 102 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 11.376A  pdb=" N   VAL A 126 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
      removed outlier: 10.049A  pdb=" N   GLU A 169 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 11.067A  pdb=" N   ILE A 128 " --> pdb=" O   THR A 167 " (cutoff:3.500A)
      removed outlier: 8.902A  pdb=" N   THR A 167 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 8.153A  pdb=" N   VAL A 130 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   ASN A 165 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   GLU A 132 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ALA A 163 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   GLN A 134 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 154
      removed outlier: 6.525A  pdb=" N   TYR A 145 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.759A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 128 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ARG H  50 " --> pdb=" O   ASN H  59 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.759A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 128 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   VAL H 120 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.764A  pdb=" N   GLY L  13 " --> pdb=" O   THR L 105 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 19 through 24
    Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 48
      removed outlier: 6.574A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    147 hydrogen bonds defined for protein.
    372 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.12

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1241
        1.34 -     1.46: 1002
        1.46 -     1.58: 1760
        1.58 -     1.70: 0
        1.70 -     1.81: 16
  Bond restraints: 4019
  Sorted by residual:
  bond pdb=" C   SER A 172 "
       pdb=" N   GLN A 173 "
    ideal  model  delta    sigma   weight residual
    1.331  1.367 -0.036 2.83e-02 1.25e+03 1.61e+00
  bond pdb=" N   ASN A  99 "
       pdb=" CA  ASN A  99 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.45e+00
  bond pdb=" CB  ASN A  99 "
       pdb=" CG  ASN A  99 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.54e-01
  bond pdb=" C   ILE H  52 "
       pdb=" O   ILE H  52 "
    ideal  model  delta    sigma   weight residual
    1.232  1.240 -0.008 1.01e-02 9.80e+03 6.60e-01
  bond pdb=" CB  CYS A 166 "
       pdb=" SG  CYS A 166 "
    ideal  model  delta    sigma   weight residual
    1.808  1.783  0.025 3.30e-02 9.18e+02 5.67e-01
  ... (remaining 4014 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.84: 5047
        0.84 -     1.68: 332
        1.68 -     2.51: 56
        2.51 -     3.35: 28
        3.35 -     4.19: 10
  Bond angle restraints: 5473
  Sorted by residual:
  angle pdb=" N   CYS A 131 "
        pdb=" CA  CYS A 131 "
        pdb=" C   CYS A 131 "
      ideal   model   delta    sigma   weight residual
     108.60  104.41    4.19 1.46e+00 4.69e-01 8.24e+00
  angle pdb=" N   TRP H 113 "
        pdb=" CA  TRP H 113 "
        pdb=" CB  TRP H 113 "
      ideal   model   delta    sigma   weight residual
     111.20  107.08    4.12 1.65e+00 3.67e-01 6.25e+00
  angle pdb=" N   ASN L  50 "
        pdb=" CA  ASN L  50 "
        pdb=" C   ASN L  50 "
      ideal   model   delta    sigma   weight residual
     112.24  109.47    2.77 1.28e+00 6.10e-01 4.70e+00
  angle pdb=" C   ILE A 233 "
        pdb=" N   ASN A 234 "
        pdb=" CA  ASN A 234 "
      ideal   model   delta    sigma   weight residual
     121.50  124.56   -3.06 1.43e+00 4.89e-01 4.59e+00
  angle pdb=" C   ASN A 148 "
        pdb=" CA  ASN A 148 "
        pdb=" CB  ASN A 148 "
      ideal   model   delta    sigma   weight residual
     109.53  113.12   -3.59 1.69e+00 3.50e-01 4.51e+00
  ... (remaining 5468 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 2077
       17.46 -    34.92: 218
       34.92 -    52.39: 63
       52.39 -    69.85: 11
       69.85 -    87.31: 4
  Dihedral angle restraints: 2373
    sinusoidal: 937
      harmonic: 1436
  Sorted by residual:
  dihedral pdb=" CB  CYS A 131 "
           pdb=" SG  CYS A 131 "
           pdb=" SG  CYS A 166 "
           pdb=" CB  CYS A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -129.75   43.75     1      1.00e+01 1.00e-02 2.66e+01
  dihedral pdb=" CA  ASN A 165 "
           pdb=" C   ASN A 165 "
           pdb=" N   CYS A 166 "
           pdb=" CA  CYS A 166 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.16  -18.84     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  VAL A 130 "
           pdb=" C   VAL A 130 "
           pdb=" N   CYS A 131 "
           pdb=" CA  CYS A 131 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.46  -18.54     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 2370 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 499
       0.054 -    0.107: 85
       0.107 -    0.161: 28
       0.161 -    0.214: 0
       0.214 -    0.268: 1
  Chirality restraints: 613
  Sorted by residual:
  chirality pdb=" C1  NAG A1301 "
            pdb=" ND2 ASN A 165 "
            pdb=" C2  NAG A1301 "
            pdb=" O5  NAG A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.13   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  ILE A 105 "
            pdb=" N   ILE A 105 "
            pdb=" C   ILE A 105 "
            pdb=" CB  ILE A 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.86e-01
  chirality pdb=" CA  ASN A  99 "
            pdb=" N   ASN A  99 "
            pdb=" C   ASN A  99 "
            pdb=" CB  ASN A  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.98e-01
  ... (remaining 610 not shown)

  Planarity restraints: 702
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 234 "   -0.025 2.00e-02 2.50e+03   2.27e-02 6.44e+00
        pdb=" CG  ASN A 234 "    0.027 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 234 "   -0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 234 "    0.025 2.00e-02 2.50e+03
        pdb=" C1  NAG A1302 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 294 "    0.027 5.00e-02 4.00e+02   4.06e-02 2.64e+00
        pdb=" N   PRO A 295 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 295 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 295 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN L  50 "    0.007 2.00e-02 2.50e+03   1.32e-02 1.75e+00
        pdb=" C   ASN L  50 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   ASN L  50 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLN L  51 "    0.008 2.00e-02 2.50e+03
  ... (remaining 699 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 326
        2.75 -     3.29: 3305
        3.29 -     3.82: 6087
        3.82 -     4.36: 7425
        4.36 -     4.90: 13596
  Nonbonded interactions: 30739
  Sorted by model distance:
  nonbonded pdb=" O   GLY H 115 "
            pdb=" OH  TYR L  36 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   SER A  98 "
            pdb=" OG  SER A  98 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OE1 GLN L   7 "
            pdb=" OG1 THR L 102 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   THR A  95 "
            pdb=" OG1 THR A  95 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" OH  TYR A 144 "
            pdb=" OD2 ASP H 102 "
     model   vdw
     2.345 3.040
  ... (remaining 30734 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.58 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.300
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     14.890
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:13.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
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      :  0.002   0.036   4027  Z= 0.108
  Angle     :  0.541   8.214   5492  Z= 0.290
  Chirality :  0.047   0.268    613
  Planarity :  0.004   0.041    699
  Dihedral  : 15.672  87.309   1440
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 19.86 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.38), residues: 487
  helix:  0.76 (0.94), residues: 23
  sheet:  1.07 (0.38), residues: 198
  loop : -0.64 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP H 107 
 HIS   0.003   0.001   HIS A  66 
 PHE   0.011   0.001   PHE A 133 
 TYR   0.009   0.001   TYR A 170 
 ARG   0.001   0.000   ARG A  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00481 (    3)
  link_NAG-ASN         : angle       4.39365 (    9)
  hydrogen bonds       : bond        0.13610 (  141)
  hydrogen bonds       : angle       6.05291 (  372)
  SS BOND              : bond        0.00282 (    5)
  SS BOND              : angle       1.38677 (   10)
  covalent geometry    : bond        0.00223 ( 4019)
  covalent geometry    : angle       0.50884 ( 5473)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.418 
Fit side-chains
REVERT: H   32 ASN cc_start: 0.8940 (m110) cc_final: 0.8548 (m-40)
  outliers start: 11
  outliers final: 10
  residues processed: 50
  average time/residue: 0.9024
  time to fit residues: 47.4723
Evaluate side-chains
  45 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 35
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain L residue   19 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    0.0050
   chunk 36 optimal weight:    0.1980
   chunk 20 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0970
   chunk 22 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.3792

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS
H   6 GLN
L   7 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.161492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.126763 restraints weight = 4175.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 1.83
r_work: 0.3217 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3083
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.0627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4027  Z= 0.104
  Angle     :  0.519   5.627   5492  Z= 0.276
  Chirality :  0.046   0.224    613
  Planarity :  0.004   0.041    699
  Dihedral  :  6.526  59.335    617
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 18.44 %
    Favored  : 78.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.38), residues: 487
  helix:  1.37 (0.95), residues: 23
  sheet:  1.09 (0.38), residues: 200
  loop : -0.72 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 107 
 HIS   0.003   0.001   HIS A  66 
 PHE   0.012   0.001   PHE A 175 
 TYR   0.010   0.001   TYR A 279 
 ARG   0.001   0.000   ARG A 246 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00377 (    3)
  link_NAG-ASN         : angle       2.89285 (    9)
  hydrogen bonds       : bond        0.03335 (  141)
  hydrogen bonds       : angle       5.08272 (  372)
  SS BOND              : bond        0.00373 (    5)
  SS BOND              : angle       1.08384 (   10)
  covalent geometry    : bond        0.00232 ( 4019)
  covalent geometry    : angle       0.50403 ( 5473)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.444 
Fit side-chains
REVERT: H   32 ASN cc_start: 0.8973 (m110) cc_final: 0.8490 (m-40)
REVERT: H   38 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7795 (ttm170)
REVERT: H   82 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7990 (tp30)
REVERT: L   96 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7972 (mp)
  outliers start: 15
  outliers final: 6
  residues processed: 49
  average time/residue: 0.9714
  time to fit residues: 50.0154
Evaluate side-chains
  43 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  228 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   63 GLU
Chi-restraints excluded: chain H residue   82 GLU
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0670
   chunk 38 optimal weight:    9.9990
   chunk 10 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.159275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.123807 restraints weight = 4163.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 1.80
r_work: 0.3192 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.0772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4027  Z= 0.142
  Angle     :  0.570   6.853   5492  Z= 0.303
  Chirality :  0.047   0.245    613
  Planarity :  0.004   0.041    699
  Dihedral  :  5.260  31.969    601
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 17.73 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.38), residues: 487
  helix:  1.48 (0.94), residues: 23
  sheet:  1.19 (0.35), residues: 228
  loop : -0.79 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 113 
 HIS   0.004   0.001   HIS A  66 
 PHE   0.018   0.002   PHE A 175 
 TYR   0.012   0.001   TYR A 279 
 ARG   0.001   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00406 (    3)
  link_NAG-ASN         : angle       2.59881 (    9)
  hydrogen bonds       : bond        0.03754 (  141)
  hydrogen bonds       : angle       5.04502 (  372)
  SS BOND              : bond        0.00567 (    5)
  SS BOND              : angle       2.30707 (   10)
  covalent geometry    : bond        0.00337 ( 4019)
  covalent geometry    : angle       0.55240 ( 5473)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 41
  time to evaluate  : 0.404 
Fit side-chains
REVERT: H   32 ASN cc_start: 0.9100 (m110) cc_final: 0.8608 (m-40)
REVERT: H   38 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7739 (ttm170)
REVERT: H   51 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7734 (tp)
REVERT: H   82 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7974 (tp30)
REVERT: L   96 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8024 (mp)
  outliers start: 20
  outliers final: 12
  residues processed: 57
  average time/residue: 0.8561
  time to fit residues: 51.1931
Evaluate side-chains
  52 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 36
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  228 ASP
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue   63 GLU
Chi-restraints excluded: chain H residue   82 GLU
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    0.3980
   chunk 44 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 1 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.159753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.126068 restraints weight = 4194.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.15
r_work: 0.3201 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3053
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3053 r_free = 0.3053    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3053 r_free = 0.3053    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3053
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.0894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4027  Z= 0.129
  Angle     :  0.544   5.394   5492  Z= 0.289
  Chirality :  0.047   0.260    613
  Planarity :  0.004   0.041    699
  Dihedral  :  5.077  32.577    601
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 17.73 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.37), residues: 487
  helix:  1.56 (0.94), residues: 23
  sheet:  1.09 (0.37), residues: 199
  loop : -0.77 (0.36), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 107 
 HIS   0.003   0.001   HIS A  66 
 PHE   0.015   0.002   PHE A 175 
 TYR   0.012   0.001   TYR A 279 
 ARG   0.001   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00709 (    3)
  link_NAG-ASN         : angle       2.67936 (    9)
  hydrogen bonds       : bond        0.03434 (  141)
  hydrogen bonds       : angle       4.96720 (  372)
  SS BOND              : bond        0.00577 (    5)
  SS BOND              : angle       1.30292 (   10)
  covalent geometry    : bond        0.00304 ( 4019)
  covalent geometry    : angle       0.53136 ( 5473)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 38
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A  129 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8414 (ttmm)
REVERT: A  154 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8231 (mt-10)
REVERT: H   32 ASN cc_start: 0.9103 (m110) cc_final: 0.8596 (m-40)
REVERT: H   38 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7706 (ttm170)
REVERT: H   51 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7701 (tp)
REVERT: H   82 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7953 (tp30)
REVERT: L   96 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7979 (mp)
  outliers start: 24
  outliers final: 13
  residues processed: 56
  average time/residue: 0.8357
  time to fit residues: 49.3434
Evaluate side-chains
  55 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 36
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  228 ASP
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue   82 GLU
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.160038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.125480 restraints weight = 4287.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.01
r_work: 0.3173 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3025
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3025
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.0972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   4027  Z= 0.155
  Angle     :  0.589   8.853   5492  Z= 0.314
  Chirality :  0.047   0.165    613
  Planarity :  0.004   0.040    699
  Dihedral  :  5.253  33.425    601
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 17.26 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.37), residues: 487
  helix:  1.48 (0.93), residues: 23
  sheet:  1.00 (0.37), residues: 200
  loop : -0.80 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H 107 
 HIS   0.004   0.001   HIS A  66 
 PHE   0.020   0.002   PHE A 175 
 TYR   0.013   0.002   TYR A 279 
 ARG   0.002   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00204 (    3)
  link_NAG-ASN         : angle       2.24419 (    9)
  hydrogen bonds       : bond        0.03764 (  141)
  hydrogen bonds       : angle       5.01175 (  372)
  SS BOND              : bond        0.00570 (    5)
  SS BOND              : angle       2.87024 (   10)
  covalent geometry    : bond        0.00376 ( 4019)
  covalent geometry    : angle       0.57015 ( 5473)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 38
  time to evaluate  : 0.610 
Fit side-chains
REVERT: A  129 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8473 (ttmm)
REVERT: A  154 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8332 (mt-10)
REVERT: H   32 ASN cc_start: 0.9124 (m110) cc_final: 0.8628 (m-40)
REVERT: H   38 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7756 (ttm170)
REVERT: H   51 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7749 (tp)
REVERT: L   96 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8083 (mp)
  outliers start: 27
  outliers final: 15
  residues processed: 60
  average time/residue: 1.2181
  time to fit residues: 76.8650
Evaluate side-chains
  54 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 34
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue   63 GLU
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 33 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0010
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.161218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.125697 restraints weight = 4191.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 1.89
r_work: 0.3209 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.0990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4027  Z= 0.124
  Angle     :  0.538   6.499   5492  Z= 0.287
  Chirality :  0.046   0.161    613
  Planarity :  0.004   0.040    699
  Dihedral  :  4.967  29.901    601
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 18.44 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.37), residues: 487
  helix:  1.60 (0.93), residues: 23
  sheet:  1.05 (0.37), residues: 199
  loop : -0.78 (0.36), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H 107 
 HIS   0.003   0.001   HIS A  66 
 PHE   0.015   0.002   PHE A 175 
 TYR   0.011   0.001   TYR A 279 
 ARG   0.001   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00319 (    3)
  link_NAG-ASN         : angle       2.28760 (    9)
  hydrogen bonds       : bond        0.03381 (  141)
  hydrogen bonds       : angle       4.95236 (  372)
  SS BOND              : bond        0.00443 (    5)
  SS BOND              : angle       2.12356 (   10)
  covalent geometry    : bond        0.00296 ( 4019)
  covalent geometry    : angle       0.52357 ( 5473)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 38
  time to evaluate  : 0.833 
Fit side-chains
REVERT: A  154 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8267 (mt-10)
REVERT: H   32 ASN cc_start: 0.9116 (m110) cc_final: 0.8617 (m-40)
REVERT: H   38 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7722 (ttm170)
REVERT: H   51 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7749 (tp)
REVERT: L   96 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8019 (mp)
  outliers start: 23
  outliers final: 16
  residues processed: 57
  average time/residue: 0.9848
  time to fit residues: 59.5323
Evaluate side-chains
  57 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 37
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0980
   chunk 15 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.160682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.125396 restraints weight = 4220.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 1.88
r_work: 0.3179 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3023
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3023
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4027  Z= 0.131
  Angle     :  0.546   5.675   5492  Z= 0.291
  Chirality :  0.046   0.163    613
  Planarity :  0.004   0.040    699
  Dihedral  :  4.907  29.828    601
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 18.68 %
    Favored  : 75.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.38), residues: 487
  helix:  1.59 (0.92), residues: 23
  sheet:  1.15 (0.35), residues: 227
  loop : -0.78 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H 107 
 HIS   0.003   0.001   HIS A  66 
 PHE   0.017   0.002   PHE A 175 
 TYR   0.012   0.001   TYR A 279 
 ARG   0.001   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00275 (    3)
  link_NAG-ASN         : angle       2.27728 (    9)
  hydrogen bonds       : bond        0.03509 (  141)
  hydrogen bonds       : angle       4.95668 (  372)
  SS BOND              : bond        0.00468 (    5)
  SS BOND              : angle       1.75620 (   10)
  covalent geometry    : bond        0.00313 ( 4019)
  covalent geometry    : angle       0.53396 ( 5473)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 39
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A  129 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8448 (ttmm)
REVERT: A  154 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8265 (mt-10)
REVERT: A  249 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8402 (tp)
REVERT: H   32 ASN cc_start: 0.9123 (m110) cc_final: 0.8631 (m-40)
REVERT: H   38 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7725 (ttm170)
REVERT: H   51 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7778 (tp)
REVERT: L   96 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8028 (mp)
  outliers start: 26
  outliers final: 16
  residues processed: 60
  average time/residue: 0.7384
  time to fit residues: 46.7975
Evaluate side-chains
  59 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 37
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   28 ILE
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    0.0770
   chunk 4 optimal weight:    2.9990
   chunk 38 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.160970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.124902 restraints weight = 4166.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.93
r_work: 0.3180 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3100
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3100
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4027  Z= 0.128
  Angle     :  0.540   5.544   5492  Z= 0.288
  Chirality :  0.046   0.169    613
  Planarity :  0.004   0.040    699
  Dihedral  :  4.828  28.721    601
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 18.91 %
    Favored  : 75.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.37), residues: 487
  helix:  1.45 (0.92), residues: 23
  sheet:  1.03 (0.37), residues: 200
  loop : -0.79 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP H 107 
 HIS   0.003   0.001   HIS A  66 
 PHE   0.016   0.002   PHE A 175 
 TYR   0.012   0.001   TYR A 279 
 ARG   0.001   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00365 (    3)
  link_NAG-ASN         : angle       2.26558 (    9)
  hydrogen bonds       : bond        0.03422 (  141)
  hydrogen bonds       : angle       4.94466 (  372)
  SS BOND              : bond        0.00464 (    5)
  SS BOND              : angle       1.50113 (   10)
  covalent geometry    : bond        0.00304 ( 4019)
  covalent geometry    : angle       0.52925 ( 5473)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 40
  time to evaluate  : 1.066 
Fit side-chains
REVERT: A  129 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8442 (ttmm)
REVERT: A  132 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8006 (mt-10)
REVERT: A  154 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8246 (mt-10)
REVERT: A  249 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8377 (tp)
REVERT: H   32 ASN cc_start: 0.9120 (m110) cc_final: 0.8604 (m-40)
REVERT: H   38 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7708 (ttm170)
REVERT: H   51 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7754 (tp)
REVERT: L   96 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8032 (mp)
  outliers start: 25
  outliers final: 18
  residues processed: 60
  average time/residue: 1.1972
  time to fit residues: 75.1691
Evaluate side-chains
  61 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 37
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue   63 GLU
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   28 ILE
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 40 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 44 optimal weight:    0.1980
   chunk 11 optimal weight:    0.1980
   chunk 41 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0020
   overall best weight:    0.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.162941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.127892 restraints weight = 4198.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.79
r_work: 0.3225 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3101
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3101
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4027  Z= 0.096
  Angle     :  0.495   4.969   5492  Z= 0.265
  Chirality :  0.045   0.168    613
  Planarity :  0.004   0.041    699
  Dihedral  :  4.508  24.123    601
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 20.57 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.38), residues: 487
  helix:  1.49 (0.93), residues: 23
  sheet:  1.08 (0.37), residues: 200
  loop : -0.73 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP H 107 
 HIS   0.003   0.001   HIS A  66 
 PHE   0.013   0.001   PHE A 133 
 TYR   0.009   0.001   TYR A 279 
 ARG   0.001   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00318 (    3)
  link_NAG-ASN         : angle       2.27759 (    9)
  hydrogen bonds       : bond        0.02926 (  141)
  hydrogen bonds       : angle       4.82598 (  372)
  SS BOND              : bond        0.00338 (    5)
  SS BOND              : angle       1.25766 (   10)
  covalent geometry    : bond        0.00218 ( 4019)
  covalent geometry    : angle       0.48407 ( 5473)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 38
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8383 (ttmm)
REVERT: A  132 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7905 (mt-10)
REVERT: A  154 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8094 (mt-10)
REVERT: A  249 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8325 (tp)
REVERT: H   32 ASN cc_start: 0.9050 (m110) cc_final: 0.8511 (m-40)
REVERT: H   38 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7752 (ttm170)
REVERT: L   96 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7922 (mp)
  outliers start: 19
  outliers final: 11
  residues processed: 52
  average time/residue: 0.9357
  time to fit residues: 50.9298
Evaluate side-chains
  56 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 40
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0170
   chunk 0 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9990
   chunk 38 optimal weight:    8.9990
   overall best weight:    0.7420

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.160394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.125953 restraints weight = 4215.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.00
r_work: 0.3171 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.1119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4027  Z= 0.144
  Angle     :  0.560   5.608   5492  Z= 0.298
  Chirality :  0.047   0.167    613
  Planarity :  0.004   0.039    699
  Dihedral  :  4.681  26.025    600
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 21.04 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.38), residues: 487
  helix:  1.34 (0.93), residues: 23
  sheet:  1.16 (0.35), residues: 228
  loop : -0.78 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP H 107 
 HIS   0.003   0.001   HIS A  66 
 PHE   0.018   0.002   PHE A 175 
 TYR   0.013   0.001   TYR A 279 
 ARG   0.002   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00417 (    3)
  link_NAG-ASN         : angle       2.25132 (    9)
  hydrogen bonds       : bond        0.03628 (  141)
  hydrogen bonds       : angle       4.92822 (  372)
  SS BOND              : bond        0.00504 (    5)
  SS BOND              : angle       1.44444 (   10)
  covalent geometry    : bond        0.00348 ( 4019)
  covalent geometry    : angle       0.55023 ( 5473)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 41
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8448 (ttmm)
REVERT: A  132 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8148 (mt-10)
REVERT: A  154 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8247 (mt-10)
REVERT: A  249 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8323 (tp)
REVERT: H   32 ASN cc_start: 0.9124 (m110) cc_final: 0.8621 (m-40)
REVERT: H   38 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7737 (ttm170)
REVERT: L   96 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8074 (mp)
  outliers start: 17
  outliers final: 10
  residues processed: 53
  average time/residue: 1.0267
  time to fit residues: 57.2247
Evaluate side-chains
  53 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0470
   chunk 23 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.161381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.126220 restraints weight = 4152.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.79
r_work: 0.3222 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4027  Z= 0.121
  Angle     :  0.535   5.360   5492  Z= 0.286
  Chirality :  0.046   0.167    613
  Planarity :  0.004   0.040    699
  Dihedral  :  4.569  23.246    600
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 20.57 %
    Favored  : 75.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.38), residues: 487
  helix:  1.37 (0.93), residues: 23
  sheet:  1.03 (0.37), residues: 200
  loop : -0.79 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP H 107 
 HIS   0.003   0.001   HIS A  66 
 PHE   0.014   0.002   PHE A 175 
 TYR   0.011   0.001   TYR A 279 
 ARG   0.001   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00449 (    3)
  link_NAG-ASN         : angle       2.23621 (    9)
  hydrogen bonds       : bond        0.03287 (  141)
  hydrogen bonds       : angle       4.86080 (  372)
  SS BOND              : bond        0.00476 (    5)
  SS BOND              : angle       1.41700 (   10)
  covalent geometry    : bond        0.00286 ( 4019)
  covalent geometry    : angle       0.52463 ( 5473)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4163.25 seconds
wall clock time: 73 minutes 40.15 seconds (4420.15 seconds total)