Starting phenix.real_space_refine
on Sat May 10 02:10:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v2c_42905/05_2025/8v2c_42905.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v2c_42905/05_2025/8v2c_42905.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v2c_42905/05_2025/8v2c_42905.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v2c_42905/05_2025/8v2c_42905.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v2c_42905/05_2025/8v2c_42905.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v2c_42905/05_2025/8v2c_42905.cif"
  }
  resolution = 3.46
  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=   0.016
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      23      5.16       5
     C    2886      2.51       5
     N     767      2.21       5
     O     924      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4600
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1343
          Classifications: {'peptide': 169}
          Link IDs: {'PTRANS': 8, 'TRANS': 160}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1583
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 13, 'TRANS': 184}
    Chain: "C"
      Number of atoms: 1492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1492
          Classifications: {'peptide': 184}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 177}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.98, per 1000 atoms: 0.87
  Number of scatterers: 4600
  At special positions: 0
  Unit cell: (87.72, 102.34, 105.78, 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      23     16.00
     O     924      8.00
     N     767      7.00
     C    2886      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  28 " - pdb=" SG  CYS A 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  71 " - pdb=" SG  CYS A 177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 144 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 172 " - pdb=" SG  CYS B 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 178 " - pdb=" SG  CYS C 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 242 " - pdb=" SG  CYS C 252 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 275 " - pdb=" SG  CYS C 282 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
    NAG-ASN
      " NAG B 701 " - " ASN B 225 "
      " NAG B 702 " - " ASN B 157 "
      " NAG C 801 " - " ASN C 239 "
      " NAG D   1 " - " ASN B 131 "
      " NAG E   1 " - " ASN C 162 "
      " NAG F   1 " - " ASN C 271 "
      " NAG G   1 " - " ASN C 304 "
      " NAG H   1 " - " ASN C 323 "
  Time building additional restraints: 1.26
  Conformation dependent library (CDL) restraints added in 509.7 milliseconds
  

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1048

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 9 sheets defined
      26.5% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 47
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 64 through 74
    Processing helix  chain 'A' and resid 80 through 87
    Processing helix  chain 'A' and resid 88 through 115
      removed outlier: 3.517A  pdb=" N   LEU A 115 " --> pdb=" O   ARG A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 144
      removed outlier: 4.475A  pdb=" N   ASP A 124 " --> pdb=" O   PHE A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 201
    Processing helix  chain 'B' and resid 213 through 216
    Processing helix  chain 'B' and resid 245 through 250
      removed outlier: 3.705A  pdb=" N   GLY B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 276
      removed outlier: 3.809A  pdb=" N   MET B 276 " --> pdb=" O   GLU B 273 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 180 through 181
      removed outlier: 3.631A  pdb=" N   CYS B 180 " --> pdb=" O   CYS B 144 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   CYS B 144 " --> pdb=" O   CYS B 180 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   ASP B 147 " --> pdb=" O   ASN B 131 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   ASN B 131 " --> pdb=" O   ASP B 147 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   LYS B 219 " --> pdb=" O   CYS B 134 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   VAL B 136 " --> pdb=" O   LYS B 219 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 172 through 173
    Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 173
    Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 229
      removed outlier: 5.746A  pdb=" N   ASN B 225 " --> pdb=" O   VAL B 243 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   VAL B 243 " --> pdb=" O   ASN B 225 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE B 282 " --> pdb=" O   LEU B 240 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 268 through 269
    Processing sheet with id=AA6, first strand: chain 'C' and resid 148 through 151
    Processing sheet with id=AA7, first strand: chain 'C' and resid 155 through 158
      removed outlier: 3.933A  pdb=" N   LYS C 155 " --> pdb=" O   VAL C 227 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR C 226 " --> pdb=" O   ILE C 212 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   SER C 177 " --> pdb=" O   GLN C 215 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241
      removed outlier: 6.707A  pdb=" N   ASN C 239 " --> pdb=" O   GLU C 255 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   GLU C 255 " --> pdb=" O   ASN C 239 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 274
      removed outlier: 3.886A  pdb=" N   TYR C 303 " --> pdb=" O   PHE C 322 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   PHE C 322 " --> pdb=" O   TYR C 303 " (cutoff:3.500A)

    190 hydrogen bonds defined for protein.
    525 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: 1.11

  Time building geometry restraints manager: 1.46 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1469
        1.34 -     1.46: 1142
        1.46 -     1.58: 2058
        1.58 -     1.70: 0
        1.70 -     1.82: 31
  Bond restraints: 4700
  Sorted by residual:
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.57e+00
  bond pdb=" C1  NAG G   2 "
       pdb=" O5  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.15e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 2.00e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.96e+00
  bond pdb=" C1  NAG B 702 "
       pdb=" O5  NAG B 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.87e+00
  ... (remaining 4695 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 6148
        1.26 -     2.53: 186
        2.53 -     3.79: 40
        3.79 -     5.06: 2
        5.06 -     6.32: 3
  Bond angle restraints: 6379
  Sorted by residual:
  angle pdb=" N   GLY B 177 "
        pdb=" CA  GLY B 177 "
        pdb=" C   GLY B 177 "
      ideal   model   delta    sigma   weight residual
     110.95  114.28   -3.33 1.70e+00 3.46e-01 3.84e+00
  angle pdb=" CA  GLU A  54 "
        pdb=" C   GLU A  54 "
        pdb=" N   PRO A  55 "
      ideal   model   delta    sigma   weight residual
     118.44  121.50   -3.06 1.59e+00 3.96e-01 3.71e+00
  angle pdb=" CA  LYS A  89 "
        pdb=" C   LYS A  89 "
        pdb=" N   PRO A  90 "
      ideal   model   delta    sigma   weight residual
     118.44  121.28   -2.84 1.59e+00 3.96e-01 3.20e+00
  angle pdb=" N   THR A 117 "
        pdb=" CA  THR A 117 "
        pdb=" C   THR A 117 "
      ideal   model   delta    sigma   weight residual
     109.81  113.57   -3.76 2.21e+00 2.05e-01 2.89e+00
  angle pdb=" N   GLU A  54 "
        pdb=" CA  GLU A  54 "
        pdb=" C   GLU A  54 "
      ideal   model   delta    sigma   weight residual
     109.81  113.41   -3.60 2.21e+00 2.05e-01 2.66e+00
  ... (remaining 6374 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.72: 2735
       21.72 -    43.44: 146
       43.44 -    65.15: 63
       65.15 -    86.87: 12
       86.87 -   108.59: 56
  Dihedral angle restraints: 3012
    sinusoidal: 1397
      harmonic: 1615
  Sorted by residual:
  dihedral pdb=" CB  CYS B 172 "
           pdb=" SG  CYS B 172 "
           pdb=" SG  CYS B 180 "
           pdb=" CB  CYS B 180 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.13  -51.13     1      1.00e+01 1.00e-02 3.58e+01
  dihedral pdb=" CB  CYS C 275 "
           pdb=" SG  CYS C 275 "
           pdb=" SG  CYS C 282 "
           pdb=" CB  CYS C 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -40.75  -45.25     1      1.00e+01 1.00e-02 2.84e+01
  dihedral pdb=" C1  NAG E   1 "
           pdb=" C2  NAG E   1 "
           pdb=" C3  NAG E   1 "
           pdb=" O3  NAG E   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.09  -66.50 -108.59     1      3.00e+01 1.11e-03 1.41e+01
  ... (remaining 3009 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 664
       0.072 -    0.143: 81
       0.143 -    0.214: 0
       0.214 -    0.286: 0
       0.286 -    0.357: 1
  Chirality restraints: 746
  Sorted by residual:
  chirality pdb=" C1  NAG C 801 "
            pdb=" ND2 ASN C 239 "
            pdb=" C2  NAG C 801 "
            pdb=" O5  NAG C 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.04   -0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CA  ILE A 150 "
            pdb=" N   ILE A 150 "
            pdb=" C   ILE A 150 "
            pdb=" CB  ILE A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.66e-01
  chirality pdb=" C1  NAG B 701 "
            pdb=" ND2 ASN B 225 "
            pdb=" C2  NAG B 701 "
            pdb=" O5  NAG B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-01 2.50e+01 4.64e-01
  ... (remaining 743 not shown)

  Planarity restraints: 810
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  64 "   -0.018 5.00e-02 4.00e+02   2.75e-02 1.21e+00
        pdb=" N   PRO A  65 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A  65 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A  65 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 213 "    0.017 5.00e-02 4.00e+02   2.55e-02 1.04e+00
        pdb=" N   PRO B 214 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B 214 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 214 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 183 "   -0.017 5.00e-02 4.00e+02   2.54e-02 1.03e+00
        pdb=" N   PRO C 184 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO C 184 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C 184 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 807 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1525
        2.85 -     3.36: 3796
        3.36 -     3.87: 6931
        3.87 -     4.39: 7285
        4.39 -     4.90: 13310
  Nonbonded interactions: 32847
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A  38 "
            pdb=" OD2 ASP B 213 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" OG1 THR C 306 "
            pdb=" O6  NAG G   1 "
     model   vdw
     2.375 3.040
  nonbonded pdb=" OE1 GLN C 270 "
            pdb=" NH2 ARG C 288 "
     model   vdw
     2.393 3.120
  nonbonded pdb=" OD1 ASP C 146 "
            pdb=" ND2 ASN C 172 "
     model   vdw
     2.425 3.120
  nonbonded pdb=" N   ASP C 251 "
            pdb=" OD1 ASP C 251 "
     model   vdw
     2.428 3.120
  ... (remaining 32842 not shown)

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

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=0.00 max=1.00 mean=0.99
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:             2.400
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     15.570
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
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      :  0.003   0.032   4720  Z= 0.151
  Angle     :  0.531   9.385   6432  Z= 0.262
  Chirality :  0.042   0.357    746
  Planarity :  0.003   0.027    802
  Dihedral  : 22.682 108.587   1943
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.71 %
    Favored  : 94.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.76 (0.33), residues: 543
  helix:  2.07 (0.45), residues: 130
  sheet: -1.48 (0.37), residues: 170
  loop : -2.82 (0.28), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 293 
 HIS   0.003   0.001   HIS B 176 
 PHE   0.005   0.001   PHE A 120 
 TYR   0.006   0.001   TYR A 183 
 ARG   0.001   0.000   ARG A 134 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00472 (    8)
  link_NAG-ASN         : angle       2.35438 (   24)
  link_BETA1-4         : bond        0.00346 (    5)
  link_BETA1-4         : angle       0.85718 (   15)
  hydrogen bonds       : bond        0.19015 (  180)
  hydrogen bonds       : angle       6.57776 (  525)
  SS BOND              : bond        0.00170 (    7)
  SS BOND              : angle       0.52330 (   14)
  covalent geometry    : bond        0.00296 ( 4700)
  covalent geometry    : angle       0.51127 ( 6379)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8007 (tm-30)
REVERT: A  149 GLU cc_start: 0.5790 (mm-30) cc_final: 0.5463 (mp0)
REVERT: C  245 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7468 (tpm170)
  outliers start: 1
  outliers final: 1
  residues processed: 90
  average time/residue: 0.1959
  time to fit residues: 21.5491
Evaluate side-chains
  57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  282 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    0.2980
   chunk 13 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9990
   chunk 21 optimal weight:    0.4980
   chunk 41 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN
A  61 ASN
B 176 HIS
C 171 GLN
C 286 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.122088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.101330 restraints weight = 7539.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 3.00
r_work: 0.3178 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3159
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4720  Z= 0.125
  Angle     :  0.708  11.114   6432  Z= 0.303
  Chirality :  0.047   0.243    746
  Planarity :  0.004   0.038    802
  Dihedral  : 24.382 111.054    868
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 11.81 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.79 (0.36), residues: 543
  helix:  3.07 (0.45), residues: 130
  sheet: -0.94 (0.38), residues: 174
  loop : -2.32 (0.34), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 293 
 HIS   0.003   0.001   HIS A  74 
 PHE   0.008   0.001   PHE C 305 
 TYR   0.015   0.001   TYR A 105 
 ARG   0.002   0.000   ARG A 185 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00245 (    8)
  link_NAG-ASN         : angle       3.77232 (   24)
  link_BETA1-4         : bond        0.00375 (    5)
  link_BETA1-4         : angle       2.06495 (   15)
  hydrogen bonds       : bond        0.03878 (  180)
  hydrogen bonds       : angle       4.62173 (  525)
  SS BOND              : bond        0.00166 (    7)
  SS BOND              : angle       0.95021 (   14)
  covalent geometry    : bond        0.00278 ( 4700)
  covalent geometry    : angle       0.66339 ( 6379)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8519 (tm-30)
REVERT: A  149 GLU cc_start: 0.5869 (mm-30) cc_final: 0.5532 (mp0)
REVERT: C  215 GLN cc_start: 0.8019 (tt0) cc_final: 0.7818 (tt0)
REVERT: C  245 ARG cc_start: 0.8365 (tpp80) cc_final: 0.7396 (tpm170)
REVERT: C  276 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7585 (tm-30)
REVERT: C  294 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6950 (mm-40)
  outliers start: 7
  outliers final: 3
  residues processed: 69
  average time/residue: 0.1470
  time to fit residues: 13.6687
Evaluate side-chains
  54 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain C residue  282 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0070
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7602

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

Flipped N/Q/H residues before XYZ refinement:
B 269 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.116112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.095378 restraints weight = 7519.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 2.99
r_work: 0.3085 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3089
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4720  Z= 0.148
  Angle     :  0.697  11.360   6432  Z= 0.303
  Chirality :  0.048   0.266    746
  Planarity :  0.004   0.037    802
  Dihedral  : 18.745 114.359    868
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 12.60 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.45 (0.36), residues: 543
  helix:  3.40 (0.45), residues: 130
  sheet: -0.77 (0.38), residues: 176
  loop : -2.14 (0.35), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 293 
 HIS   0.002   0.001   HIS C 193 
 PHE   0.012   0.001   PHE A 114 
 TYR   0.012   0.001   TYR A 183 
 ARG   0.002   0.000   ARG C 327 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01120 (    8)
  link_NAG-ASN         : angle       2.28761 (   24)
  link_BETA1-4         : bond        0.00433 (    5)
  link_BETA1-4         : angle       2.04242 (   15)
  hydrogen bonds       : bond        0.04510 (  180)
  hydrogen bonds       : angle       4.27745 (  525)
  SS BOND              : bond        0.00248 (    7)
  SS BOND              : angle       0.97312 (   14)
  covalent geometry    : bond        0.00334 ( 4700)
  covalent geometry    : angle       0.67671 ( 6379)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7189 (tp)
REVERT: A  149 GLU cc_start: 0.5863 (mm-30) cc_final: 0.5565 (mp0)
REVERT: C  245 ARG cc_start: 0.8420 (tpp80) cc_final: 0.7375 (tpm170)
REVERT: C  276 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8109 (tm-30)
  outliers start: 14
  outliers final: 10
  residues processed: 66
  average time/residue: 0.1306
  time to fit residues: 12.0370
Evaluate side-chains
  61 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  185 ILE
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  318 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0870
   chunk 20 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0270
   chunk 29 optimal weight:    0.7980
   chunk 36 optimal weight:    0.4980
   overall best weight:    0.4216

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

Flipped N/Q/H residues before XYZ refinement:
C 181 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.117883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.097524 restraints weight = 7538.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.94
r_work: 0.3107 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3111
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3111
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4720  Z= 0.109
  Angle     :  0.688  11.121   6432  Z= 0.290
  Chirality :  0.046   0.268    746
  Planarity :  0.003   0.041    802
  Dihedral  : 15.562  99.883    868
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.76 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.08 (0.37), residues: 543
  helix:  3.68 (0.45), residues: 130
  sheet: -0.48 (0.39), residues: 176
  loop : -1.94 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 293 
 HIS   0.001   0.000   HIS C 193 
 PHE   0.008   0.001   PHE B 295 
 TYR   0.009   0.001   TYR A  97 
 ARG   0.002   0.000   ARG C 327 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00892 (    8)
  link_NAG-ASN         : angle       3.05452 (   24)
  link_BETA1-4         : bond        0.00639 (    5)
  link_BETA1-4         : angle       2.27762 (   15)
  hydrogen bonds       : bond        0.03629 (  180)
  hydrogen bonds       : angle       3.92650 (  525)
  SS BOND              : bond        0.00182 (    7)
  SS BOND              : angle       0.81143 (   14)
  covalent geometry    : bond        0.00233 ( 4700)
  covalent geometry    : angle       0.65470 ( 6379)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8807 (tp30) cc_final: 0.8427 (tm-30)
REVERT: A  144 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7140 (tp)
REVERT: A  149 GLU cc_start: 0.5893 (mm-30) cc_final: 0.5611 (mp0)
REVERT: C  215 GLN cc_start: 0.8043 (tt0) cc_final: 0.7805 (tt0)
REVERT: C  245 ARG cc_start: 0.8383 (tpp80) cc_final: 0.7340 (tpm170)
REVERT: C  276 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7646 (tm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 61
  average time/residue: 0.1329
  time to fit residues: 11.1254
Evaluate side-chains
  58 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  275 CYS
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  319 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0570
   chunk 29 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.6106

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

Flipped N/Q/H residues before XYZ refinement:
C 267 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.108161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.087608 restraints weight = 7937.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 3.00
r_work: 0.2952 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   4720  Z= 0.238
  Angle     :  0.819  11.898   6432  Z= 0.368
  Chirality :  0.049   0.241    746
  Planarity :  0.005   0.034    802
  Dihedral  : 13.329  96.097    868
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.34 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.25 (0.37), residues: 543
  helix:  3.35 (0.45), residues: 130
  sheet: -0.48 (0.39), residues: 173
  loop : -2.00 (0.36), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 293 
 HIS   0.005   0.001   HIS C 326 
 PHE   0.018   0.002   PHE A 114 
 TYR   0.020   0.002   TYR A 183 
 ARG   0.006   0.001   ARG C 327 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01010 (    8)
  link_NAG-ASN         : angle       3.10227 (   24)
  link_BETA1-4         : bond        0.00654 (    5)
  link_BETA1-4         : angle       2.54598 (   15)
  hydrogen bonds       : bond        0.06773 (  180)
  hydrogen bonds       : angle       4.62343 (  525)
  SS BOND              : bond        0.00338 (    7)
  SS BOND              : angle       1.39074 (   14)
  covalent geometry    : bond        0.00569 ( 4700)
  covalent geometry    : angle       0.78793 ( 6379)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7511 (tp)
REVERT: A  149 GLU cc_start: 0.5966 (mm-30) cc_final: 0.5750 (mp0)
REVERT: A  195 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7264 (ttp-110)
REVERT: C  276 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8033 (tm-30)
REVERT: C  327 ARG cc_start: 0.6856 (mtt-85) cc_final: 0.5612 (mmp-170)
  outliers start: 14
  outliers final: 12
  residues processed: 58
  average time/residue: 0.1533
  time to fit residues: 11.8409
Evaluate side-chains
  55 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  319 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0010
   chunk 2 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0030
   chunk 7 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
C 267 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.113010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.092531 restraints weight = 7588.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.96
r_work: 0.3036 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3042
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3042 r_free = 0.3042    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3042 r_free = 0.3042    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3042
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4720  Z= 0.111
  Angle     :  0.701  13.149   6432  Z= 0.302
  Chirality :  0.044   0.222    746
  Planarity :  0.003   0.037    802
  Dihedral  : 12.212  94.131    868
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.50 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.06 (0.38), residues: 543
  helix:  3.75 (0.46), residues: 130
  sheet: -0.45 (0.39), residues: 176
  loop : -1.78 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 293 
 HIS   0.001   0.000   HIS C 193 
 PHE   0.009   0.001   PHE B 295 
 TYR   0.019   0.001   TYR A 105 
 ARG   0.002   0.000   ARG C 327 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00684 (    8)
  link_NAG-ASN         : angle       2.80364 (   24)
  link_BETA1-4         : bond        0.00764 (    5)
  link_BETA1-4         : angle       2.52655 (   15)
  hydrogen bonds       : bond        0.04338 (  180)
  hydrogen bonds       : angle       4.02744 (  525)
  SS BOND              : bond        0.00187 (    7)
  SS BOND              : angle       0.84252 (   14)
  covalent geometry    : bond        0.00233 ( 4700)
  covalent geometry    : angle       0.67026 ( 6379)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7393 (tp)
REVERT: A  149 GLU cc_start: 0.5874 (mm-30) cc_final: 0.5641 (mp0)
REVERT: C  276 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7834 (tm-30)
REVERT: C  327 ARG cc_start: 0.6616 (mtt-85) cc_final: 0.5396 (mmp-170)
  outliers start: 10
  outliers final: 8
  residues processed: 51
  average time/residue: 0.1496
  time to fit residues: 10.7954
Evaluate side-chains
  50 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  319 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0030
   chunk 46 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 13 optimal weight:    0.2980
   chunk 34 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.5790

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.112726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.092160 restraints weight = 7566.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 2.97
r_work: 0.3033 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3039
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3039
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4720  Z= 0.118
  Angle     :  0.654  10.642   6432  Z= 0.288
  Chirality :  0.043   0.219    746
  Planarity :  0.003   0.035    802
  Dihedral  : 11.002  90.528    868
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.11 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.24 (0.38), residues: 543
  helix:  3.87 (0.46), residues: 130
  sheet: -0.38 (0.39), residues: 175
  loop : -1.61 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 293 
 HIS   0.002   0.000   HIS A 146 
 PHE   0.010   0.001   PHE A 114 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.003   0.000   ARG C 327 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00631 (    8)
  link_NAG-ASN         : angle       2.72619 (   24)
  link_BETA1-4         : bond        0.00756 (    5)
  link_BETA1-4         : angle       2.62204 (   15)
  hydrogen bonds       : bond        0.04170 (  180)
  hydrogen bonds       : angle       3.89373 (  525)
  SS BOND              : bond        0.00198 (    7)
  SS BOND              : angle       0.90884 (   14)
  covalent geometry    : bond        0.00265 ( 4700)
  covalent geometry    : angle       0.62083 ( 6379)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7395 (tp)
REVERT: A  149 GLU cc_start: 0.5864 (mm-30) cc_final: 0.5642 (mp0)
REVERT: B  215 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8795 (p)
REVERT: C  276 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7731 (tm-30)
REVERT: C  327 ARG cc_start: 0.6420 (mtt-85) cc_final: 0.5266 (mmp-170)
  outliers start: 13
  outliers final: 9
  residues processed: 54
  average time/residue: 0.1297
  time to fit residues: 9.7723
Evaluate side-chains
  54 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  319 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 25 optimal weight:    0.1980
   chunk 48 optimal weight:    0.8980
   chunk 5 optimal weight:    0.1980
   chunk 41 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C 189 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.113258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.092622 restraints weight = 7602.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.99
r_work: 0.3038 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4720  Z= 0.115
  Angle     :  0.654  13.619   6432  Z= 0.288
  Chirality :  0.043   0.218    746
  Planarity :  0.003   0.036    802
  Dihedral  : 10.361  88.015    868
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.90 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.34 (0.38), residues: 543
  helix:  3.90 (0.45), residues: 130
  sheet: -0.34 (0.39), residues: 176
  loop : -1.51 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 181 
 HIS   0.001   0.000   HIS A 146 
 PHE   0.008   0.001   PHE B 295 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.002   0.000   ARG C 327 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00586 (    8)
  link_NAG-ASN         : angle       2.59912 (   24)
  link_BETA1-4         : bond        0.00872 (    5)
  link_BETA1-4         : angle       2.56285 (   15)
  hydrogen bonds       : bond        0.03975 (  180)
  hydrogen bonds       : angle       3.83478 (  525)
  SS BOND              : bond        0.00341 (    7)
  SS BOND              : angle       0.90354 (   14)
  covalent geometry    : bond        0.00255 ( 4700)
  covalent geometry    : angle       0.62337 ( 6379)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7364 (tp)
REVERT: A  149 GLU cc_start: 0.5866 (mm-30) cc_final: 0.5647 (mp0)
REVERT: A  195 ARG cc_start: 0.7405 (ttm-80) cc_final: 0.6886 (ttm170)
REVERT: B  215 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8774 (p)
REVERT: C  276 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7714 (tm-30)
REVERT: C  327 ARG cc_start: 0.6416 (mtt-85) cc_final: 0.5303 (mmp-170)
  outliers start: 11
  outliers final: 7
  residues processed: 56
  average time/residue: 0.1500
  time to fit residues: 11.2981
Evaluate side-chains
  54 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  319 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C 181 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.112131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.091591 restraints weight = 7692.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.99
r_work: 0.3017 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4720  Z= 0.128
  Angle     :  0.660  14.799   6432  Z= 0.293
  Chirality :  0.043   0.215    746
  Planarity :  0.003   0.035    802
  Dihedral  :  9.969  84.474    868
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.50 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.35 (0.38), residues: 543
  helix:  3.91 (0.45), residues: 130
  sheet: -0.33 (0.39), residues: 175
  loop : -1.49 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 293 
 HIS   0.002   0.000   HIS A 146 
 PHE   0.010   0.001   PHE A 114 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.003   0.000   ARG C 327 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00590 (    8)
  link_NAG-ASN         : angle       2.53252 (   24)
  link_BETA1-4         : bond        0.00784 (    5)
  link_BETA1-4         : angle       2.46318 (   15)
  hydrogen bonds       : bond        0.04335 (  180)
  hydrogen bonds       : angle       3.87854 (  525)
  SS BOND              : bond        0.00217 (    7)
  SS BOND              : angle       0.96948 (   14)
  covalent geometry    : bond        0.00295 ( 4700)
  covalent geometry    : angle       0.63137 ( 6379)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7429 (tp)
REVERT: A  149 GLU cc_start: 0.5941 (mm-30) cc_final: 0.5734 (mp0)
REVERT: A  195 ARG cc_start: 0.7465 (ttm-80) cc_final: 0.6927 (ttm170)
REVERT: B  215 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8802 (p)
REVERT: C  276 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7755 (tm-30)
REVERT: C  327 ARG cc_start: 0.6480 (mtt-85) cc_final: 0.5330 (mmp-170)
  outliers start: 13
  outliers final: 8
  residues processed: 56
  average time/residue: 0.1580
  time to fit residues: 11.7784
Evaluate side-chains
  54 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  319 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.111471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.092421 restraints weight = 7551.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 2.56
r_work: 0.3032 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2902
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2902 r_free = 0.2902    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2902 r_free = 0.2902    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2902
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4720  Z= 0.136
  Angle     :  0.666  14.613   6432  Z= 0.299
  Chirality :  0.044   0.214    746
  Planarity :  0.004   0.036    802
  Dihedral  :  9.800  81.916    868
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.50 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.37 (0.38), residues: 543
  helix:  3.88 (0.45), residues: 130
  sheet: -0.33 (0.39), residues: 176
  loop : -1.43 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 293 
 HIS   0.002   0.001   HIS A 146 
 PHE   0.009   0.001   PHE A 114 
 TYR   0.020   0.001   TYR A 105 
 ARG   0.004   0.000   ARG B 260 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00567 (    8)
  link_NAG-ASN         : angle       2.50217 (   24)
  link_BETA1-4         : bond        0.00782 (    5)
  link_BETA1-4         : angle       2.36734 (   15)
  hydrogen bonds       : bond        0.04511 (  180)
  hydrogen bonds       : angle       3.91404 (  525)
  SS BOND              : bond        0.00243 (    7)
  SS BOND              : angle       1.04702 (   14)
  covalent geometry    : bond        0.00316 ( 4700)
  covalent geometry    : angle       0.63883 ( 6379)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7416 (tp)
REVERT: A  149 GLU cc_start: 0.6019 (mm-30) cc_final: 0.5819 (mp0)
REVERT: A  195 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.6933 (ttm170)
REVERT: B  215 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8766 (p)
REVERT: C  276 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7767 (tm-30)
REVERT: C  327 ARG cc_start: 0.6535 (mtt-85) cc_final: 0.5278 (mmp-170)
  outliers start: 11
  outliers final: 9
  residues processed: 54
  average time/residue: 0.1543
  time to fit residues: 11.0523
Evaluate side-chains
  54 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  319 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0470
   chunk 42 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 15 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
C 181 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.112803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.093742 restraints weight = 7562.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.56
r_work: 0.3056 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2925
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2925 r_free = 0.2925    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2925 r_free = 0.2925    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2925
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4720  Z= 0.115
  Angle     :  0.651  14.878   6432  Z= 0.291
  Chirality :  0.043   0.209    746
  Planarity :  0.003   0.036    802
  Dihedral  :  9.566  78.902    868
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.31 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.47 (0.38), residues: 543
  helix:  4.01 (0.45), residues: 130
  sheet: -0.31 (0.39), residues: 176
  loop : -1.37 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 181 
 HIS   0.001   0.000   HIS A 146 
 PHE   0.008   0.001   PHE A 114 
 TYR   0.009   0.001   TYR A 183 
 ARG   0.002   0.000   ARG C 327 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00512 (    8)
  link_NAG-ASN         : angle       2.41210 (   24)
  link_BETA1-4         : bond        0.00830 (    5)
  link_BETA1-4         : angle       2.30219 (   15)
  hydrogen bonds       : bond        0.03940 (  180)
  hydrogen bonds       : angle       3.79865 (  525)
  SS BOND              : bond        0.00196 (    7)
  SS BOND              : angle       0.91472 (   14)
  covalent geometry    : bond        0.00258 ( 4700)
  covalent geometry    : angle       0.62548 ( 6379)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2422.65 seconds
wall clock time: 42 minutes 55.69 seconds (2575.69 seconds total)