Starting phenix.real_space_refine
on Thu Jul 24 13:33:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p54_13194/07_2025/7p54_13194.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p54_13194/07_2025/7p54_13194.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p54_13194/07_2025/7p54_13194.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p54_13194/07_2025/7p54_13194.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p54_13194/07_2025/7p54_13194.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p54_13194/07_2025/7p54_13194.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    4030      2.51       5
     N     986      2.21       5
     O    1182      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6248
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3040
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 397, 3040
          Classifications: {'peptide': 397}
          Link IDs: {'PTRANS': 9, 'TRANS': 387}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3040
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 397, 3040
          Classifications: {'peptide': 397}
          Link IDs: {'PTRANS': 9, 'TRANS': 387}
          Chain breaks: 1
    Chain: "C"
      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: "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: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "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
  Time building chain proxies: 5.09, per 1000 atoms: 0.81
  Number of scatterers: 6248
  At special positions: 0
  Unit cell: (93.744, 70.308, 128.898, 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      50     16.00
     O    1182      8.00
     N     986      7.00
     C    4030      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 382 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 300 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 274 " - pdb=" SG  CYS B 382 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 300 " - pdb=" SG  CYS B 367 " 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 C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 601 " - " ASN A 283 "
      " NAG A 602 " - " ASN A  31 "
      " NAG B 601 " - " ASN B 283 "
      " NAG B 602 " - " ASN B  31 "
      " NAG C   1 " - " ASN A 352 "
      " NAG D   1 " - " ASN A 129 "
      " NAG E   1 " - " ASN B 352 "
      " NAG F   1 " - " ASN B 129 "
  Time building additional restraints: 2.00
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1480

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 0 sheets defined
      89.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 19
    Processing helix  chain 'A' and resid 38 through 72
    Processing helix  chain 'A' and resid 89 through 161
      removed outlier: 4.269A  pdb=" N   LEU A 150 " --> pdb=" O   MET A 146 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLU A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE A 160 " --> pdb=" O   ARG A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 187
      removed outlier: 3.744A  pdb=" N   LEU A 171 " --> pdb=" O   TYR A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 237
    Processing helix  chain 'A' and resid 238 through 276
      removed outlier: 3.560A  pdb=" N   SER A 244 " --> pdb=" O   CYS A 240 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ALA A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 285
    Processing helix  chain 'A' and resid 290 through 299
    Processing helix  chain 'A' and resid 308 through 337
      removed outlier: 3.580A  pdb=" N   VAL A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
      Proline residue:  A 335  - end of helix
    Processing helix  chain 'A' and resid 341 through 365
    Processing helix  chain 'A' and resid 366 through 383
      removed outlier: 4.482A  pdb=" N   LEU A 370 " --> pdb=" O   ASP A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 409
    Processing helix  chain 'A' and resid 409 through 416
      removed outlier: 3.614A  pdb=" N   ALA A 413 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 19
    Processing helix  chain 'B' and resid 38 through 72
    Processing helix  chain 'B' and resid 89 through 161
      removed outlier: 4.283A  pdb=" N   LEU B 150 " --> pdb=" O   MET B 146 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   GLU B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE B 160 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 187
      removed outlier: 3.773A  pdb=" N   LEU B 171 " --> pdb=" O   TYR B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 237
    Processing helix  chain 'B' and resid 239 through 276
      removed outlier: 4.272A  pdb=" N   ALA B 276 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 285
    Processing helix  chain 'B' and resid 290 through 300
    Processing helix  chain 'B' and resid 308 through 337
      removed outlier: 3.597A  pdb=" N   VAL B 334 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
      Proline residue:  B 335  - end of helix
    Processing helix  chain 'B' and resid 340 through 365
      removed outlier: 3.772A  pdb=" N   LEU B 344 " --> pdb=" O   ALA B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 383
      removed outlier: 4.559A  pdb=" N   LEU B 370 " --> pdb=" O   ASP B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 409
    Processing helix  chain 'B' and resid 409 through 416
      removed outlier: 3.647A  pdb=" N   ALA B 413 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)

    581 hydrogen bonds defined for protein.
    1743 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: 1.90

  Time building geometry restraints manager: 2.32 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1935
        1.34 -     1.46: 1538
        1.46 -     1.58: 2839
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 6378
  Sorted by residual:
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.53e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.43e+00
  bond pdb=" C1  NAG B 602 "
       pdb=" O5  NAG B 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.33e+00
  bond pdb=" C1  NAG A 602 "
       pdb=" O5  NAG A 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.82e+00
  bond pdb=" C1  NAG B 601 "
       pdb=" O5  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.61e+00
  ... (remaining 6373 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 8390
        1.38 -     2.76: 254
        2.76 -     4.13: 34
        4.13 -     5.51: 11
        5.51 -     6.89: 3
  Bond angle restraints: 8692
  Sorted by residual:
  angle pdb=" C   VAL B  23 "
        pdb=" N   GLY B  24 "
        pdb=" CA  GLY B  24 "
      ideal   model   delta    sigma   weight residual
     121.44  117.03    4.41 1.45e+00 4.76e-01 9.25e+00
  angle pdb=" N   GLN A 325 "
        pdb=" CA  GLN A 325 "
        pdb=" CB  GLN A 325 "
      ideal   model   delta    sigma   weight residual
     110.16  114.31   -4.15 1.48e+00 4.57e-01 7.87e+00
  angle pdb=" N   ARG B 368 "
        pdb=" CA  ARG B 368 "
        pdb=" C   ARG B 368 "
      ideal   model   delta    sigma   weight residual
     111.11  114.34   -3.23 1.20e+00 6.94e-01 7.25e+00
  angle pdb=" N   GLY B  37 "
        pdb=" CA  GLY B  37 "
        pdb=" C   GLY B  37 "
      ideal   model   delta    sigma   weight residual
     114.25  111.02    3.23 1.30e+00 5.92e-01 6.18e+00
  angle pdb=" C   CYS B 367 "
        pdb=" N   ARG B 368 "
        pdb=" CA  ARG B 368 "
      ideal   model   delta    sigma   weight residual
     120.54  123.89   -3.35 1.35e+00 5.49e-01 6.16e+00
  ... (remaining 8687 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 3460
       16.06 -    32.12: 290
       32.12 -    48.18: 91
       48.18 -    64.23: 25
       64.23 -    80.29: 8
  Dihedral angle restraints: 3874
    sinusoidal: 1570
      harmonic: 2304
  Sorted by residual:
  dihedral pdb=" CB  CYS A 300 "
           pdb=" SG  CYS A 300 "
           pdb=" SG  CYS A 367 "
           pdb=" CB  CYS A 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -162.49   76.49     1      1.00e+01 1.00e-02 7.36e+01
  dihedral pdb=" CB  CYS B 300 "
           pdb=" SG  CYS B 300 "
           pdb=" SG  CYS B 367 "
           pdb=" CB  CYS B 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.61   55.61     1      1.00e+01 1.00e-02 4.18e+01
  dihedral pdb=" CB  CYS A 274 "
           pdb=" SG  CYS A 274 "
           pdb=" SG  CYS A 382 "
           pdb=" CB  CYS A 382 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  128.88  -35.88     1      1.00e+01 1.00e-02 1.82e+01
  ... (remaining 3871 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 985
       0.063 -    0.126: 84
       0.126 -    0.188: 1
       0.188 -    0.251: 0
       0.251 -    0.314: 2
  Chirality restraints: 1072
  Sorted by residual:
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN B 129 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 129 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CA  GLN A 325 "
            pdb=" N   GLN A 325 "
            pdb=" C   GLN A 325 "
            pdb=" CB  GLN A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.29e-01
  ... (remaining 1069 not shown)

  Planarity restraints: 1066
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  20 "   -0.055 5.00e-02 4.00e+02   8.28e-02 1.10e+01
        pdb=" N   PRO A  21 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO A  21 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A  21 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  20 "   -0.053 5.00e-02 4.00e+02   8.04e-02 1.03e+01
        pdb=" N   PRO B  21 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO B  21 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO B  21 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 147 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.66e+00
        pdb=" C   LYS B 147 "    0.028 2.00e-02 2.50e+03
        pdb=" O   LYS B 147 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   VAL B 148 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1063 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 737
        2.74 -     3.28: 6440
        3.28 -     3.82: 11254
        3.82 -     4.36: 11217
        4.36 -     4.90: 20634
  Nonbonded interactions: 50282
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 278 "
            pdb=" OH  TYR A 374 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OD1 ASN B 111 "
            pdb=" NH1 ARG B 212 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" OD2 ASP A  38 "
            pdb=" OG  SER A  40 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   ILE B 281 "
            pdb=" OG1 THR B 285 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OD1 ASN A 111 "
            pdb=" NH1 ARG A 212 "
     model   vdw
     2.243 3.120
  ... (remaining 50277 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 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.140
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
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      :  0.004   0.038   6394  Z= 0.173
  Angle     :  0.586   7.623   8736  Z= 0.302
  Chirality :  0.038   0.314   1072
  Planarity :  0.005   0.083   1058
  Dihedral  : 13.935  80.293   2382
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.08 (0.29), residues: 786
  helix:  3.32 (0.18), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.34 (0.49), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 213 
 HIS   0.002   0.001   HIS A  18 
 PHE   0.012   0.002   PHE B 395 
 TYR   0.010   0.001   TYR A   8 
 ARG   0.007   0.001   ARG B 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00337 (    8)
  link_NAG-ASN         : angle       1.63199 (   24)
  link_BETA1-4         : bond        0.01212 (    4)
  link_BETA1-4         : angle       4.04926 (   12)
  hydrogen bonds       : bond        0.09394 (  581)
  hydrogen bonds       : angle       4.11908 ( 1743)
  SS BOND              : bond        0.00444 (    4)
  SS BOND              : angle       3.15677 (    8)
  covalent geometry    : bond        0.00358 ( 6378)
  covalent geometry    : angle       0.55278 ( 8692)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A   16 TRP cc_start: 0.6870 (m100) cc_final: 0.6646 (m100)
REVERT: A  207 TYR cc_start: 0.7718 (t80) cc_final: 0.7392 (t80)
REVERT: A  213 TRP cc_start: 0.8415 (t60) cc_final: 0.7703 (t-100)
REVERT: A  245 MET cc_start: 0.6533 (mmp) cc_final: 0.6259 (mmp)
REVERT: A  353 SER cc_start: 0.8925 (t) cc_final: 0.8714 (t)
REVERT: B   12 TRP cc_start: 0.8176 (p-90) cc_final: 0.7966 (p-90)
REVERT: B  213 TRP cc_start: 0.8324 (t60) cc_final: 0.7643 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.2120
  time to fit residues: 37.2584
Evaluate side-chains
  116 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 32 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
B  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.150981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.120879 restraints weight = 6858.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.34
r_work: 0.3259 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.0861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6394  Z= 0.146
  Angle     :  0.524   6.703   8736  Z= 0.264
  Chirality :  0.038   0.239   1072
  Planarity :  0.004   0.052   1058
  Dihedral  :  7.328  59.841   1096
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  8.03 %
    Favored  : 90.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.20 (0.29), residues: 786
  helix:  3.47 (0.18), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.79 (0.51), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  16 
 HIS   0.003   0.001   HIS A  22 
 PHE   0.017   0.002   PHE A  62 
 TYR   0.020   0.001   TYR B   8 
 ARG   0.005   0.001   ARG A 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00285 (    8)
  link_NAG-ASN         : angle       1.91921 (   24)
  link_BETA1-4         : bond        0.01164 (    4)
  link_BETA1-4         : angle       3.37797 (   12)
  hydrogen bonds       : bond        0.04004 (  581)
  hydrogen bonds       : angle       3.58709 ( 1743)
  SS BOND              : bond        0.00728 (    4)
  SS BOND              : angle       1.88905 (    8)
  covalent geometry    : bond        0.00320 ( 6378)
  covalent geometry    : angle       0.49644 ( 8692)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.634 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8184 (t80) cc_final: 0.7776 (t80)
REVERT: A  213 TRP cc_start: 0.8561 (t60) cc_final: 0.7669 (t-100)
REVERT: A  332 PHE cc_start: 0.7906 (m-10) cc_final: 0.7689 (m-10)
REVERT: A  336 LEU cc_start: 0.8870 (mp) cc_final: 0.8649 (mp)
REVERT: B    8 TYR cc_start: 0.7729 (t80) cc_final: 0.7451 (t80)
REVERT: B   16 TRP cc_start: 0.8039 (m100) cc_final: 0.7822 (m100)
REVERT: B  213 TRP cc_start: 0.8557 (t60) cc_final: 0.7589 (t-100)
REVERT: B  283 ASN cc_start: 0.8218 (t0) cc_final: 0.7883 (t0)
REVERT: B  322 MET cc_start: 0.8412 (mtp) cc_final: 0.8053 (mtp)
  outliers start: 9
  outliers final: 6
  residues processed: 127
  average time/residue: 0.1906
  time to fit residues: 31.9700
Evaluate side-chains
  123 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 64 optimal weight:    0.2980
   chunk 16 optimal weight:    0.5980
   chunk 65 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 68 optimal weight:    0.3980
   chunk 53 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3865 r_free = 0.3865 target = 0.159586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.130313 restraints weight = 6864.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.28
r_work: 0.3260 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.1068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6394  Z= 0.123
  Angle     :  0.496   7.039   8736  Z= 0.245
  Chirality :  0.038   0.241   1072
  Planarity :  0.004   0.040   1058
  Dihedral  :  6.667  57.669   1096
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.36 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.31 (0.29), residues: 786
  helix:  3.57 (0.18), residues: 668
  sheet:  None (None), residues: 0
  loop : -2.05 (0.50), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  16 
 HIS   0.002   0.000   HIS A 371 
 PHE   0.022   0.002   PHE A  62 
 TYR   0.017   0.001   TYR A   8 
 ARG   0.004   0.000   ARG A  26 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00313 (    8)
  link_NAG-ASN         : angle       1.68322 (   24)
  link_BETA1-4         : bond        0.01352 (    4)
  link_BETA1-4         : angle       3.40767 (   12)
  hydrogen bonds       : bond        0.03772 (  581)
  hydrogen bonds       : angle       3.49323 ( 1743)
  SS BOND              : bond        0.00612 (    4)
  SS BOND              : angle       1.33752 (    8)
  covalent geometry    : bond        0.00256 ( 6378)
  covalent geometry    : angle       0.47103 ( 8692)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 130
  time to evaluate  : 0.614 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8236 (t80) cc_final: 0.7807 (t80)
REVERT: A  213 TRP cc_start: 0.8527 (t60) cc_final: 0.7659 (t-100)
REVERT: A  245 MET cc_start: 0.6500 (mmp) cc_final: 0.5964 (mmp)
REVERT: A  283 ASN cc_start: 0.7958 (t0) cc_final: 0.7679 (t0)
REVERT: A  332 PHE cc_start: 0.8051 (m-10) cc_final: 0.7727 (m-10)
REVERT: A  336 LEU cc_start: 0.8899 (mp) cc_final: 0.8694 (mp)
REVERT: B    8 TYR cc_start: 0.7407 (t80) cc_final: 0.7050 (t80)
REVERT: B   16 TRP cc_start: 0.7981 (m100) cc_final: 0.7765 (m100)
REVERT: B  213 TRP cc_start: 0.8547 (t60) cc_final: 0.7600 (t-100)
REVERT: B  283 ASN cc_start: 0.8339 (t0) cc_final: 0.8001 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 133
  average time/residue: 0.1836
  time to fit residues: 31.7576
Evaluate side-chains
  132 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    0.0670
   chunk 28 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 56 optimal weight:    0.3980
   chunk 14 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 70 optimal weight:    0.2980
   overall best weight:    0.3918

-------------------------------------------------------------------------------
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 = 0.3863 r_free = 0.3863 target = 0.159713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.129884 restraints weight = 6938.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.32
r_work: 0.3291 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6394  Z= 0.114
  Angle     :  0.472   6.694   8736  Z= 0.235
  Chirality :  0.036   0.240   1072
  Planarity :  0.004   0.036   1058
  Dihedral  :  6.230  56.779   1096
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.39 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.42 (0.29), residues: 786
  helix:  3.60 (0.18), residues: 678
  sheet:  None (None), residues: 0
  loop : -2.24 (0.52), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  16 
 HIS   0.002   0.000   HIS A 371 
 PHE   0.024   0.002   PHE A  62 
 TYR   0.016   0.001   TYR A   8 
 ARG   0.004   0.000   ARG A 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00249 (    8)
  link_NAG-ASN         : angle       1.62833 (   24)
  link_BETA1-4         : bond        0.01300 (    4)
  link_BETA1-4         : angle       3.37302 (   12)
  hydrogen bonds       : bond        0.03623 (  581)
  hydrogen bonds       : angle       3.45392 ( 1743)
  SS BOND              : bond        0.00557 (    4)
  SS BOND              : angle       1.02975 (    8)
  covalent geometry    : bond        0.00229 ( 6378)
  covalent geometry    : angle       0.44701 ( 8692)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.719 
Fit side-chains
REVERT: A  166 ASP cc_start: 0.8518 (p0) cc_final: 0.8309 (p0)
REVERT: A  207 TYR cc_start: 0.8245 (t80) cc_final: 0.7833 (t80)
REVERT: A  213 TRP cc_start: 0.8473 (t60) cc_final: 0.7672 (t-100)
REVERT: A  245 MET cc_start: 0.6488 (mmp) cc_final: 0.5899 (mmp)
REVERT: A  283 ASN cc_start: 0.8069 (t0) cc_final: 0.7778 (t0)
REVERT: A  332 PHE cc_start: 0.8066 (m-10) cc_final: 0.7716 (m-10)
REVERT: A  336 LEU cc_start: 0.8869 (mp) cc_final: 0.8661 (mp)
REVERT: B    8 TYR cc_start: 0.7323 (t80) cc_final: 0.7004 (t80)
REVERT: B   16 TRP cc_start: 0.8020 (m100) cc_final: 0.7764 (m100)
REVERT: B  213 TRP cc_start: 0.8512 (t60) cc_final: 0.7617 (t-100)
REVERT: B  272 ASP cc_start: 0.8290 (m-30) cc_final: 0.8072 (m-30)
REVERT: B  283 ASN cc_start: 0.8429 (t0) cc_final: 0.8080 (t0)
  outliers start: 10
  outliers final: 10
  residues processed: 136
  average time/residue: 0.2152
  time to fit residues: 38.1289
Evaluate side-chains
  137 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  300 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3820 r_free = 0.3820 target = 0.155559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.125829 restraints weight = 7033.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.32
r_work: 0.3260 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6394  Z= 0.150
  Angle     :  0.518   6.820   8736  Z= 0.255
  Chirality :  0.038   0.233   1072
  Planarity :  0.003   0.033   1058
  Dihedral  :  5.978  55.614   1096
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.21 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.32 (0.29), residues: 786
  helix:  3.46 (0.18), residues: 686
  sheet:  None (None), residues: 0
  loop : -2.15 (0.56), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  13 
 HIS   0.003   0.001   HIS A 371 
 PHE   0.028   0.002   PHE B  62 
 TYR   0.015   0.001   TYR A   8 
 ARG   0.003   0.001   ARG A 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00220 (    8)
  link_NAG-ASN         : angle       1.69916 (   24)
  link_BETA1-4         : bond        0.01195 (    4)
  link_BETA1-4         : angle       3.41457 (   12)
  hydrogen bonds       : bond        0.03733 (  581)
  hydrogen bonds       : angle       3.49292 ( 1743)
  SS BOND              : bond        0.00787 (    4)
  SS BOND              : angle       1.46284 (    8)
  covalent geometry    : bond        0.00334 ( 6378)
  covalent geometry    : angle       0.49349 ( 8692)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.904 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8341 (t80) cc_final: 0.7833 (t80)
REVERT: A  213 TRP cc_start: 0.8550 (t60) cc_final: 0.7656 (t-100)
REVERT: A  245 MET cc_start: 0.6706 (mmp) cc_final: 0.6031 (mmp)
REVERT: A  283 ASN cc_start: 0.8153 (t0) cc_final: 0.7845 (t0)
REVERT: A  325 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.6651 (mp10)
REVERT: A  332 PHE cc_start: 0.8103 (m-10) cc_final: 0.7701 (m-10)
REVERT: B    8 TYR cc_start: 0.7530 (t80) cc_final: 0.7176 (t80)
REVERT: B   16 TRP cc_start: 0.8009 (m100) cc_final: 0.7738 (m100)
REVERT: B  213 TRP cc_start: 0.8584 (t60) cc_final: 0.7605 (t-100)
REVERT: B  283 ASN cc_start: 0.8458 (t0) cc_final: 0.8183 (t0)
REVERT: B  332 PHE cc_start: 0.8100 (m-10) cc_final: 0.7818 (m-10)
  outliers start: 17
  outliers final: 14
  residues processed: 133
  average time/residue: 0.2351
  time to fit residues: 41.1137
Evaluate side-chains
  139 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  300 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0970
   chunk 8 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.158343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.128940 restraints weight = 6860.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.28
r_work: 0.3302 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6394  Z= 0.125
  Angle     :  0.500   6.940   8736  Z= 0.247
  Chirality :  0.037   0.242   1072
  Planarity :  0.003   0.033   1058
  Dihedral  :  5.769  54.244   1096
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.42 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.39 (0.29), residues: 786
  helix:  3.51 (0.18), residues: 686
  sheet:  None (None), residues: 0
  loop : -2.15 (0.56), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  16 
 HIS   0.003   0.001   HIS A 371 
 PHE   0.028   0.002   PHE B  62 
 TYR   0.015   0.001   TYR A   8 
 ARG   0.003   0.000   ARG A 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00205 (    8)
  link_NAG-ASN         : angle       1.58645 (   24)
  link_BETA1-4         : bond        0.01276 (    4)
  link_BETA1-4         : angle       3.36247 (   12)
  hydrogen bonds       : bond        0.03655 (  581)
  hydrogen bonds       : angle       3.46702 ( 1743)
  SS BOND              : bond        0.00667 (    4)
  SS BOND              : angle       1.30705 (    8)
  covalent geometry    : bond        0.00265 ( 6378)
  covalent geometry    : angle       0.47685 ( 8692)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.7200 (t80) cc_final: 0.6909 (t80)
REVERT: A  207 TYR cc_start: 0.8311 (t80) cc_final: 0.7850 (t80)
REVERT: A  213 TRP cc_start: 0.8529 (t60) cc_final: 0.7650 (t-100)
REVERT: A  283 ASN cc_start: 0.8151 (t0) cc_final: 0.7835 (t0)
REVERT: A  325 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.6558 (mp10)
REVERT: A  332 PHE cc_start: 0.8190 (m-10) cc_final: 0.7920 (m-10)
REVERT: B    8 TYR cc_start: 0.7448 (t80) cc_final: 0.7154 (t80)
REVERT: B   16 TRP cc_start: 0.7986 (m100) cc_final: 0.7702 (m100)
REVERT: B  213 TRP cc_start: 0.8568 (t60) cc_final: 0.7603 (t-100)
REVERT: B  283 ASN cc_start: 0.8469 (t0) cc_final: 0.8191 (t0)
REVERT: B  332 PHE cc_start: 0.8105 (m-10) cc_final: 0.7813 (m-10)
  outliers start: 16
  outliers final: 15
  residues processed: 132
  average time/residue: 0.1935
  time to fit residues: 33.2956
Evaluate side-chains
  138 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  300 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0670
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 76 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.3850 r_free = 0.3850 target = 0.158427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.128740 restraints weight = 6864.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.30
r_work: 0.3343 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6394  Z= 0.125
  Angle     :  0.503   7.262   8736  Z= 0.248
  Chirality :  0.037   0.242   1072
  Planarity :  0.003   0.032   1058
  Dihedral  :  5.501  51.004   1096
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.73 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.44 (0.29), residues: 786
  helix:  3.51 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -2.00 (0.57), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  16 
 HIS   0.003   0.001   HIS A 371 
 PHE   0.029   0.002   PHE A  62 
 TYR   0.014   0.001   TYR A   8 
 ARG   0.009   0.001   ARG A 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00214 (    8)
  link_NAG-ASN         : angle       1.57189 (   24)
  link_BETA1-4         : bond        0.01196 (    4)
  link_BETA1-4         : angle       3.36414 (   12)
  hydrogen bonds       : bond        0.03586 (  581)
  hydrogen bonds       : angle       3.45067 ( 1743)
  SS BOND              : bond        0.00670 (    4)
  SS BOND              : angle       1.35916 (    8)
  covalent geometry    : bond        0.00267 ( 6378)
  covalent geometry    : angle       0.47957 ( 8692)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.800 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.7359 (t80) cc_final: 0.7019 (t80)
REVERT: A  166 ASP cc_start: 0.8672 (p0) cc_final: 0.8458 (p0)
REVERT: A  207 TYR cc_start: 0.8331 (t80) cc_final: 0.7863 (t80)
REVERT: A  213 TRP cc_start: 0.8524 (t60) cc_final: 0.7664 (t-100)
REVERT: A  283 ASN cc_start: 0.8203 (t0) cc_final: 0.7888 (t0)
REVERT: A  325 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.6581 (mp10)
REVERT: A  332 PHE cc_start: 0.8263 (m-10) cc_final: 0.7998 (m-10)
REVERT: B    8 TYR cc_start: 0.7521 (t80) cc_final: 0.7271 (t80)
REVERT: B   16 TRP cc_start: 0.7975 (m100) cc_final: 0.7702 (m100)
REVERT: B  213 TRP cc_start: 0.8563 (t60) cc_final: 0.7626 (t-100)
REVERT: B  283 ASN cc_start: 0.8512 (t0) cc_final: 0.8240 (t0)
REVERT: B  325 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.6885 (mp10)
REVERT: B  332 PHE cc_start: 0.8191 (m-10) cc_final: 0.7903 (m-10)
  outliers start: 19
  outliers final: 16
  residues processed: 134
  average time/residue: 0.2948
  time to fit residues: 51.1938
Evaluate side-chains
  137 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  325 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3828 r_free = 0.3828 target = 0.156312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.126994 restraints weight = 6921.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.27
r_work: 0.3210 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6394  Z= 0.158
  Angle     :  0.538   6.987   8736  Z= 0.264
  Chirality :  0.039   0.244   1072
  Planarity :  0.003   0.038   1058
  Dihedral  :  5.308  45.716   1096
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.94 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.31 (0.29), residues: 786
  helix:  3.42 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -2.02 (0.57), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  13 
 HIS   0.003   0.001   HIS A 371 
 PHE   0.030   0.002   PHE A  62 
 TYR   0.013   0.002   TYR A   8 
 ARG   0.003   0.001   ARG B 156 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00220 (    8)
  link_NAG-ASN         : angle       1.71070 (   24)
  link_BETA1-4         : bond        0.01111 (    4)
  link_BETA1-4         : angle       3.41437 (   12)
  hydrogen bonds       : bond        0.03741 (  581)
  hydrogen bonds       : angle       3.52331 ( 1743)
  SS BOND              : bond        0.00880 (    4)
  SS BOND              : angle       1.68408 (    8)
  covalent geometry    : bond        0.00354 ( 6378)
  covalent geometry    : angle       0.51391 ( 8692)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.782 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.7495 (t80) cc_final: 0.7283 (t80)
REVERT: A  164 ARG cc_start: 0.7143 (mtp85) cc_final: 0.6363 (mtp85)
REVERT: A  207 TYR cc_start: 0.8368 (t80) cc_final: 0.7857 (t80)
REVERT: A  213 TRP cc_start: 0.8606 (t60) cc_final: 0.7613 (t-100)
REVERT: A  283 ASN cc_start: 0.8157 (t0) cc_final: 0.7831 (t0)
REVERT: A  325 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.6504 (mp10)
REVERT: B   16 TRP cc_start: 0.7941 (m100) cc_final: 0.7585 (m100)
REVERT: B  213 TRP cc_start: 0.8621 (t60) cc_final: 0.7570 (t-100)
REVERT: B  283 ASN cc_start: 0.8472 (t0) cc_final: 0.8198 (t0)
REVERT: B  325 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.6866 (mp10)
REVERT: B  332 PHE cc_start: 0.8183 (m-10) cc_final: 0.7883 (m-10)
  outliers start: 20
  outliers final: 18
  residues processed: 134
  average time/residue: 0.2300
  time to fit residues: 40.6144
Evaluate side-chains
  140 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  325 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3833 r_free = 0.3833 target = 0.156969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.127742 restraints weight = 6919.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.29
r_work: 0.3207 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6394  Z= 0.138
  Angle     :  0.522   7.298   8736  Z= 0.256
  Chirality :  0.038   0.249   1072
  Planarity :  0.003   0.037   1058
  Dihedral  :  5.142  39.073   1096
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.09 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.39 (0.29), residues: 786
  helix:  3.47 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.97 (0.57), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  16 
 HIS   0.003   0.001   HIS A 371 
 PHE   0.030   0.002   PHE A  62 
 TYR   0.019   0.001   TYR B   8 
 ARG   0.004   0.000   ARG A 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00203 (    8)
  link_NAG-ASN         : angle       1.61825 (   24)
  link_BETA1-4         : bond        0.01174 (    4)
  link_BETA1-4         : angle       3.39925 (   12)
  hydrogen bonds       : bond        0.03671 (  581)
  hydrogen bonds       : angle       3.49154 ( 1743)
  SS BOND              : bond        0.00724 (    4)
  SS BOND              : angle       1.49812 (    8)
  covalent geometry    : bond        0.00304 ( 6378)
  covalent geometry    : angle       0.49864 ( 8692)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 1.102 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.8044 (mtm110) cc_final: 0.7757 (mpp80)
REVERT: A  164 ARG cc_start: 0.7074 (mtp85) cc_final: 0.6243 (mtp85)
REVERT: A  207 TYR cc_start: 0.8346 (t80) cc_final: 0.7838 (t80)
REVERT: A  213 TRP cc_start: 0.8574 (t60) cc_final: 0.7593 (t-100)
REVERT: A  283 ASN cc_start: 0.8147 (t0) cc_final: 0.7813 (t0)
REVERT: A  325 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.6450 (mp10)
REVERT: A  332 PHE cc_start: 0.8356 (m-80) cc_final: 0.7994 (m-10)
REVERT: B   16 TRP cc_start: 0.7926 (m100) cc_final: 0.7567 (m100)
REVERT: B  213 TRP cc_start: 0.8607 (t60) cc_final: 0.7563 (t-100)
REVERT: B  283 ASN cc_start: 0.8513 (t0) cc_final: 0.8225 (t0)
REVERT: B  325 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.6845 (mp10)
REVERT: B  332 PHE cc_start: 0.8193 (m-10) cc_final: 0.7904 (m-10)
  outliers start: 22
  outliers final: 19
  residues processed: 134
  average time/residue: 0.3635
  time to fit residues: 63.8731
Evaluate side-chains
  139 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain B residue  378 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0970
   chunk 38 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 71 optimal weight:    0.4980
   chunk 69 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3842 r_free = 0.3842 target = 0.158077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.128846 restraints weight = 6946.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 2.28
r_work: 0.3233 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6394  Z= 0.125
  Angle     :  0.511   7.243   8736  Z= 0.251
  Chirality :  0.038   0.246   1072
  Planarity :  0.003   0.036   1058
  Dihedral  :  4.942  38.671   1096
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.09 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.47 (0.29), residues: 786
  helix:  3.52 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.94 (0.57), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  16 
 HIS   0.003   0.001   HIS A 371 
 PHE   0.030   0.002   PHE A  62 
 TYR   0.020   0.001   TYR B   8 
 ARG   0.004   0.000   ARG B 156 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00215 (    8)
  link_NAG-ASN         : angle       1.53565 (   24)
  link_BETA1-4         : bond        0.01186 (    4)
  link_BETA1-4         : angle       3.39348 (   12)
  hydrogen bonds       : bond        0.03584 (  581)
  hydrogen bonds       : angle       3.46784 ( 1743)
  SS BOND              : bond        0.00657 (    4)
  SS BOND              : angle       1.41293 (    8)
  covalent geometry    : bond        0.00269 ( 6378)
  covalent geometry    : angle       0.48819 ( 8692)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.811 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.6977 (t80) cc_final: 0.6697 (t80)
REVERT: A   26 ARG cc_start: 0.8054 (mtm110) cc_final: 0.7767 (mpp80)
REVERT: A  176 GLN cc_start: 0.7602 (mm-40) cc_final: 0.7236 (tt0)
REVERT: A  207 TYR cc_start: 0.8273 (t80) cc_final: 0.7797 (t80)
REVERT: A  213 TRP cc_start: 0.8552 (t60) cc_final: 0.7566 (t-100)
REVERT: A  283 ASN cc_start: 0.8119 (t0) cc_final: 0.7774 (t0)
REVERT: A  325 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.6396 (mp10)
REVERT: B   16 TRP cc_start: 0.7902 (m100) cc_final: 0.7529 (m100)
REVERT: B   26 ARG cc_start: 0.7620 (mpp80) cc_final: 0.7282 (mpp80)
REVERT: B  213 TRP cc_start: 0.8590 (t60) cc_final: 0.7542 (t-100)
REVERT: B  283 ASN cc_start: 0.8456 (t0) cc_final: 0.8179 (t0)
REVERT: B  325 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.6801 (mp10)
REVERT: B  332 PHE cc_start: 0.8246 (m-10) cc_final: 0.7971 (m-10)
  outliers start: 20
  outliers final: 18
  residues processed: 136
  average time/residue: 0.3189
  time to fit residues: 57.4227
Evaluate side-chains
  140 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 1.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain B residue  378 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0020
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.5588

-------------------------------------------------------------------------------
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 = 0.3844 r_free = 0.3844 target = 0.158217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.128981 restraints weight = 7040.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.29
r_work: 0.3357 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6394  Z= 0.126
  Angle     :  0.511   7.133   8736  Z= 0.251
  Chirality :  0.038   0.245   1072
  Planarity :  0.003   0.035   1058
  Dihedral  :  4.895  38.643   1096
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 19.39 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.47 (0.29), residues: 786
  helix:  3.52 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.93 (0.57), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  16 
 HIS   0.003   0.001   HIS A 371 
 PHE   0.030   0.002   PHE A  62 
 TYR   0.017   0.001   TYR B   8 
 ARG   0.008   0.001   ARG A 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    8)
  link_NAG-ASN         : angle       1.52652 (   24)
  link_BETA1-4         : bond        0.01182 (    4)
  link_BETA1-4         : angle       3.39393 (   12)
  hydrogen bonds       : bond        0.03562 (  581)
  hydrogen bonds       : angle       3.47003 ( 1743)
  SS BOND              : bond        0.00628 (    4)
  SS BOND              : angle       1.41531 (    8)
  covalent geometry    : bond        0.00271 ( 6378)
  covalent geometry    : angle       0.48786 ( 8692)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3959.31 seconds
wall clock time: 73 minutes 46.17 seconds (4426.17 seconds total)