Starting phenix.real_space_refine
on Wed Jul 23 20:24:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xrp_33416/07_2025/7xrp_33416.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xrp_33416/07_2025/7xrp_33416.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xrp_33416/07_2025/7xrp_33416.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xrp_33416/07_2025/7xrp_33416.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xrp_33416/07_2025/7xrp_33416.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xrp_33416/07_2025/7xrp_33416.cif"
  }
  resolution = 3.88
  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=   0.011
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      14      5.16       5
     C    2655      2.51       5
     N     674      2.21       5
     O     786      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4129
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1684
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 11, 'TRANS': 197}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 935
          Classifications: {'peptide': 124}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "F"
      Number of atoms: 1454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1454
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 9, 'TRANS': 172}
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      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: 5.13, per 1000 atoms: 1.24
  Number of scatterers: 4129
  At special positions: 0
  Unit cell: (73.91, 77.8, 113.588, 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      14     16.00
     O     786      8.00
     N     674      7.00
     C    2655      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 336 " - pdb=" SG  CYS F 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 379 " - pdb=" SG  CYS F 432 " distance=2.06

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 401 " - " ASN A 165 "
      " NAG A 402 " - " ASN A 282 "
      " NAG A 403 " - " ASN A 122 "
      " NAG F 601 " - " ASN F 343 "
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 473.5 milliseconds
  

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  952

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 9 sheets defined
      5.4% alpha, 30.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'B' and resid 62 through 65
      removed outlier: 3.510A  pdb=" N   LYS B  65 " --> pdb=" O   ASP B  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 62 through 65'
    Processing helix  chain 'B' and resid 87 through 91
    Processing helix  chain 'F' and resid 338 through 343
      removed outlier: 3.959A  pdb=" N   PHE F 342 " --> pdb=" O   PHE F 338 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASN F 343 " --> pdb=" O   GLY F 339 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 338 through 343'
    Processing helix  chain 'F' and resid 403 through 410
      removed outlier: 3.708A  pdb=" N   GLU F 406 " --> pdb=" O   ARG F 403 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   ARG F 408 " --> pdb=" O   ASP F 405 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 502 through 506
      removed outlier: 3.761A  pdb=" N   GLN F 506 " --> pdb=" O   VAL F 503 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31
      removed outlier: 3.590A  pdb=" N   SER A  31 " --> pdb=" O   SER A  60 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   SER A  60 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   THR A  63 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   VAL A 267 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   THR A 208 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   VAL A 193 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ILE A 203 " --> pdb=" O   VAL A 227 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   VAL A 227 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55
      removed outlier: 3.713A  pdb=" N   THR A  51 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ASP A  53 " --> pdb=" O   ARG A 273 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLN A 271 " --> pdb=" O   PHE A  55 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.778A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LYS A 129 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL A 120 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6
      removed outlier: 3.562A  pdb=" N   VAL B  79 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   THR B  69 " --> pdb=" O   GLN B  82 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13
      removed outlier: 3.601A  pdb=" N   THR B 122 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL B  12 " --> pdb=" O   THR B 122 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   SER B 124 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL B 121 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA B  92 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   GLN B  39 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY B  35 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   LEU B  99 " --> pdb=" O   PHE B  33 " (cutoff:3.500A)
      removed outlier: 5.536A  pdb=" N   PHE B  33 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13
      removed outlier: 3.601A  pdb=" N   THR B 122 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL B  12 " --> pdb=" O   THR B 122 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   SER B 124 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL B 121 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA B  92 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 50
    Processing sheet with id=AA8, first strand: chain 'F' and resid 354 through 357
      removed outlier: 5.047A  pdb=" N   ASN F 394 " --> pdb=" O   GLU F 516 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   GLU F 516 " --> pdb=" O   ASN F 394 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   LEU F 513 " --> pdb=" O   CYS F 432 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   VAL F 433 " --> pdb=" O   LYS F 378 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 452 through 454

    95 hydrogen bonds defined for protein.
    219 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.99

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 666
        1.30 -     1.44: 1271
        1.44 -     1.57: 2278
        1.57 -     1.70: 1
        1.70 -     1.83: 15
  Bond restraints: 4231
  Sorted by residual:
  bond pdb=" CA  ALA F 352 "
       pdb=" C   ALA F 352 "
    ideal  model  delta    sigma   weight residual
    1.528  1.442  0.086 1.04e-02 9.25e+03 6.82e+01
  bond pdb=" CA  SER F 349 "
       pdb=" C   SER F 349 "
    ideal  model  delta    sigma   weight residual
    1.526  1.425  0.100 1.36e-02 5.41e+03 5.46e+01
  bond pdb=" CA  ARG F 346 "
       pdb=" C   ARG F 346 "
    ideal  model  delta    sigma   weight residual
    1.522  1.446  0.076 1.23e-02 6.61e+03 3.81e+01
  bond pdb=" CA  PHE F 347 "
       pdb=" C   PHE F 347 "
    ideal  model  delta    sigma   weight residual
    1.522  1.449  0.074 1.23e-02 6.61e+03 3.58e+01
  bond pdb=" CA  ALA F 348 "
       pdb=" C   ALA F 348 "
    ideal  model  delta    sigma   weight residual
    1.528  1.456  0.072 1.38e-02 5.25e+03 2.71e+01
  ... (remaining 4226 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.09: 5709
        5.09 -    10.19: 34
       10.19 -    15.28: 4
       15.28 -    20.37: 0
       20.37 -    25.46: 1
  Bond angle restraints: 5748
  Sorted by residual:
  angle pdb=" N   ARG A 214 "
        pdb=" CA  ARG A 214 "
        pdb=" C   ARG A 214 "
      ideal   model   delta    sigma   weight residual
     109.76   84.30   25.46 1.59e+00 3.96e-01 2.56e+02
  angle pdb=" N   VAL F 350 "
        pdb=" CA  VAL F 350 "
        pdb=" C   VAL F 350 "
      ideal   model   delta    sigma   weight residual
     110.62  118.46   -7.84 1.02e+00 9.61e-01 5.90e+01
  angle pdb=" N   ASN A 122 "
        pdb=" CA  ASN A 122 "
        pdb=" C   ASN A 122 "
      ideal   model   delta    sigma   weight residual
     111.28  118.92   -7.64 1.09e+00 8.42e-01 4.91e+01
  angle pdb=" N   TYR F 473 "
        pdb=" CA  TYR F 473 "
        pdb=" C   TYR F 473 "
      ideal   model   delta    sigma   weight residual
     113.38  121.61   -8.23 1.23e+00 6.61e-01 4.47e+01
  angle pdb=" N   VAL A 130 "
        pdb=" CA  VAL A 130 "
        pdb=" C   VAL A 130 "
      ideal   model   delta    sigma   weight residual
     113.10  107.19    5.91 9.70e-01 1.06e+00 3.72e+01
  ... (remaining 5743 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 2217
       17.34 -    34.67: 241
       34.67 -    52.01: 47
       52.01 -    69.35: 5
       69.35 -    86.68: 4
  Dihedral angle restraints: 2514
    sinusoidal: 1022
      harmonic: 1492
  Sorted by residual:
  dihedral pdb=" CA  CYS F 336 "
           pdb=" C   CYS F 336 "
           pdb=" N   PRO F 337 "
           pdb=" CA  PRO F 337 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.94  -31.06     0      5.00e+00 4.00e-02 3.86e+01
  dihedral pdb=" CA  ASN F 360 "
           pdb=" C   ASN F 360 "
           pdb=" N   CYS F 361 "
           pdb=" CA  CYS F 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.27   25.73     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  PHE F 490 "
           pdb=" C   PHE F 490 "
           pdb=" N   PRO F 491 "
           pdb=" CA  PRO F 491 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.44  -21.56     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 2511 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 546
       0.095 -    0.190: 71
       0.190 -    0.284: 14
       0.284 -    0.379: 4
       0.379 -    0.474: 4
  Chirality restraints: 639
  Sorted by residual:
  chirality pdb=" CA  PRO A 217 "
            pdb=" N   PRO A 217 "
            pdb=" C   PRO A 217 "
            pdb=" CB  PRO A 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.24    0.47 2.00e-01 2.50e+01 5.61e+00
  chirality pdb=" CA  PHE F 429 "
            pdb=" N   PHE F 429 "
            pdb=" C   PHE F 429 "
            pdb=" CB  PHE F 429 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.42e+00
  chirality pdb=" CA  VAL F 350 "
            pdb=" N   VAL F 350 "
            pdb=" C   VAL F 350 "
            pdb=" CB  VAL F 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.03    0.42 2.00e-01 2.50e+01 4.32e+00
  ... (remaining 636 not shown)

  Planarity restraints: 739
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 403 "   -0.344 2.00e-02 2.50e+03   2.97e-01 1.10e+03
        pdb=" C7  NAG A 403 "    0.082 2.00e-02 2.50e+03
        pdb=" C8  NAG A 403 "   -0.135 2.00e-02 2.50e+03
        pdb=" N2  NAG A 403 "    0.529 2.00e-02 2.50e+03
        pdb=" O7  NAG A 403 "   -0.132 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 401 "   -0.316 2.00e-02 2.50e+03   2.74e-01 9.36e+02
        pdb=" C7  NAG A 401 "    0.071 2.00e-02 2.50e+03
        pdb=" C8  NAG A 401 "   -0.148 2.00e-02 2.50e+03
        pdb=" N2  NAG A 401 "    0.488 2.00e-02 2.50e+03
        pdb=" O7  NAG A 401 "   -0.096 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F 601 "   -0.276 2.00e-02 2.50e+03   2.30e-01 6.61e+02
        pdb=" C7  NAG F 601 "    0.076 2.00e-02 2.50e+03
        pdb=" C8  NAG F 601 "   -0.185 2.00e-02 2.50e+03
        pdb=" N2  NAG F 601 "    0.385 2.00e-02 2.50e+03
        pdb=" O7  NAG F 601 "    0.000 2.00e-02 2.50e+03
  ... (remaining 736 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1059
        2.79 -     3.32: 3382
        3.32 -     3.84: 6407
        3.84 -     4.37: 6913
        4.37 -     4.90: 12570
  Nonbonded interactions: 30331
  Sorted by model distance:
  nonbonded pdb=" O   THR A  51 "
            pdb=" OG1 THR A 274 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" N   ARG A 214 "
            pdb=" O   ARG A 214 "
     model   vdw
     2.271 2.496
  nonbonded pdb=" O   ASP A 290 "
            pdb=" OG  SER A 297 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OG  SER F 383 "
            pdb=" O   THR F 385 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   SER B 103 "
            pdb=" OG  SER B 103 "
     model   vdw
     2.286 3.040
  ... (remaining 30326 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             26.840
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.890
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
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      :  0.008   0.100   4240  Z= 0.489
  Angle     :  1.144  25.464   5770  Z= 0.702
  Chirality :  0.079   0.474    639
  Planarity :  0.019   0.297    735
  Dihedral  : 14.361  86.684   1547
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 12.87 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    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: -4.63 (0.29), residues: 499
  helix: -5.03 (0.29), residues: 24
  sheet: -3.31 (0.33), residues: 154
  loop : -2.90 (0.28), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP F 436 
 HIS   0.004   0.001   HIS B  30 
 PHE   0.036   0.002   PHE F 400 
 TYR   0.020   0.002   TYR F 351 
 ARG   0.002   0.001   ARG F 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00206 (    4)
  link_NAG-ASN         : angle       1.39048 (   12)
  hydrogen bonds       : bond        0.31823 (   92)
  hydrogen bonds       : angle      10.91849 (  219)
  SS BOND              : bond        0.01196 (    5)
  SS BOND              : angle       2.83083 (   10)
  covalent geometry    : bond        0.00788 ( 4231)
  covalent geometry    : angle       1.13860 ( 5748)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 128
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 LYS cc_start: 0.7900 (mttm) cc_final: 0.7665 (tmtt)
REVERT: B   39 GLN cc_start: 0.6561 (tt0) cc_final: 0.6258 (pp30)
REVERT: B  115 TRP cc_start: 0.7598 (m100) cc_final: 0.7101 (m100)
REVERT: F  355 ARG cc_start: 0.8556 (ttt90) cc_final: 0.8178 (ttm-80)
REVERT: F  449 TYR cc_start: 0.8004 (m-80) cc_final: 0.7562 (m-80)
REVERT: F  456 PHE cc_start: 0.8398 (m-80) cc_final: 0.8031 (m-80)
REVERT: F  498 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7866 (mm-40)
  outliers start: 2
  outliers final: 0
  residues processed: 129
  average time/residue: 0.2398
  time to fit residues: 36.0748
Evaluate side-chains
  90 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
B  30 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.150151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.120305 restraints weight = 6366.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.123466 restraints weight = 4682.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.124461 restraints weight = 3258.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4240  Z= 0.154
  Angle     :  0.695   9.118   5770  Z= 0.355
  Chirality :  0.046   0.168    639
  Planarity :  0.005   0.061    735
  Dihedral  :  6.618  58.940    646
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 18.74 %
    Favored  : 76.98 %
  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: -4.01 (0.33), residues: 499
  helix: -4.51 (0.44), residues: 30
  sheet: -2.67 (0.34), residues: 186
  loop : -2.43 (0.33), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP F 436 
 HIS   0.005   0.001   HIS B  30 
 PHE   0.021   0.002   PHE F 338 
 TYR   0.015   0.001   TYR B  80 
 ARG   0.006   0.001   ARG A 273 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00408 (    4)
  link_NAG-ASN         : angle       2.54037 (   12)
  hydrogen bonds       : bond        0.04237 (   92)
  hydrogen bonds       : angle       7.56468 (  219)
  SS BOND              : bond        0.00655 (    5)
  SS BOND              : angle       1.14151 (   10)
  covalent geometry    : bond        0.00355 ( 4231)
  covalent geometry    : angle       0.68493 ( 5748)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.472 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7955 (mttm) cc_final: 0.7702 (tmtt)
REVERT: A   91 TYR cc_start: 0.9068 (t80) cc_final: 0.8826 (t80)
REVERT: A  129 LYS cc_start: 0.7370 (ttpt) cc_final: 0.7160 (ttpt)
REVERT: A  227 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8439 (m)
REVERT: A  275 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7649 (m-10)
REVERT: B   20 LEU cc_start: 0.8442 (mm) cc_final: 0.8128 (mm)
REVERT: B   38 ARG cc_start: 0.7841 (ptm160) cc_final: 0.7153 (tmm-80)
REVERT: B   39 GLN cc_start: 0.6273 (tt0) cc_final: 0.5513 (pp30)
REVERT: B   46 GLU cc_start: 0.6858 (tp30) cc_final: 0.6560 (tp30)
REVERT: B   95 TYR cc_start: 0.8222 (m-80) cc_final: 0.7873 (m-80)
REVERT: B  115 TRP cc_start: 0.7649 (m100) cc_final: 0.7318 (m100)
REVERT: F  338 PHE cc_start: 0.8122 (p90) cc_final: 0.7872 (p90)
REVERT: F  355 ARG cc_start: 0.8255 (ttt90) cc_final: 0.7882 (ttm-80)
REVERT: F  417 LYS cc_start: 0.8153 (ttmt) cc_final: 0.7925 (ttpp)
REVERT: F  421 TYR cc_start: 0.8409 (m-10) cc_final: 0.8200 (m-80)
REVERT: F  444 LYS cc_start: 0.7175 (tptp) cc_final: 0.6868 (tptp)
REVERT: F  449 TYR cc_start: 0.7894 (m-80) cc_final: 0.7370 (m-80)
REVERT: F  456 PHE cc_start: 0.8375 (m-80) cc_final: 0.8087 (m-80)
REVERT: F  465 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8028 (mt-10)
REVERT: F  498 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7709 (mm-40)
  outliers start: 19
  outliers final: 8
  residues processed: 121
  average time/residue: 0.2922
  time to fit residues: 41.2322
Evaluate side-chains
  98 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  465 GLU
Chi-restraints excluded: chain F residue  510 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0970
   chunk 5 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0060
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
B  30 HIS
F 422 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.154810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.125466 restraints weight = 6404.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.127984 restraints weight = 3736.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.130097 restraints weight = 3086.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4240  Z= 0.126
  Angle     :  0.639   9.916   5770  Z= 0.325
  Chirality :  0.044   0.155    639
  Planarity :  0.004   0.043    735
  Dihedral  :  5.464  36.943    646
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 21.44 %
    Favored  : 74.27 %
  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: -3.72 (0.33), residues: 499
  helix: -4.29 (0.48), residues: 30
  sheet: -2.30 (0.35), residues: 178
  loop : -2.40 (0.33), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 436 
 HIS   0.005   0.001   HIS B  30 
 PHE   0.015   0.001   PHE F 338 
 TYR   0.020   0.001   TYR A 170 
 ARG   0.009   0.001   ARG F 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00165 (    4)
  link_NAG-ASN         : angle       1.80538 (   12)
  hydrogen bonds       : bond        0.03384 (   92)
  hydrogen bonds       : angle       6.84564 (  219)
  SS BOND              : bond        0.00207 (    5)
  SS BOND              : angle       1.46883 (   10)
  covalent geometry    : bond        0.00295 ( 4231)
  covalent geometry    : angle       0.63177 ( 5748)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.802 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7999 (mttm) cc_final: 0.7704 (tmtt)
REVERT: A   91 TYR cc_start: 0.9028 (t80) cc_final: 0.8823 (t80)
REVERT: A  170 TYR cc_start: 0.7357 (t80) cc_final: 0.7129 (t80)
REVERT: B   20 LEU cc_start: 0.8591 (mm) cc_final: 0.8346 (mm)
REVERT: B   38 ARG cc_start: 0.7960 (ptm160) cc_final: 0.7253 (tmm-80)
REVERT: B   39 GLN cc_start: 0.6175 (tt0) cc_final: 0.5421 (pp30)
REVERT: B   46 GLU cc_start: 0.6806 (tp30) cc_final: 0.6575 (tp30)
REVERT: B   95 TYR cc_start: 0.8213 (m-80) cc_final: 0.7852 (m-80)
REVERT: B  115 TRP cc_start: 0.7630 (m100) cc_final: 0.7357 (m100)
REVERT: F  408 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7064 (ptp90)
REVERT: F  417 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7921 (ttpp)
REVERT: F  444 LYS cc_start: 0.7205 (tptp) cc_final: 0.6885 (tptp)
REVERT: F  449 TYR cc_start: 0.7826 (m-80) cc_final: 0.7288 (m-80)
REVERT: F  498 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7712 (mm-40)
  outliers start: 19
  outliers final: 11
  residues processed: 105
  average time/residue: 0.2887
  time to fit residues: 35.9564
Evaluate side-chains
  98 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  500 THR
Chi-restraints excluded: chain F residue  510 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 7 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0000
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 43 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
B  30 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.154924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.125347 restraints weight = 6419.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.127714 restraints weight = 3852.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.129657 restraints weight = 3304.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4240  Z= 0.125
  Angle     :  0.604   8.063   5770  Z= 0.307
  Chirality :  0.044   0.155    639
  Planarity :  0.004   0.037    735
  Dihedral  :  5.326  43.820    646
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 25.28 %
    Favored  : 71.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.54 (0.34), residues: 499
  helix: -4.09 (0.51), residues: 30
  sheet: -2.25 (0.35), residues: 181
  loop : -2.22 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 436 
 HIS   0.006   0.001   HIS B  30 
 PHE   0.018   0.001   PHE F 338 
 TYR   0.017   0.001   TYR B  60 
 ARG   0.007   0.001   ARG F 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00152 (    4)
  link_NAG-ASN         : angle       1.76771 (   12)
  hydrogen bonds       : bond        0.03030 (   92)
  hydrogen bonds       : angle       6.49630 (  219)
  SS BOND              : bond        0.00267 (    5)
  SS BOND              : angle       1.28584 (   10)
  covalent geometry    : bond        0.00293 ( 4231)
  covalent geometry    : angle       0.59778 ( 5748)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 LYS cc_start: 0.8002 (mttm) cc_final: 0.7712 (tmtt)
REVERT: B   20 LEU cc_start: 0.8566 (mm) cc_final: 0.8201 (mm)
REVERT: B   38 ARG cc_start: 0.7970 (ptm160) cc_final: 0.7230 (tmm-80)
REVERT: B   95 TYR cc_start: 0.8155 (m-80) cc_final: 0.7736 (m-80)
REVERT: F  417 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7989 (ttpp)
REVERT: F  421 TYR cc_start: 0.8408 (m-10) cc_final: 0.8100 (m-10)
REVERT: F  444 LYS cc_start: 0.7236 (tptp) cc_final: 0.6944 (tptp)
REVERT: F  449 TYR cc_start: 0.7790 (m-80) cc_final: 0.7263 (m-80)
REVERT: F  454 ARG cc_start: 0.7910 (ttm170) cc_final: 0.7628 (mtm180)
REVERT: F  498 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7760 (mm-40)
  outliers start: 15
  outliers final: 12
  residues processed: 98
  average time/residue: 0.4090
  time to fit residues: 49.3454
Evaluate side-chains
  91 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  392 PHE
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  500 THR
Chi-restraints excluded: chain F residue  510 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
B  30 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.151255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.121396 restraints weight = 6574.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.124255 restraints weight = 4126.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.126446 restraints weight = 3206.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4240  Z= 0.178
  Angle     :  0.638   7.084   5770  Z= 0.328
  Chirality :  0.045   0.153    639
  Planarity :  0.004   0.047    735
  Dihedral  :  5.847  53.774    646
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 24.83 %
    Favored  : 71.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.51 (0.34), residues: 499
  helix: -3.97 (0.55), residues: 30
  sheet: -2.42 (0.34), residues: 186
  loop : -2.05 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP F 353 
 HIS   0.006   0.001   HIS B  30 
 PHE   0.015   0.002   PHE F 338 
 TYR   0.027   0.002   TYR A 170 
 ARG   0.007   0.001   ARG F 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00147 (    4)
  link_NAG-ASN         : angle       1.94838 (   12)
  hydrogen bonds       : bond        0.03207 (   92)
  hydrogen bonds       : angle       6.66970 (  219)
  SS BOND              : bond        0.00321 (    5)
  SS BOND              : angle       1.49154 (   10)
  covalent geometry    : bond        0.00421 ( 4231)
  covalent geometry    : angle       0.62973 ( 5748)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.469 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.8031 (mttm) cc_final: 0.7746 (tmtt)
REVERT: A  129 LYS cc_start: 0.7444 (ttpt) cc_final: 0.6944 (tttm)
REVERT: A  275 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7636 (m-10)
REVERT: B   20 LEU cc_start: 0.8647 (mm) cc_final: 0.8290 (mm)
REVERT: B   38 ARG cc_start: 0.8073 (ptm160) cc_final: 0.7327 (tmm-80)
REVERT: F  364 ASP cc_start: 0.7953 (p0) cc_final: 0.7578 (p0)
REVERT: F  417 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7971 (ttpp)
REVERT: F  449 TYR cc_start: 0.7795 (m-80) cc_final: 0.7254 (m-80)
  outliers start: 17
  outliers final: 12
  residues processed: 96
  average time/residue: 0.2252
  time to fit residues: 25.6172
Evaluate side-chains
  88 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  392 PHE
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0870
   chunk 26 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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 = 0.3834 r_free = 0.3834 target = 0.153545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.123961 restraints weight = 6411.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.126887 restraints weight = 4002.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.128954 restraints weight = 3162.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.3736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4240  Z= 0.138
  Angle     :  0.598   6.778   5770  Z= 0.309
  Chirality :  0.044   0.146    639
  Planarity :  0.004   0.027    735
  Dihedral  :  5.037  26.054    646
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 25.28 %
    Favored  : 70.88 %
  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: -3.39 (0.35), residues: 499
  helix: -3.76 (0.62), residues: 30
  sheet: -2.36 (0.35), residues: 181
  loop : -1.98 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 353 
 HIS   0.001   0.000   HIS A  49 
 PHE   0.018   0.001   PHE F 400 
 TYR   0.027   0.002   TYR F 423 
 ARG   0.006   0.001   ARG A  34 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00155 (    4)
  link_NAG-ASN         : angle       1.62634 (   12)
  hydrogen bonds       : bond        0.02969 (   92)
  hydrogen bonds       : angle       6.31957 (  219)
  SS BOND              : bond        0.00287 (    5)
  SS BOND              : angle       1.26469 (   10)
  covalent geometry    : bond        0.00326 ( 4231)
  covalent geometry    : angle       0.59199 ( 5748)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.429 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7986 (mttm) cc_final: 0.7731 (tmtt)
REVERT: B    3 GLN cc_start: 0.8611 (pm20) cc_final: 0.8403 (pm20)
REVERT: B   20 LEU cc_start: 0.8618 (mm) cc_final: 0.8292 (mm)
REVERT: B   38 ARG cc_start: 0.8022 (ptm160) cc_final: 0.7324 (tmm-80)
REVERT: F  417 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7911 (ttpp)
REVERT: F  449 TYR cc_start: 0.7850 (m-80) cc_final: 0.7341 (m-80)
  outliers start: 17
  outliers final: 13
  residues processed: 92
  average time/residue: 0.2242
  time to fit residues: 24.3858
Evaluate side-chains
  82 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  392 PHE
Chi-restraints excluded: chain F residue  402 ILE
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0670
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.7118

-------------------------------------------------------------------------------
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 = 0.153166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.123695 restraints weight = 6395.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.126189 restraints weight = 3952.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.128148 restraints weight = 3312.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.3812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4240  Z= 0.144
  Angle     :  0.595   7.218   5770  Z= 0.308
  Chirality :  0.044   0.146    639
  Planarity :  0.004   0.043    735
  Dihedral  :  4.888  22.440    646
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 26.19 %
    Favored  : 69.75 %
  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: -3.34 (0.35), residues: 499
  helix: -3.69 (0.63), residues: 30
  sheet: -2.32 (0.36), residues: 181
  loop : -1.95 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F 436 
 HIS   0.001   0.000   HIS B  30 
 PHE   0.019   0.001   PHE F 400 
 TYR   0.025   0.002   TYR F 423 
 ARG   0.011   0.001   ARG A  34 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00163 (    4)
  link_NAG-ASN         : angle       1.51658 (   12)
  hydrogen bonds       : bond        0.02913 (   92)
  hydrogen bonds       : angle       6.25889 (  219)
  SS BOND              : bond        0.00254 (    5)
  SS BOND              : angle       1.23594 (   10)
  covalent geometry    : bond        0.00342 ( 4231)
  covalent geometry    : angle       0.59005 ( 5748)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.476 
Fit side-chains
REVERT: A  129 LYS cc_start: 0.7498 (ttpt) cc_final: 0.7218 (tttt)
REVERT: A  275 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7644 (m-10)
REVERT: B    3 GLN cc_start: 0.8596 (pm20) cc_final: 0.8353 (pm20)
REVERT: B   20 LEU cc_start: 0.8639 (mm) cc_final: 0.8314 (mm)
REVERT: B   38 ARG cc_start: 0.8056 (ptm160) cc_final: 0.7389 (tmm-80)
REVERT: F  417 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7896 (ttpp)
REVERT: F  449 TYR cc_start: 0.7859 (m-80) cc_final: 0.7357 (m-80)
  outliers start: 18
  outliers final: 15
  residues processed: 90
  average time/residue: 0.2059
  time to fit residues: 22.3378
Evaluate side-chains
  86 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  392 PHE
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  30 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.153036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.124442 restraints weight = 6430.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.126747 restraints weight = 4056.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.128040 restraints weight = 3597.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4240  Z= 0.154
  Angle     :  0.615   7.336   5770  Z= 0.318
  Chirality :  0.044   0.146    639
  Planarity :  0.004   0.042    735
  Dihedral  :  4.843  21.250    646
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 26.19 %
    Favored  : 69.75 %
  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: -3.31 (0.35), residues: 499
  helix: -3.77 (0.59), residues: 30
  sheet: -2.30 (0.36), residues: 181
  loop : -1.92 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP F 436 
 HIS   0.006   0.001   HIS B  30 
 PHE   0.018   0.001   PHE F 400 
 TYR   0.027   0.002   TYR F 423 
 ARG   0.012   0.001   ARG A  34 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00156 (    4)
  link_NAG-ASN         : angle       1.48110 (   12)
  hydrogen bonds       : bond        0.02918 (   92)
  hydrogen bonds       : angle       6.24317 (  219)
  SS BOND              : bond        0.00268 (    5)
  SS BOND              : angle       1.24524 (   10)
  covalent geometry    : bond        0.00367 ( 4231)
  covalent geometry    : angle       0.61036 ( 5748)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.473 
Fit side-chains
REVERT: A   91 TYR cc_start: 0.9129 (t80) cc_final: 0.8819 (t80)
REVERT: A  129 LYS cc_start: 0.7541 (ttpt) cc_final: 0.7245 (tttt)
REVERT: A  226 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7943 (tp)
REVERT: A  275 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7663 (m-10)
REVERT: B    3 GLN cc_start: 0.8604 (pm20) cc_final: 0.8378 (pm20)
REVERT: B   20 LEU cc_start: 0.8560 (mm) cc_final: 0.8261 (mm)
REVERT: B   30 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.7661 (m-70)
REVERT: B   38 ARG cc_start: 0.8097 (ptm160) cc_final: 0.7422 (tmm-80)
REVERT: F  498 GLN cc_start: 0.8135 (mm110) cc_final: 0.7929 (mm-40)
  outliers start: 18
  outliers final: 14
  residues processed: 89
  average time/residue: 0.2068
  time to fit residues: 22.1298
Evaluate side-chains
  85 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue   30 HIS
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain F residue  383 SER
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  392 PHE
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 1 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B  30 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.153614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.124256 restraints weight = 6482.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.127148 restraints weight = 3953.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.128587 restraints weight = 3246.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.4039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4240  Z= 0.145
  Angle     :  0.619   7.526   5770  Z= 0.318
  Chirality :  0.044   0.145    639
  Planarity :  0.004   0.043    735
  Dihedral  :  4.769  20.913    646
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 26.86 %
    Favored  : 69.07 %
  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: -3.30 (0.35), residues: 499
  helix: -3.65 (0.62), residues: 30
  sheet: -2.31 (0.35), residues: 184
  loop : -1.90 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 436 
 HIS   0.010   0.001   HIS B  30 
 PHE   0.017   0.001   PHE F 400 
 TYR   0.031   0.002   TYR F 423 
 ARG   0.007   0.001   ARG A  34 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00156 (    4)
  link_NAG-ASN         : angle       1.40188 (   12)
  hydrogen bonds       : bond        0.02855 (   92)
  hydrogen bonds       : angle       6.14814 (  219)
  SS BOND              : bond        0.00234 (    5)
  SS BOND              : angle       1.21140 (   10)
  covalent geometry    : bond        0.00351 ( 4231)
  covalent geometry    : angle       0.61470 ( 5748)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A   91 TYR cc_start: 0.9116 (t80) cc_final: 0.8826 (t80)
REVERT: A  129 LYS cc_start: 0.7490 (ttpt) cc_final: 0.7212 (tttt)
REVERT: A  275 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7632 (m-10)
REVERT: B    3 GLN cc_start: 0.8573 (pm20) cc_final: 0.8323 (pm20)
REVERT: B   20 LEU cc_start: 0.8610 (mm) cc_final: 0.8303 (mm)
  outliers start: 18
  outliers final: 15
  residues processed: 90
  average time/residue: 0.2196
  time to fit residues: 23.5925
Evaluate side-chains
  88 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain F residue  383 SER
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  392 PHE
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0870
   chunk 20 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
B  30 HIS
** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.154497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.125976 restraints weight = 6382.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.128185 restraints weight = 3956.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.129283 restraints weight = 3629.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.4205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4240  Z= 0.137
  Angle     :  0.633   7.477   5770  Z= 0.324
  Chirality :  0.044   0.161    639
  Planarity :  0.004   0.041    735
  Dihedral  :  4.700  21.025    646
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 27.77 %
    Favored  : 68.85 %
  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: -3.21 (0.35), residues: 499
  helix: -3.58 (0.64), residues: 30
  sheet: -2.25 (0.36), residues: 182
  loop : -1.85 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 436 
 HIS   0.006   0.001   HIS B  30 
 PHE   0.017   0.001   PHE F 338 
 TYR   0.039   0.002   TYR A 170 
 ARG   0.007   0.001   ARG F 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00162 (    4)
  link_NAG-ASN         : angle       1.28678 (   12)
  hydrogen bonds       : bond        0.02876 (   92)
  hydrogen bonds       : angle       6.01548 (  219)
  SS BOND              : bond        0.00230 (    5)
  SS BOND              : angle       1.15205 (   10)
  covalent geometry    : bond        0.00331 ( 4231)
  covalent geometry    : angle       0.63008 ( 5748)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.417 
Fit side-chains
REVERT: A  129 LYS cc_start: 0.7467 (ttpt) cc_final: 0.7211 (tttt)
REVERT: A  309 GLU cc_start: 0.7839 (mp0) cc_final: 0.7637 (mp0)
REVERT: B    3 GLN cc_start: 0.8553 (pm20) cc_final: 0.8320 (pm20)
REVERT: B   20 LEU cc_start: 0.8538 (mm) cc_final: 0.8267 (mm)
REVERT: F  408 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7225 (ptp90)
REVERT: F  449 TYR cc_start: 0.7925 (m-80) cc_final: 0.7469 (m-80)
  outliers start: 15
  outliers final: 14
  residues processed: 90
  average time/residue: 0.1847
  time to fit residues: 20.2777
Evaluate side-chains
  88 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  392 PHE
Chi-restraints excluded: chain F residue  408 ARG
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.153270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.124679 restraints weight = 6444.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.126813 restraints weight = 4108.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.128051 restraints weight = 3712.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.4251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4240  Z= 0.160
  Angle     :  0.659   7.425   5770  Z= 0.337
  Chirality :  0.045   0.159    639
  Planarity :  0.004   0.034    735
  Dihedral  :  4.917  23.734    646
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 27.09 %
    Favored  : 69.07 %
  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: -3.14 (0.35), residues: 499
  helix: -3.55 (0.64), residues: 30
  sheet: -2.13 (0.35), residues: 186
  loop : -1.85 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP F 436 
 HIS   0.001   0.000   HIS A  66 
 PHE   0.019   0.001   PHE F 400 
 TYR   0.035   0.002   TYR A 170 
 ARG   0.007   0.001   ARG F 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00137 (    4)
  link_NAG-ASN         : angle       1.42854 (   12)
  hydrogen bonds       : bond        0.02962 (   92)
  hydrogen bonds       : angle       6.17378 (  219)
  SS BOND              : bond        0.00259 (    5)
  SS BOND              : angle       1.24705 (   10)
  covalent geometry    : bond        0.00386 ( 4231)
  covalent geometry    : angle       0.65479 ( 5748)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2268.88 seconds
wall clock time: 41 minutes 1.61 seconds (2461.61 seconds total)