Starting phenix.real_space_refine
on Tue Feb  3 18:07:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xgo_66856/02_2026/9xgo_66856.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xgo_66856/02_2026/9xgo_66856.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9xgo_66856/02_2026/9xgo_66856.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xgo_66856/02_2026/9xgo_66856.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xgo_66856/02_2026/9xgo_66856.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xgo_66856/02_2026/9xgo_66856.map"
  }
  resolution = 3.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.038
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      26      5.16       5
     C    3734      2.51       5
     N     969      2.21       5
     O    1130      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5859
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "H"
      Number of atoms: 938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 938
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
    Chain: "L"
      Number of atoms: 822
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 822
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 4, 'TRANS': 107}
    Chain: "N"
      Number of atoms: 2228
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2228
          Classifications: {'peptide': 276}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 263}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 1773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1773
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 207}
    Chain: "N"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "R"
      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: 1.78, per 1000 atoms: 0.30
  Number of scatterers: 5859
  At special positions: 0
  Unit cell: (116.64, 88.56, 87.48, 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      26     16.00
     O    1130      8.00
     N     969      7.00
     C    3734      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  21 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  15 " - pdb=" SG  CYS N 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 131 " - pdb=" SG  CYS N 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 291 " - pdb=" SG  CYS N 301 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 391 " - pdb=" SG  CYS R 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 480 " - pdb=" SG  CYS R 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG N 401 " - " ASN N 165 "
      " NAG N 402 " - " ASN N 122 "
      " NAG N 403 " - " ASN N  61 "
      " NAG N 404 " - " ASN N 234 "
      " NAG N 405 " - " ASN N 282 "
      " NAG N 406 " - " ASN N  74 "
      " NAG R 601 " - " ASN R 343 "
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 389.4 milliseconds
  

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1352

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 14 sheets defined
      7.0% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'L' and resid 25 through 32
      removed outlier: 3.786A  pdb=" N   TYR L  32 " --> pdb=" O   ASP L  28 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 81 through 86
      removed outlier: 4.105A  pdb=" N   ALA L  86 " --> pdb=" O   GLU L  83 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 294 through 302
    Processing helix  chain 'R' and resid 349 through 353
      removed outlier: 3.748A  pdb=" N   TRP R 353 " --> pdb=" O   VAL R 350 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 365 through 372
      removed outlier: 3.724A  pdb=" N   TYR R 369 " --> pdb=" O   TYR R 365 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ALA R 372 " --> pdb=" O   ILE R 368 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 383 through 388
      removed outlier: 4.011A  pdb=" N   ASN R 388 " --> pdb=" O   PRO R 384 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 403 through 411
      removed outlier: 3.582A  pdb=" N   VAL R 407 " --> pdb=" O   GLY R 404 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   SER R 408 " --> pdb=" O   ASN R 405 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE R 410 " --> pdb=" O   VAL R 407 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 5
    Processing sheet with id=AA2, first strand: chain 'H' and resid 9 through 11
      removed outlier: 3.683A  pdb=" N   GLU H   9 " --> pdb=" O   LEU H 116 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLN H  38 " --> pdb=" O   VAL H  92 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   TRP H  35 " --> pdb=" O   MET H  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 11
      removed outlier: 3.683A  pdb=" N   GLU H   9 " --> pdb=" O   LEU H 116 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 11 through 12
    Processing sheet with id=AA5, first strand: chain 'L' and resid 39 through 40
    Processing sheet with id=AA6, first strand: chain 'L' and resid 91 through 93
      removed outlier: 3.547A  pdb=" N   LEU L 100 " --> pdb=" O   SER L  92 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'N' and resid 20 through 22
      removed outlier: 3.597A  pdb=" N   THR N  22 " --> pdb=" O   HIS N  66 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   HIS N  66 " --> pdb=" O   THR N  22 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 28 through 31
      removed outlier: 3.809A  pdb=" N   SER N  60 " --> pdb=" O   SER N  31 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 48 through 49
      removed outlier: 3.705A  pdb=" N   ASP N 287 " --> pdb=" O   LYS N 278 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 52 through 55
    Processing sheet with id=AB2, first strand: chain 'N' and resid 103 through 104
      removed outlier: 3.649A  pdb=" N   GLY N 103 " --> pdb=" O   LEU N 241 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLU N 154 " --> pdb=" O   TYR N 145 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 189 through 197
      removed outlier: 4.144A  pdb=" N   THR N 208 " --> pdb=" O   LEU N 189 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL N 193 " --> pdb=" O   TYR N 204 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   PHE N 201 " --> pdb=" O   ASP N 228 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   ASP N 228 " --> pdb=" O   PHE N 201 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   ILE N 203 " --> pdb=" O   LEU N 226 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 355 through 358
      removed outlier: 3.642A  pdb=" N   TYR R 396 " --> pdb=" O   SER R 514 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 452 through 454

    98 hydrogen bonds defined for protein.
    225 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: 0.84

  Time building geometry restraints manager: 0.74 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: 1843
        1.34 -     1.46: 1393
        1.46 -     1.57: 2740
        1.57 -     1.69: 0
        1.69 -     1.81: 33
  Bond restraints: 6009
  Sorted by residual:
  bond pdb=" C1  NAG R 601 "
       pdb=" O5  NAG R 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 2.02e+00
  bond pdb=" C1  NAG N 404 "
       pdb=" O5  NAG N 404 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.95e+00
  bond pdb=" CG  LEU N 216 "
       pdb=" CD1 LEU N 216 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.91e+00
  bond pdb=" C1  NAG N 405 "
       pdb=" O5  NAG N 405 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.61e+00
  bond pdb=" C1  NAG N 403 "
       pdb=" O5  NAG N 403 "
    ideal  model  delta    sigma   weight residual
    1.406  1.430 -0.024 2.00e-02 2.50e+03 1.49e+00
  ... (remaining 6004 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 7914
        1.91 -     3.81: 216
        3.81 -     5.72: 27
        5.72 -     7.63: 7
        7.63 -     9.54: 1
  Bond angle restraints: 8165
  Sorted by residual:
  angle pdb=" CA  ARG R 403 "
        pdb=" CB  ARG R 403 "
        pdb=" CG  ARG R 403 "
      ideal   model   delta    sigma   weight residual
     114.10  121.72   -7.62 2.00e+00 2.50e-01 1.45e+01
  angle pdb=" N   SER R 438 "
        pdb=" CA  SER R 438 "
        pdb=" C   SER R 438 "
      ideal   model   delta    sigma   weight residual
     114.09  109.22    4.87 1.55e+00 4.16e-01 9.86e+00
  angle pdb=" N   CYS R 391 "
        pdb=" CA  CYS R 391 "
        pdb=" C   CYS R 391 "
      ideal   model   delta    sigma   weight residual
     108.60  113.06   -4.46 1.46e+00 4.69e-01 9.34e+00
  angle pdb=" CA  CYS R 391 "
        pdb=" CB  CYS R 391 "
        pdb=" SG  CYS R 391 "
      ideal   model   delta    sigma   weight residual
     114.40  121.27   -6.87 2.30e+00 1.89e-01 8.92e+00
  angle pdb=" C   THR N  76 "
        pdb=" N   LYS N  77 "
        pdb=" CA  LYS N  77 "
      ideal   model   delta    sigma   weight residual
     121.54  127.18   -5.64 1.91e+00 2.74e-01 8.71e+00
  ... (remaining 8160 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.98: 3227
       16.98 -    33.96: 314
       33.96 -    50.94: 63
       50.94 -    67.93: 13
       67.93 -    84.91: 7
  Dihedral angle restraints: 3624
    sinusoidal: 1500
      harmonic: 2124
  Sorted by residual:
  dihedral pdb=" CB  CYS R 391 "
           pdb=" SG  CYS R 391 "
           pdb=" SG  CYS R 525 "
           pdb=" CB  CYS R 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -2.47  -83.53     1      1.00e+01 1.00e-02 8.52e+01
  dihedral pdb=" CB  CYS N  15 "
           pdb=" SG  CYS N  15 "
           pdb=" SG  CYS N 136 "
           pdb=" CB  CYS N 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.34  -76.34     1      1.00e+01 1.00e-02 7.33e+01
  dihedral pdb=" CA  ASN N  81 "
           pdb=" C   ASN N  81 "
           pdb=" N   PRO N  82 "
           pdb=" CA  PRO N  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.26   35.74     0      5.00e+00 4.00e-02 5.11e+01
  ... (remaining 3621 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 805
       0.078 -    0.156: 96
       0.156 -    0.234: 4
       0.234 -    0.312: 0
       0.312 -    0.390: 1
  Chirality restraints: 906
  Sorted by residual:
  chirality pdb=" C1  NAG R 601 "
            pdb=" ND2 ASN R 343 "
            pdb=" C2  NAG R 601 "
            pdb=" O5  NAG R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.80e+00
  chirality pdb=" CB  THR N  33 "
            pdb=" CA  THR N  33 "
            pdb=" OG1 THR N  33 "
            pdb=" CG2 THR N  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  TYR N 265 "
            pdb=" N   TYR N 265 "
            pdb=" C   TYR N 265 "
            pdb=" CB  TYR N 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.22e-01
  ... (remaining 903 not shown)

  Planarity restraints: 1049
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN N  81 "    0.082 5.00e-02 4.00e+02   1.27e-01 2.56e+01
        pdb=" N   PRO N  82 "   -0.219 5.00e-02 4.00e+02
        pdb=" CA  PRO N  82 "    0.069 5.00e-02 4.00e+02
        pdb=" CD  PRO N  82 "    0.068 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR N 266 "    0.011 2.00e-02 2.50e+03   1.76e-02 6.18e+00
        pdb=" CG  TYR N 266 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR N 266 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR N 266 "    0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR N 266 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR N 266 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR N 266 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR N 266 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR N 265 "   -0.027 2.00e-02 2.50e+03   1.67e-02 5.55e+00
        pdb=" CG  TYR N 265 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR N 265 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR N 265 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR N 265 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR N 265 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR N 265 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR N 265 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1046 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 185
        2.68 -     3.23: 5979
        3.23 -     3.79: 8909
        3.79 -     4.34: 11932
        4.34 -     4.90: 19483
  Nonbonded interactions: 46488
  Sorted by model distance:
  nonbonded pdb=" O   THR L   5 "
            pdb=" OG1 THR L  23 "
     model   vdw
     2.119 3.040
  nonbonded pdb=" O   THR R 393 "
            pdb=" OG1 THR R 523 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" OG  SER L  65 "
            pdb=" OG1 THR L  76 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" OG1 THR L  94 "
            pdb=" O   SER L  96 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" OG  SER L  17 "
            pdb=" O   ASN R 481 "
     model   vdw
     2.189 3.040
  ... (remaining 46483 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:             4.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.230
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
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      :  0.005   0.046   6025  Z= 0.211
  Angle     :  0.768   9.537   8204  Z= 0.399
  Chirality :  0.049   0.390    906
  Planarity :  0.006   0.127   1042
  Dihedral  : 13.771  84.907   2245
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 19.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.68 %
    Favored  : 85.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.15 (0.31), residues: 722
  helix: -1.70 (0.86), residues: 33
  sheet: -1.98 (0.41), residues: 172
  loop : -2.31 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 403 
 TYR   0.038   0.002   TYR N 266 
 PHE   0.012   0.002   PHE N  79 
 TRP   0.011   0.002   TRP N  64 
 HIS   0.011   0.002   HIS N  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 6009)
  covalent geometry    : angle       0.74197 ( 8165)
  SS BOND              : bond        0.00254 (    9)
  SS BOND              : angle       2.74947 (   18)
  hydrogen bonds       : bond        0.27136 (   94)
  hydrogen bonds       : angle      10.42509 (  225)
  link_NAG-ASN         : bond        0.00575 (    7)
  link_NAG-ASN         : angle       3.11519 (   21)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.229 
Fit side-chains
REVERT: H   98 ASP cc_start: 0.9120 (p0) cc_final: 0.8791 (p0)
REVERT: H  107 TYR cc_start: 0.8593 (m-10) cc_final: 0.8375 (m-10)
REVERT: L   33 ASN cc_start: 0.9356 (t0) cc_final: 0.8961 (t0)
REVERT: R  424 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8430 (ttpp)
REVERT: R  461 LEU cc_start: 0.8942 (tt) cc_final: 0.8593 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0718
  time to fit residues: 9.7276
Evaluate side-chains
  80 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0870
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
H  59 ASN
** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 422 ASN ** 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 = 0.3733 r_free = 0.3733 target = 0.115960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.096036 restraints weight = 14546.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.098882 restraints weight = 8109.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.100768 restraints weight = 5586.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.101955 restraints weight = 4359.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.102824 restraints weight = 3704.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6025  Z= 0.140
  Angle     :  0.683   9.262   8204  Z= 0.353
  Chirality :  0.046   0.368    906
  Planarity :  0.005   0.092   1042
  Dihedral  :  6.685  51.586    949
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.88 %
    Favored  : 87.12 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.87 %
    Favored  : 87.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.11 (0.31), residues: 722
  helix: -1.98 (0.82), residues: 33
  sheet: -1.71 (0.41), residues: 177
  loop : -2.36 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  56 
 TYR   0.026   0.002   TYR L  51 
 PHE   0.012   0.001   PHE N 106 
 TRP   0.009   0.001   TRP N  64 
 HIS   0.005   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6009)
  covalent geometry    : angle       0.65970 ( 8165)
  SS BOND              : bond        0.00444 (    9)
  SS BOND              : angle       2.16099 (   18)
  hydrogen bonds       : bond        0.04242 (   94)
  hydrogen bonds       : angle       6.78194 (  225)
  link_NAG-ASN         : bond        0.00568 (    7)
  link_NAG-ASN         : angle       2.96709 (   21)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.230 
Fit side-chains
REVERT: H  107 TYR cc_start: 0.8467 (m-10) cc_final: 0.8263 (m-10)
REVERT: L   33 ASN cc_start: 0.9316 (t0) cc_final: 0.8813 (t0)
REVERT: L   40 GLN cc_start: 0.8488 (tp40) cc_final: 0.7749 (tp40)
REVERT: N  142 ASP cc_start: 0.7468 (m-30) cc_final: 0.7180 (m-30)
REVERT: R  424 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8467 (ttpp)
  outliers start: 11
  outliers final: 9
  residues processed: 104
  average time/residue: 0.0659
  time to fit residues: 9.2250
Evaluate side-chains
  95 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   92 VAL
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain L residue   20 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   41 HIS
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain R residue  354 ASN
Chi-restraints excluded: chain R residue  401 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 47 optimal weight:    0.0980
   chunk 46 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 19 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0980
   chunk 67 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  81 ASN
** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 417 ASN
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.114164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.094051 restraints weight = 14504.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.096846 restraints weight = 8156.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.098664 restraints weight = 5664.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.099859 restraints weight = 4459.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.100684 restraints weight = 3787.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6025  Z= 0.165
  Angle     :  0.688   9.498   8204  Z= 0.353
  Chirality :  0.046   0.379    906
  Planarity :  0.005   0.068   1042
  Dihedral  :  6.324  51.834    949
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 13.30 %
    Favored  : 86.57 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.12 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.20 (0.31), residues: 722
  helix: -1.91 (0.82), residues: 33
  sheet: -1.74 (0.40), residues: 178
  loop : -2.45 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 403 
 TYR   0.028   0.002   TYR N 265 
 PHE   0.042   0.002   PHE N 157 
 TRP   0.009   0.001   TRP N  64 
 HIS   0.005   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 6009)
  covalent geometry    : angle       0.66562 ( 8165)
  SS BOND              : bond        0.00257 (    9)
  SS BOND              : angle       2.11106 (   18)
  hydrogen bonds       : bond        0.03723 (   94)
  hydrogen bonds       : angle       6.15529 (  225)
  link_NAG-ASN         : bond        0.00520 (    7)
  link_NAG-ASN         : angle       3.01061 (   21)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.236 
Fit side-chains
REVERT: L   16 GLN cc_start: 0.7971 (tp-100) cc_final: 0.7744 (tp-100)
REVERT: L   33 ASN cc_start: 0.9286 (t0) cc_final: 0.8761 (t0)
REVERT: N  142 ASP cc_start: 0.7547 (m-30) cc_final: 0.7296 (m-30)
REVERT: R  424 LYS cc_start: 0.8809 (ttpt) cc_final: 0.8504 (ttpp)
REVERT: R  461 LEU cc_start: 0.8882 (tt) cc_final: 0.8554 (tt)
  outliers start: 13
  outliers final: 9
  residues processed: 99
  average time/residue: 0.0706
  time to fit residues: 9.5831
Evaluate side-chains
  98 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   92 VAL
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain L residue   20 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   41 HIS
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain R residue  354 ASN
Chi-restraints excluded: chain R residue  401 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.113814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.093702 restraints weight = 14394.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.096494 restraints weight = 8200.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.098294 restraints weight = 5724.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.099464 restraints weight = 4512.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.100301 restraints weight = 3845.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6025  Z= 0.174
  Angle     :  0.690   9.467   8204  Z= 0.356
  Chirality :  0.047   0.386    906
  Planarity :  0.005   0.072   1042
  Dihedral  :  6.271  51.829    949
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.85 %
    Favored  : 86.15 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 16.54 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.23 (0.31), residues: 722
  helix: -1.82 (0.85), residues: 33
  sheet: -1.78 (0.40), residues: 178
  loop : -2.47 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 454 
 TYR   0.027   0.001   TYR N 265 
 PHE   0.018   0.002   PHE N 220 
 TRP   0.008   0.002   TRP N  64 
 HIS   0.005   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 6009)
  covalent geometry    : angle       0.66698 ( 8165)
  SS BOND              : bond        0.00261 (    9)
  SS BOND              : angle       2.13669 (   18)
  hydrogen bonds       : bond        0.03357 (   94)
  hydrogen bonds       : angle       5.95918 (  225)
  link_NAG-ASN         : bond        0.00536 (    7)
  link_NAG-ASN         : angle       3.06214 (   21)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.167 
Fit side-chains
REVERT: L   16 GLN cc_start: 0.8024 (tp-100) cc_final: 0.7777 (tp-100)
REVERT: L   33 ASN cc_start: 0.9225 (t0) cc_final: 0.8674 (t0)
REVERT: R  424 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8480 (ttpp)
  outliers start: 25
  outliers final: 12
  residues processed: 108
  average time/residue: 0.0666
  time to fit residues: 9.9087
Evaluate side-chains
  99 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   92 VAL
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain L residue   20 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   41 HIS
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  105 THR
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain N residue  175 PHE
Chi-restraints excluded: chain R residue  354 ASN
Chi-restraints excluded: chain R residue  401 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 51 optimal weight:    0.0970
   chunk 1 optimal weight:    0.3980
   chunk 17 optimal weight:    0.4980
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 54 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 67 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 417 ASN
** R 422 ASN ** 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 = 0.3748 r_free = 0.3748 target = 0.116776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.096820 restraints weight = 14581.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.099676 restraints weight = 8120.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.101579 restraints weight = 5623.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.102843 restraints weight = 4379.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.103668 restraints weight = 3685.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6025  Z= 0.126
  Angle     :  0.682  14.740   8204  Z= 0.346
  Chirality :  0.046   0.374    906
  Planarity :  0.004   0.056   1042
  Dihedral  :  5.975  53.586    949
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.88 %
    Favored  : 87.12 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.95 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.15 (0.31), residues: 722
  helix: -1.49 (0.92), residues: 33
  sheet: -1.93 (0.37), residues: 197
  loop : -2.33 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  56 
 TYR   0.026   0.001   TYR L  51 
 PHE   0.012   0.001   PHE N 106 
 TRP   0.007   0.001   TRP H 111 
 HIS   0.003   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6009)
  covalent geometry    : angle       0.65939 ( 8165)
  SS BOND              : bond        0.00203 (    9)
  SS BOND              : angle       1.97827 (   18)
  hydrogen bonds       : bond        0.02770 (   94)
  hydrogen bonds       : angle       5.59124 (  225)
  link_NAG-ASN         : bond        0.00551 (    7)
  link_NAG-ASN         : angle       3.01920 (   21)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.285 
Fit side-chains
REVERT: L   16 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7849 (tp-100)
REVERT: L   33 ASN cc_start: 0.9230 (t0) cc_final: 0.8672 (t0)
REVERT: L   37 TRP cc_start: 0.8696 (m100) cc_final: 0.8289 (m100)
  outliers start: 19
  outliers final: 12
  residues processed: 112
  average time/residue: 0.0708
  time to fit residues: 10.7816
Evaluate side-chains
  102 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain L residue   20 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   41 HIS
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  105 THR
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain R residue  354 ASN
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  539 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 12 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  81 ASN
** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 409 GLN
R 417 ASN
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.115058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.094879 restraints weight = 14476.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.097739 restraints weight = 8114.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.099608 restraints weight = 5621.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.100819 restraints weight = 4416.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.101640 restraints weight = 3748.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6025  Z= 0.160
  Angle     :  0.706  12.788   8204  Z= 0.363
  Chirality :  0.047   0.378    906
  Planarity :  0.005   0.095   1042
  Dihedral  :  6.100  52.497    949
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.57 %
    Favored  : 86.43 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.84 %
    Favored  : 77.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.14 (0.31), residues: 722
  helix: -1.51 (0.91), residues: 33
  sheet: -1.71 (0.39), residues: 178
  loop : -2.43 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 454 
 TYR   0.026   0.001   TYR L  51 
 PHE   0.020   0.002   PHE N 220 
 TRP   0.007   0.001   TRP R 436 
 HIS   0.005   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 6009)
  covalent geometry    : angle       0.68444 ( 8165)
  SS BOND              : bond        0.00252 (    9)
  SS BOND              : angle       2.00845 (   18)
  hydrogen bonds       : bond        0.02921 (   94)
  hydrogen bonds       : angle       5.62192 (  225)
  link_NAG-ASN         : bond        0.00528 (    7)
  link_NAG-ASN         : angle       2.99881 (   21)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.230 
Fit side-chains
REVERT: L   16 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7845 (tp-100)
REVERT: L   33 ASN cc_start: 0.9221 (t0) cc_final: 0.8631 (t0)
REVERT: R  424 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8345 (ttpp)
REVERT: R  461 LEU cc_start: 0.8783 (tp) cc_final: 0.8399 (tt)
  outliers start: 19
  outliers final: 15
  residues processed: 105
  average time/residue: 0.0639
  time to fit residues: 9.2229
Evaluate side-chains
  103 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain L residue   20 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   41 HIS
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  105 THR
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  175 PHE
Chi-restraints excluded: chain R residue  354 ASN
Chi-restraints excluded: chain R residue  391 CYS
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  525 CYS
Chi-restraints excluded: chain R residue  539 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 13 optimal weight:    7.9990
   chunk 26 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 16 optimal weight:    0.4980
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  81 ASN
** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 422 ASN ** 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 = 0.3673 r_free = 0.3673 target = 0.111931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.091611 restraints weight = 14721.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.094362 restraints weight = 8303.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.096151 restraints weight = 5807.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.097330 restraints weight = 4596.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.098017 restraints weight = 3920.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6025  Z= 0.229
  Angle     :  0.758  11.694   8204  Z= 0.389
  Chirality :  0.049   0.394    906
  Planarity :  0.006   0.101   1042
  Dihedral  :  6.475  51.280    949
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 14.82 %
    Favored  : 85.04 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 21.10 %
    Favored  : 75.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.19 (0.31), residues: 722
  helix: -1.69 (0.89), residues: 33
  sheet: -1.64 (0.40), residues: 167
  loop : -2.49 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  56 
 TYR   0.029   0.002   TYR N 265 
 PHE   0.036   0.002   PHE N 157 
 TRP   0.012   0.002   TRP N 258 
 HIS   0.006   0.002   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 6009)
  covalent geometry    : angle       0.73528 ( 8165)
  SS BOND              : bond        0.00316 (    9)
  SS BOND              : angle       2.27738 (   18)
  hydrogen bonds       : bond        0.03298 (   94)
  hydrogen bonds       : angle       5.82908 (  225)
  link_NAG-ASN         : bond        0.00538 (    7)
  link_NAG-ASN         : angle       3.17612 (   21)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.167 
Fit side-chains
REVERT: H  110 TYR cc_start: 0.7895 (m-80) cc_final: 0.7442 (m-80)
REVERT: L   16 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7850 (tp-100)
REVERT: L   33 ASN cc_start: 0.9226 (t0) cc_final: 0.8580 (t0)
REVERT: N  142 ASP cc_start: 0.7549 (m-30) cc_final: 0.7315 (m-30)
REVERT: R  424 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8315 (ttpp)
REVERT: R  461 LEU cc_start: 0.8703 (tp) cc_final: 0.8246 (tt)
  outliers start: 21
  outliers final: 14
  residues processed: 100
  average time/residue: 0.0722
  time to fit residues: 9.7512
Evaluate side-chains
  97 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain L residue   20 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   41 HIS
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  105 THR
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain R residue  354 ASN
Chi-restraints excluded: chain R residue  391 CYS
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  525 CYS
Chi-restraints excluded: chain R residue  539 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 13 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0570
   chunk 64 optimal weight:    5.9990
   chunk 33 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.116492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.096536 restraints weight = 14596.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.099378 restraints weight = 8122.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.101242 restraints weight = 5630.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.102447 restraints weight = 4406.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.103226 restraints weight = 3742.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6025  Z= 0.127
  Angle     :  0.711  14.232   8204  Z= 0.356
  Chirality :  0.047   0.377    906
  Planarity :  0.005   0.079   1042
  Dihedral  :  6.029  53.630    949
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 13.02 %
    Favored  : 86.84 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 21.57 %
    Favored  : 75.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.16 (0.31), residues: 722
  helix: -1.39 (0.92), residues: 34
  sheet: -1.97 (0.37), residues: 192
  loop : -2.33 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  86 
 TYR   0.025   0.001   TYR L  51 
 PHE   0.033   0.001   PHE N 157 
 TRP   0.009   0.001   TRP H 111 
 HIS   0.003   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6009)
  covalent geometry    : angle       0.69076 ( 8165)
  SS BOND              : bond        0.00231 (    9)
  SS BOND              : angle       1.91453 (   18)
  hydrogen bonds       : bond        0.02587 (   94)
  hydrogen bonds       : angle       5.50396 (  225)
  link_NAG-ASN         : bond        0.00573 (    7)
  link_NAG-ASN         : angle       2.99012 (   21)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.229 
Fit side-chains
REVERT: L   33 ASN cc_start: 0.9201 (t0) cc_final: 0.8586 (t0)
REVERT: L   38 TYR cc_start: 0.8202 (m-80) cc_final: 0.7980 (m-80)
REVERT: N  142 ASP cc_start: 0.7446 (m-30) cc_final: 0.7203 (m-30)
REVERT: N  153 MET cc_start: 0.8166 (mmt) cc_final: 0.7950 (mmm)
REVERT: R  461 LEU cc_start: 0.8580 (tp) cc_final: 0.8218 (tt)
  outliers start: 18
  outliers final: 15
  residues processed: 107
  average time/residue: 0.0693
  time to fit residues: 10.1057
Evaluate side-chains
  99 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain L residue   20 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   41 HIS
Chi-restraints excluded: chain L residue   53 VAL
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  105 THR
Chi-restraints excluded: chain N residue   79 PHE
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain R residue  354 ASN
Chi-restraints excluded: chain R residue  391 CYS
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  525 CYS
Chi-restraints excluded: chain R residue  539 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0670
   chunk 23 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 11 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 55 optimal weight:    0.2980
   overall best weight:    0.5520

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

Flipped N/Q/H residues before XYZ refinement:
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  81 ASN
** N 121 ASN ** 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 = 0.3753 r_free = 0.3753 target = 0.117144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.097000 restraints weight = 14698.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.099861 restraints weight = 8200.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.101752 restraints weight = 5679.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.102971 restraints weight = 4448.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.103782 restraints weight = 3772.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6025  Z= 0.130
  Angle     :  0.712  13.459   8204  Z= 0.356
  Chirality :  0.047   0.371    906
  Planarity :  0.005   0.075   1042
  Dihedral  :  5.920  53.715    949
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 12.60 %
    Favored  : 87.26 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 22.05 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.04 (0.31), residues: 722
  helix: -1.23 (0.93), residues: 34
  sheet: -1.91 (0.37), residues: 192
  loop : -2.24 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  86 
 TYR   0.026   0.001   TYR L  51 
 PHE   0.014   0.001   PHE R 392 
 TRP   0.006   0.001   TRP H 111 
 HIS   0.004   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6009)
  covalent geometry    : angle       0.69227 ( 8165)
  SS BOND              : bond        0.00202 (    9)
  SS BOND              : angle       1.89049 (   18)
  hydrogen bonds       : bond        0.02579 (   94)
  hydrogen bonds       : angle       5.37477 (  225)
  link_NAG-ASN         : bond        0.00553 (    7)
  link_NAG-ASN         : angle       2.92180 (   21)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.243 
Fit side-chains
REVERT: H   86 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7627 (tmm-80)
REVERT: L   33 ASN cc_start: 0.9198 (t0) cc_final: 0.8809 (t0)
REVERT: N  173 GLN cc_start: 0.8686 (tp40) cc_final: 0.8313 (tp40)
REVERT: N  303 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6593 (mm)
  outliers start: 17
  outliers final: 14
  residues processed: 100
  average time/residue: 0.0715
  time to fit residues: 9.9705
Evaluate side-chains
  100 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain L residue   20 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   41 HIS
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  105 THR
Chi-restraints excluded: chain N residue   79 PHE
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain N residue  303 LEU
Chi-restraints excluded: chain R residue  354 ASN
Chi-restraints excluded: chain R residue  391 CYS
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  525 CYS
Chi-restraints excluded: chain R residue  539 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 71 optimal weight:    0.0670
   chunk 37 optimal weight:    0.5980
   chunk 16 optimal weight:    0.1980
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0470
   chunk 45 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 13 optimal weight:    0.1980
   overall best weight:    0.2216

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

Flipped N/Q/H residues before XYZ refinement:
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.120758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.100990 restraints weight = 14535.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.103927 restraints weight = 8052.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.105831 restraints weight = 5519.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.107073 restraints weight = 4309.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.107823 restraints weight = 3639.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6025  Z= 0.119
  Angle     :  0.708  12.696   8204  Z= 0.355
  Chirality :  0.047   0.362    906
  Planarity :  0.005   0.064   1042
  Dihedral  :  5.744  54.380    949
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.08 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 22.52 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.94 (0.31), residues: 722
  helix: -0.12 (1.10), residues: 28
  sheet: -2.01 (0.37), residues: 193
  loop : -2.15 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG N  78 
 TYR   0.023   0.001   TYR L  51 
 PHE   0.036   0.001   PHE N 157 
 TRP   0.008   0.001   TRP H  46 
 HIS   0.002   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6009)
  covalent geometry    : angle       0.69079 ( 8165)
  SS BOND              : bond        0.00198 (    9)
  SS BOND              : angle       1.72674 (   18)
  hydrogen bonds       : bond        0.02322 (   94)
  hydrogen bonds       : angle       5.21212 (  225)
  link_NAG-ASN         : bond        0.00579 (    7)
  link_NAG-ASN         : angle       2.79106 (   21)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.250 
Fit side-chains
REVERT: H   86 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7601 (tmm-80)
REVERT: L   33 ASN cc_start: 0.9130 (t0) cc_final: 0.8705 (t0)
REVERT: L   37 TRP cc_start: 0.8539 (m100) cc_final: 0.8196 (m100)
REVERT: L   38 TYR cc_start: 0.8107 (m-80) cc_final: 0.7860 (m-80)
REVERT: L   52 ASP cc_start: 0.8572 (t0) cc_final: 0.8352 (t0)
REVERT: N   52 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8638 (tm-30)
REVERT: N  153 MET cc_start: 0.8011 (mmt) cc_final: 0.7756 (mmm)
REVERT: N  173 GLN cc_start: 0.8686 (tp40) cc_final: 0.8334 (tp40)
REVERT: N  303 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6585 (mm)
  outliers start: 14
  outliers final: 13
  residues processed: 113
  average time/residue: 0.0795
  time to fit residues: 12.0858
Evaluate side-chains
  107 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   99 ILE
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain L residue   20 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   41 HIS
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  105 THR
Chi-restraints excluded: chain N residue   79 PHE
Chi-restraints excluded: chain N residue  303 LEU
Chi-restraints excluded: chain R residue  354 ASN
Chi-restraints excluded: chain R residue  391 CYS
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  525 CYS
Chi-restraints excluded: chain R residue  539 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 55 optimal weight:    0.0770
   chunk 20 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 17 optimal weight:    0.1980
   chunk 51 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0170
   chunk 58 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0970
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.2574

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

Flipped N/Q/H residues before XYZ refinement:
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.121187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.101218 restraints weight = 14404.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.104147 restraints weight = 8102.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.106062 restraints weight = 5588.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.107287 restraints weight = 4365.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.108037 restraints weight = 3694.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.3266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6025  Z= 0.119
  Angle     :  0.703  12.778   8204  Z= 0.352
  Chirality :  0.047   0.358    906
  Planarity :  0.005   0.093   1042
  Dihedral  :  5.690  54.212    949
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.94 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 22.99 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.86 (0.31), residues: 722
  helix: -0.07 (1.10), residues: 28
  sheet: -1.49 (0.39), residues: 180
  loop : -2.32 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG N  78 
 TYR   0.030   0.001   TYR N 170 
 PHE   0.028   0.001   PHE R 456 
 TRP   0.008   0.001   TRP H  46 
 HIS   0.003   0.001   HIS R 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6009)
  covalent geometry    : angle       0.68658 ( 8165)
  SS BOND              : bond        0.00180 (    9)
  SS BOND              : angle       1.61538 (   18)
  hydrogen bonds       : bond        0.02331 (   94)
  hydrogen bonds       : angle       5.01333 (  225)
  link_NAG-ASN         : bond        0.00572 (    7)
  link_NAG-ASN         : angle       2.72029 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1148.35 seconds
wall clock time: 20 minutes 39.25 seconds (1239.25 seconds total)