Starting phenix.real_space_refine
on Wed Sep 17 04:16:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bj2_44627/09_2025/9bj2_44627.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bj2_44627/09_2025/9bj2_44627.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bj2_44627/09_2025/9bj2_44627.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bj2_44627/09_2025/9bj2_44627.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bj2_44627/09_2025/9bj2_44627.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bj2_44627/09_2025/9bj2_44627.map"
  }
  resolution = 2.8
  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=  -0.000 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      13      5.16       5
     C    2498      2.51       5
     N     651      2.21       5
     O     758      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3920
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2107
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 13, 'TRANS': 250}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "H"
      Number of atoms: 991
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 991
          Classifications: {'peptide': 129}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 124}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "L"
      Number of atoms: 780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 780
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 7, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   SER H 131 " occ=0.58
      ... (4 atoms not shown)
      pdb=" OG  SER H 131 " occ=0.58
  Time building chain proxies: 1.15, per 1000 atoms: 0.29
  Number of scatterers: 3920
  At special positions: 0
  Unit cell: (76.689, 83.5058, 105.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      13     16.00
     O     758      8.00
     N     651      7.00
     C    2498      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 165 "
      " NAG A1302 " - " ASN A 234 "
      " NAG A1303 " - " ASN A 122 "
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 151.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 11 sheets defined
      7.0% alpha, 45.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 254 through 256
      No H-bonds generated for 'chain 'A' and resid 254 through 256'
    Processing helix  chain 'A' and resid 294 through 303
    Processing helix  chain 'H' and resid 25 through 31
      removed outlier: 3.528A  pdb=" N   PHE H  29 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 65
      removed outlier: 4.009A  pdb=" N   GLN H  65 " --> pdb=" O   GLN H  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 65'
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'H' and resid 102 through 109
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30
    Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 30
      removed outlier: 8.216A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ALA A 263 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55
      removed outlier: 4.051A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.579A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ALA A 243 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   ARG A 102 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 11.376A  pdb=" N   VAL A 126 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
      removed outlier: 10.049A  pdb=" N   GLU A 169 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 11.067A  pdb=" N   ILE A 128 " --> pdb=" O   THR A 167 " (cutoff:3.500A)
      removed outlier: 8.902A  pdb=" N   THR A 167 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 8.153A  pdb=" N   VAL A 130 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   ASN A 165 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   GLU A 132 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ALA A 163 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   GLN A 134 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 154
      removed outlier: 6.525A  pdb=" N   TYR A 145 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.759A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 128 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ARG H  50 " --> pdb=" O   ASN H  59 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.759A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 128 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   VAL H 120 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.764A  pdb=" N   GLY L  13 " --> pdb=" O   THR L 105 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 19 through 24
    Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 48
      removed outlier: 6.574A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    147 hydrogen bonds defined for protein.
    372 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.62

  Time building geometry restraints manager: 0.44 seconds

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

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

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

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

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.58 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.820
  Find NCS groups from input model:        0.010
  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:7.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4027  Z= 0.108
  Angle     :  0.541   8.214   5492  Z= 0.290
  Chirality :  0.047   0.268    613
  Planarity :  0.004   0.041    699
  Dihedral  : 15.672  87.309   1440
  Min Nonbonded Distance : 2.208

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

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.38), residues: 487
  helix:  0.76 (0.94), residues: 23
  sheet:  1.07 (0.38), residues: 198
  loop : -0.64 (0.38), residues: 266

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

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

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

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.206 
Fit side-chains
REVERT: H   32 ASN cc_start: 0.8940 (m110) cc_final: 0.8548 (m-40)
  outliers start: 11
  outliers final: 10
  residues processed: 50
  average time/residue: 0.4438
  time to fit residues: 23.1987
Evaluate side-chains
  45 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 35
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain L residue   19 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0010
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.9188

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.157742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.122707 restraints weight = 4236.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.07
r_work: 0.3135 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3008
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3008
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.0812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4027  Z= 0.170
  Angle     :  0.611   6.144   5492  Z= 0.322
  Chirality :  0.049   0.223    613
  Planarity :  0.004   0.042    699
  Dihedral  :  6.973  57.640    617
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 17.73 %
    Favored  : 77.78 %
  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 aren not related in a simple way.
  whole:  0.28 (0.38), residues: 487
  helix:  1.11 (0.95), residues: 23
  sheet:  1.06 (0.35), residues: 228
  loop : -0.81 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  38 
 TYR   0.014   0.002   TYR A 279 
 PHE   0.022   0.002   PHE A 175 
 TRP   0.011   0.002   TRP H 113 
 HIS   0.004   0.002   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 4019)
  covalent geometry    : angle       0.59696 ( 5473)
  SS BOND              : bond        0.00607 (    5)
  SS BOND              : angle       1.20041 (   10)
  hydrogen bonds       : bond        0.04275 (  141)
  hydrogen bonds       : angle       5.26031 (  372)
  link_NAG-ASN         : bond        0.00455 (    3)
  link_NAG-ASN         : angle       3.07725 (    9)

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

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 39
  time to evaluate  : 0.157 
Fit side-chains
REVERT: H   38 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7819 (ttm170)
REVERT: L   96 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8053 (mp)
  outliers start: 19
  outliers final: 11
  residues processed: 55
  average time/residue: 0.4140
  time to fit residues: 23.8405
Evaluate side-chains
  46 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 33
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue   63 GLU
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0970
   chunk 6 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.5978

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.159352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.124198 restraints weight = 4218.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 1.98
r_work: 0.3175 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.0825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4027  Z= 0.128
  Angle     :  0.560   7.345   5492  Z= 0.299
  Chirality :  0.047   0.249    613
  Planarity :  0.004   0.041    699
  Dihedral  :  5.805  47.911    607
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 18.20 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.38), residues: 487
  helix:  1.37 (0.94), residues: 23
  sheet:  1.00 (0.38), residues: 200
  loop : -0.81 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  38 
 TYR   0.011   0.001   TYR A 279 
 PHE   0.015   0.002   PHE A 175 
 TRP   0.011   0.001   TRP H 113 
 HIS   0.003   0.001   HIS H  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 4019)
  covalent geometry    : angle       0.54109 ( 5473)
  SS BOND              : bond        0.00523 (    5)
  SS BOND              : angle       2.54985 (   10)
  hydrogen bonds       : bond        0.03564 (  141)
  hydrogen bonds       : angle       5.06073 (  372)
  link_NAG-ASN         : bond        0.00389 (    3)
  link_NAG-ASN         : angle       2.45837 (    9)

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

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 39
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A  154 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8250 (mt-10)
REVERT: H   32 ASN cc_start: 0.9124 (m110) cc_final: 0.8622 (m-40)
REVERT: H   38 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7788 (ttm170)
REVERT: L   96 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8034 (mp)
  outliers start: 20
  outliers final: 11
  residues processed: 54
  average time/residue: 0.4042
  time to fit residues: 22.8638
Evaluate side-chains
  51 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 37
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  228 ASP
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 45 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.159732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.124974 restraints weight = 4152.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.74
r_work: 0.3199 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3051
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3051
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.0968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4027  Z= 0.147
  Angle     :  0.574   5.959   5492  Z= 0.305
  Chirality :  0.048   0.271    613
  Planarity :  0.004   0.041    699
  Dihedral  :  5.334  34.692    602
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 17.97 %
    Favored  : 75.65 %
  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 aren not related in a simple way.
  whole:  0.08 (0.37), residues: 487
  helix:  1.35 (0.93), residues: 23
  sheet:  0.97 (0.38), residues: 200
  loop : -0.82 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  38 
 TYR   0.013   0.001   TYR A 279 
 PHE   0.019   0.002   PHE A 175 
 TRP   0.011   0.002   TRP H 113 
 HIS   0.004   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4019)
  covalent geometry    : angle       0.56299 ( 5473)
  SS BOND              : bond        0.00521 (    5)
  SS BOND              : angle       1.27522 (   10)
  hydrogen bonds       : bond        0.03734 (  141)
  hydrogen bonds       : angle       5.05119 (  372)
  link_NAG-ASN         : bond        0.00838 (    3)
  link_NAG-ASN         : angle       2.60747 (    9)

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

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 40
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  154 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8320 (mt-10)
REVERT: H   32 ASN cc_start: 0.9119 (m110) cc_final: 0.8621 (m-40)
REVERT: H   38 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7794 (ttm170)
REVERT: H   51 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7757 (tp)
REVERT: L   96 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7996 (mp)
  outliers start: 27
  outliers final: 15
  residues processed: 61
  average time/residue: 0.4523
  time to fit residues: 28.8925
Evaluate side-chains
  55 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 36
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  228 ASP
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   63 GLU
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 45 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.0586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.158256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.123791 restraints weight = 4219.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.99
r_work: 0.3165 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   4027  Z= 0.190
  Angle     :  0.641   9.699   5492  Z= 0.340
  Chirality :  0.049   0.172    613
  Planarity :  0.004   0.042    699
  Dihedral  :  5.676  38.062    602
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 17.97 %
    Favored  : 75.65 %
  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 aren not related in a simple way.
  whole: -0.04 (0.37), residues: 487
  helix:  1.21 (0.93), residues: 23
  sheet:  0.87 (0.37), residues: 202
  loop : -0.89 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  38 
 TYR   0.015   0.002   TYR A 279 
 PHE   0.024   0.002   PHE A 175 
 TRP   0.012   0.002   TRP H 113 
 HIS   0.004   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 4019)
  covalent geometry    : angle       0.62032 ( 5473)
  SS BOND              : bond        0.00688 (    5)
  SS BOND              : angle       3.17313 (   10)
  hydrogen bonds       : bond        0.04188 (  141)
  hydrogen bonds       : angle       5.14978 (  372)
  link_NAG-ASN         : bond        0.00330 (    3)
  link_NAG-ASN         : angle       2.34374 (    9)

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

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 36
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A  154 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8443 (mt-10)
REVERT: H   38 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7784 (ttm170)
REVERT: H   51 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7801 (tp)
REVERT: L   96 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8085 (mp)
  outliers start: 27
  outliers final: 17
  residues processed: 59
  average time/residue: 0.4143
  time to fit residues: 25.6878
Evaluate side-chains
  53 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 32
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue   63 GLU
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   28 ILE
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    0.1980
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.160135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.125862 restraints weight = 4270.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.99
r_work: 0.3176 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3028
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3028 r_free = 0.3028    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3028 r_free = 0.3028    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3028
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   4027  Z= 0.141
  Angle     :  0.587   9.764   5492  Z= 0.311
  Chirality :  0.047   0.163    613
  Planarity :  0.004   0.041    699
  Dihedral  :  5.405  33.598    602
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 18.44 %
    Favored  : 75.41 %
  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 aren not related in a simple way.
  whole: -0.00 (0.37), residues: 487
  helix:  1.38 (0.94), residues: 23
  sheet:  0.90 (0.38), residues: 199
  loop : -0.86 (0.36), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  38 
 TYR   0.012   0.001   TYR A 279 
 PHE   0.018   0.002   PHE A 133 
 TRP   0.012   0.002   TRP H 107 
 HIS   0.003   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4019)
  covalent geometry    : angle       0.56206 ( 5473)
  SS BOND              : bond        0.00478 (    5)
  SS BOND              : angle       3.19593 (   10)
  hydrogen bonds       : bond        0.03600 (  141)
  hydrogen bonds       : angle       5.04548 (  372)
  link_NAG-ASN         : bond        0.00235 (    3)
  link_NAG-ASN         : angle       2.64962 (    9)

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

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 37
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  154 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8327 (mt-10)
REVERT: H   38 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7790 (ttm170)
REVERT: L   96 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8011 (mp)
  outliers start: 26
  outliers final: 18
  residues processed: 59
  average time/residue: 0.4100
  time to fit residues: 25.4187
Evaluate side-chains
  55 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 34
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   28 ILE
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0980
   chunk 11 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.158639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.123700 restraints weight = 4322.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 1.95
r_work: 0.3193 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3073
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3073
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.1093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   4027  Z= 0.142
  Angle     :  0.572   7.333   5492  Z= 0.304
  Chirality :  0.047   0.165    613
  Planarity :  0.004   0.041    699
  Dihedral  :  5.315  33.150    602
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 18.20 %
    Favored  : 75.41 %
  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 aren not related in a simple way.
  whole: -0.02 (0.37), residues: 487
  helix:  1.40 (0.92), residues: 23
  sheet:  0.89 (0.38), residues: 199
  loop : -0.88 (0.36), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  38 
 TYR   0.012   0.001   TYR A 279 
 PHE   0.017   0.002   PHE A 175 
 TRP   0.016   0.002   TRP H 107 
 HIS   0.003   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 4019)
  covalent geometry    : angle       0.55562 ( 5473)
  SS BOND              : bond        0.00521 (    5)
  SS BOND              : angle       2.41663 (   10)
  hydrogen bonds       : bond        0.03582 (  141)
  hydrogen bonds       : angle       5.01531 (  372)
  link_NAG-ASN         : bond        0.00388 (    3)
  link_NAG-ASN         : angle       2.38369 (    9)

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

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 37
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A  129 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8460 (mtmm)
REVERT: A  154 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8348 (mt-10)
REVERT: H   38 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7770 (ttm170)
REVERT: H   51 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7862 (tp)
REVERT: L   96 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8022 (mp)
  outliers start: 27
  outliers final: 19
  residues processed: 58
  average time/residue: 0.3983
  time to fit residues: 24.1637
Evaluate side-chains
  59 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 35
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   28 ILE
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 27 optimal weight:    8.9990
   chunk 10 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 21 optimal weight:    0.4980
   chunk 44 optimal weight:    6.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.7180

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

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

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 = 0.158723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.124624 restraints weight = 4284.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.95
r_work: 0.3160 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3018
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3018
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.1117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4027  Z= 0.144
  Angle     :  0.572   6.226   5492  Z= 0.304
  Chirality :  0.047   0.165    613
  Planarity :  0.004   0.041    699
  Dihedral  :  5.236  32.779    602
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 18.44 %
    Favored  : 75.65 %
  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 aren not related in a simple way.
  whole: -0.08 (0.37), residues: 487
  helix:  1.35 (0.92), residues: 23
  sheet:  0.85 (0.38), residues: 200
  loop : -0.92 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  38 
 TYR   0.013   0.001   TYR A 279 
 PHE   0.018   0.002   PHE A 175 
 TRP   0.019   0.002   TRP H 107 
 HIS   0.003   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 4019)
  covalent geometry    : angle       0.55730 ( 5473)
  SS BOND              : bond        0.00517 (    5)
  SS BOND              : angle       2.07106 (   10)
  hydrogen bonds       : bond        0.03599 (  141)
  hydrogen bonds       : angle       4.99669 (  372)
  link_NAG-ASN         : bond        0.00352 (    3)
  link_NAG-ASN         : angle       2.38715 (    9)

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

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 38
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  154 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8328 (mt-10)
REVERT: H   32 ASN cc_start: 0.9148 (m110) cc_final: 0.8610 (m-40)
REVERT: H   38 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7744 (ttm170)
REVERT: H   51 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7816 (tp)
REVERT: L   96 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7989 (mp)
  outliers start: 25
  outliers final: 19
  residues processed: 58
  average time/residue: 0.3770
  time to fit residues: 23.0715
Evaluate side-chains
  58 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 35
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   28 ILE
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 45 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    1.2984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.157411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.123199 restraints weight = 4255.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.97
r_work: 0.3159 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3011
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3011
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.074   4027  Z= 0.227
  Angle     :  0.708  11.758   5492  Z= 0.372
  Chirality :  0.050   0.177    613
  Planarity :  0.005   0.044    699
  Dihedral  :  5.836  37.397    602
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 18.44 %
    Favored  : 75.41 %
  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 aren not related in a simple way.
  whole: -0.23 (0.37), residues: 487
  helix:  0.94 (0.92), residues: 23
  sheet:  0.91 (0.38), residues: 196
  loop : -1.13 (0.35), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  38 
 TYR   0.016   0.002   TYR A 279 
 PHE   0.028   0.003   PHE A 175 
 TRP   0.025   0.002   TRP H 107 
 HIS   0.005   0.002   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 ( 4019)
  covalent geometry    : angle       0.68155 ( 5473)
  SS BOND              : bond        0.00687 (    5)
  SS BOND              : angle       3.78992 (   10)
  hydrogen bonds       : bond        0.04499 (  141)
  hydrogen bonds       : angle       5.19691 (  372)
  link_NAG-ASN         : bond        0.00236 (    3)
  link_NAG-ASN         : angle       2.73224 (    9)

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

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 35
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: H   38 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7770 (ttm170)
REVERT: H   51 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7873 (tp)
REVERT: L   96 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8124 (mp)
  outliers start: 26
  outliers final: 18
  residues processed: 57
  average time/residue: 0.4094
  time to fit residues: 24.4710
Evaluate side-chains
  54 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 33
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   28 ILE
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 28 optimal weight:    0.2980
   chunk 6 optimal weight:    0.7980
   chunk 17 optimal weight:    0.4980
   chunk 31 optimal weight:    0.3980
   chunk 12 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 40 optimal weight:    0.2980
   overall best weight:    0.4180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.161969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.126421 restraints weight = 4240.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.93
r_work: 0.3186 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   4027  Z= 0.113
  Angle     :  0.547   8.141   5492  Z= 0.292
  Chirality :  0.046   0.164    613
  Planarity :  0.004   0.042    699
  Dihedral  :  5.108  29.232    602
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 20.57 %
    Favored  : 75.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.38), residues: 487
  helix:  1.32 (0.95), residues: 23
  sheet:  1.00 (0.38), residues: 195
  loop : -0.99 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  54 
 TYR   0.010   0.001   TYR H  95 
 PHE   0.013   0.001   PHE A 133 
 TRP   0.026   0.001   TRP H 107 
 HIS   0.003   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4019)
  covalent geometry    : angle       0.52674 ( 5473)
  SS BOND              : bond        0.00393 (    5)
  SS BOND              : angle       2.62964 (   10)
  hydrogen bonds       : bond        0.03078 (  141)
  hydrogen bonds       : angle       4.92858 (  372)
  link_NAG-ASN         : bond        0.00122 (    3)
  link_NAG-ASN         : angle       2.53184 (    9)

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

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 39
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.8642 (mtmm) cc_final: 0.8425 (mttt)
REVERT: H   32 ASN cc_start: 0.9121 (m110) cc_final: 0.8572 (m-40)
REVERT: H   38 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7731 (ttm170)
REVERT: L   96 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7961 (mp)
  outliers start: 18
  outliers final: 13
  residues processed: 53
  average time/residue: 0.4409
  time to fit residues: 24.4712
Evaluate side-chains
  52 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   24 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   60 SER
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0970
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.7578

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.159975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.126420 restraints weight = 4232.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.90
r_work: 0.3148 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3051
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3051
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   4027  Z= 0.151
  Angle     :  0.600   9.296   5492  Z= 0.318
  Chirality :  0.047   0.166    613
  Planarity :  0.004   0.041    699
  Dihedral  :  5.258  32.498    602
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 21.28 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.37), residues: 487
  helix:  1.21 (0.93), residues: 23
  sheet:  1.00 (0.38), residues: 195
  loop : -1.01 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  38 
 TYR   0.012   0.001   TYR A 279 
 PHE   0.019   0.002   PHE A 175 
 TRP   0.026   0.002   TRP H 107 
 HIS   0.003   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 4019)
  covalent geometry    : angle       0.57855 ( 5473)
  SS BOND              : bond        0.00488 (    5)
  SS BOND              : angle       3.00666 (   10)
  hydrogen bonds       : bond        0.03654 (  141)
  hydrogen bonds       : angle       4.97533 (  372)
  link_NAG-ASN         : bond        0.00180 (    3)
  link_NAG-ASN         : angle       2.45944 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1905.90 seconds
wall clock time: 33 minutes 17.77 seconds (1997.77 seconds total)