Starting phenix.real_space_refine
on Sun Apr 27 11:58:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n62_24192/04_2025/7n62_24192_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n62_24192/04_2025/7n62_24192.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n62_24192/04_2025/7n62_24192.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n62_24192/04_2025/7n62_24192.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n62_24192/04_2025/7n62_24192_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n62_24192/04_2025/7n62_24192_neut.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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      17      5.16       5
     C    3569      2.51       5
     N     933      2.21       5
     O    1094      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 5613
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2235
          Classifications: {'peptide': 277}
          Link IDs: {'PTRANS': 14, 'TRANS': 262}
    Chain: "H"
      Number of atoms: 1689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1689
          Classifications: {'peptide': 223}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211}
    Chain: "L"
      Number of atoms: 1619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1619
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199}
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 3.74, per 1000 atoms: 0.67
  Number of scatterers: 5613
  At special positions: 0
  Unit cell: (64.35, 95.7, 122.925, 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      17     16.00
     O    1094      8.00
     N     933      7.00
     C    3569      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 150 " - pdb=" SG  CYS H 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " 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  17 "
      " NAG A1302 " - " ASN A  61 "
      " NAG A1303 " - " ASN A 122 "
      " NAG A1304 " - " ASN A 165 "
      " NAG A1305 " - " ASN A 234 "
  Time building additional restraints: 2.07
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1314

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 16 sheets defined
      5.3% alpha, 35.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.558A  pdb=" N   PHE H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 195 through 199
    Processing helix  chain 'L' and resid 29 through 32
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.775A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 127
    Processing helix  chain 'L' and resid 182 through 188
      removed outlier: 4.097A  pdb=" N   LYS L 188 " --> pdb=" O   ALA L 184 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28
      removed outlier: 3.628A  pdb=" N   LYS A 195 " --> pdb=" O   LYS A 202 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   VAL A 227 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85
      removed outlier: 3.649A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   ALA A 243 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 5.785A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85
      removed outlier: 5.651A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121
    Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 145
      removed outlier: 4.062A  pdb=" N   TYR A 144 " --> pdb=" O   MET A 153 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   MET A 153 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12
      removed outlier: 5.865A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 132 through 133
      removed outlier: 4.376A  pdb=" N   LEU H 148 " --> pdb=" O   VAL H 192 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL H 192 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 132 through 133
      removed outlier: 4.376A  pdb=" N   LEU H 148 " --> pdb=" O   VAL H 192 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL H 192 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER H 187 " --> pdb=" O   VAL H 179 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 161 through 164
    Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12
    Processing sheet with id=AB5, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.530A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 114 through 118
      removed outlier: 5.631A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 153 through 154
      removed outlier: 3.731A  pdb=" N   LYS L 145 " --> pdb=" O   THR L 197 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   CYS L 194 " --> pdb=" O   LYS L 207 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL L 205 " --> pdb=" O   VAL L 196 " (cutoff:3.500A)

    180 hydrogen bonds defined for protein.
    429 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.56

  Time building geometry restraints manager: 1.76 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: 1779
        1.34 -     1.46: 1526
        1.46 -     1.59: 2431
        1.59 -     1.71: 0
        1.71 -     1.83: 22
  Bond restraints: 5758
  Sorted by residual:
  bond pdb=" N   GLU H   6 "
       pdb=" CA  GLU H   6 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.23e-02 6.61e+03 6.33e+00
  bond pdb=" N   ASP A 253 "
       pdb=" CA  ASP A 253 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.50e-02 4.44e+03 5.06e+00
  bond pdb=" C   ALA H  92 "
       pdb=" N   VAL H  93 "
    ideal  model  delta    sigma   weight residual
    1.334  1.313  0.021 1.24e-02 6.50e+03 2.83e+00
  bond pdb=" CB  PRO H 159 "
       pdb=" CG  PRO H 159 "
    ideal  model  delta    sigma   weight residual
    1.506  1.567 -0.061 3.90e-02 6.57e+02 2.41e+00
  bond pdb=" CB  TRP H  36 "
       pdb=" CG  TRP H  36 "
    ideal  model  delta    sigma   weight residual
    1.498  1.455  0.043 3.10e-02 1.04e+03 1.97e+00
  ... (remaining 5753 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 7408
        1.64 -     3.28: 354
        3.28 -     4.92: 51
        4.92 -     6.56: 14
        6.56 -     8.20: 5
  Bond angle restraints: 7832
  Sorted by residual:
  angle pdb=" C   GLU H 158 "
        pdb=" N   PRO H 159 "
        pdb=" CD  PRO H 159 "
      ideal   model   delta    sigma   weight residual
     120.60  113.12    7.48 2.20e+00 2.07e-01 1.16e+01
  angle pdb=" N   TYR A 144 "
        pdb=" CA  TYR A 144 "
        pdb=" C   TYR A 144 "
      ideal   model   delta    sigma   weight residual
     108.46  113.39   -4.93 1.51e+00 4.39e-01 1.07e+01
  angle pdb=" CA  PRO H 159 "
        pdb=" N   PRO H 159 "
        pdb=" CD  PRO H 159 "
      ideal   model   delta    sigma   weight residual
     111.50  107.46    4.04 1.40e+00 5.10e-01 8.34e+00
  angle pdb=" CA  GLU A  96 "
        pdb=" CB  GLU A  96 "
        pdb=" CG  GLU A  96 "
      ideal   model   delta    sigma   weight residual
     114.10  119.83   -5.73 2.00e+00 2.50e-01 8.21e+00
  angle pdb=" C   GLU H 158 "
        pdb=" N   PRO H 159 "
        pdb=" CA  PRO H 159 "
      ideal   model   delta    sigma   weight residual
     127.00  133.63   -6.63 2.40e+00 1.74e-01 7.62e+00
  ... (remaining 7827 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 3112
       17.83 -    35.66: 280
       35.66 -    53.49: 54
       53.49 -    71.32: 8
       71.32 -    89.14: 4
  Dihedral angle restraints: 3458
    sinusoidal: 1396
      harmonic: 2062
  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
      93.00   36.85   56.15     1      1.00e+01 1.00e-02 4.25e+01
  dihedral pdb=" CA  THR A  19 "
           pdb=" C   THR A  19 "
           pdb=" N   THR A  20 "
           pdb=" CA  THR A  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.77   27.23     0      5.00e+00 4.00e-02 2.97e+01
  dihedral pdb=" CA  PRO A  82 "
           pdb=" C   PRO A  82 "
           pdb=" N   VAL A  83 "
           pdb=" CA  VAL A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.13   25.87     0      5.00e+00 4.00e-02 2.68e+01
  ... (remaining 3455 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 839
       0.106 -    0.213: 32
       0.213 -    0.319: 2
       0.319 -    0.425: 1
       0.425 -    0.532: 1
  Chirality restraints: 875
  Sorted by residual:
  chirality pdb=" C1  NAG A1304 "
            pdb=" ND2 ASN A 165 "
            pdb=" C2  NAG A1304 "
            pdb=" O5  NAG A1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.87   -0.53 2.00e-01 2.50e+01 7.07e+00
  chirality pdb=" CB  ILE A 210 "
            pdb=" CA  ILE A 210 "
            pdb=" CG1 ILE A 210 "
            pdb=" CG2 ILE A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" CB  ILE L  76 "
            pdb=" CA  ILE L  76 "
            pdb=" CG1 ILE L  76 "
            pdb=" CG2 ILE L  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.54e+00
  ... (remaining 872 not shown)

  Planarity restraints: 1005
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO L 119 "   -0.061 5.00e-02 4.00e+02   9.15e-02 1.34e+01
        pdb=" N   PRO L 120 "    0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO L 120 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO L 120 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 158 "   -0.057 5.00e-02 4.00e+02   8.38e-02 1.12e+01
        pdb=" N   PRO H 159 "    0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO H 159 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO H 159 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA H 135 "   -0.036 5.00e-02 4.00e+02   5.52e-02 4.87e+00
        pdb=" N   PRO H 136 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO H 136 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO H 136 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1002 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 764
        2.74 -     3.28: 6066
        3.28 -     3.82: 9555
        3.82 -     4.36: 11231
        4.36 -     4.90: 18714
  Nonbonded interactions: 46330
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 156 "
            pdb=" OH  TYR A 160 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OE1 GLN L 166 "
            pdb=" OG  SER L 171 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" NH2 ARG A 158 "
            pdb=" OD1 ASP H 101 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" O   GLN A  14 "
            pdb=" NH1 ARG A 158 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   TYR L 186 "
            pdb=" OH  TYR L 192 "
     model   vdw
     2.229 3.040
  ... (remaining 46325 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             14.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.400
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
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      :  0.006   0.061   5769  Z= 0.297
  Angle     :  0.855  14.301   7859  Z= 0.450
  Chirality :  0.053   0.532    875
  Planarity :  0.006   0.092   1000
  Dihedral  : 13.902  89.144   2126
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 21.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.87 %
    Favored  : 85.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.31), residues: 706
  helix: -2.65 (1.15), residues: 14
  sheet: -1.13 (0.31), residues: 269
  loop : -2.35 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A 258 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.020   0.002   PHE L  72 
 TYR   0.035   0.002   TYR A 144 
 ARG   0.005   0.001   ARG H  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00803 (    5)
  link_NAG-ASN         : angle       5.12659 (   15)
  hydrogen bonds       : bond        0.28264 (  169)
  hydrogen bonds       : angle      11.20079 (  429)
  SS BOND              : bond        0.00386 (    6)
  SS BOND              : angle       1.43064 (   12)
  covalent geometry    : bond        0.00641 ( 5758)
  covalent geometry    : angle       0.82457 ( 7832)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 THR cc_start: 0.6470 (t) cc_final: 0.6260 (t)
REVERT: A   56 LEU cc_start: 0.9064 (tp) cc_final: 0.8691 (tp)
REVERT: A  100 ILE cc_start: 0.9421 (tt) cc_final: 0.9202 (tt)
REVERT: H   90 ASP cc_start: 0.9094 (m-30) cc_final: 0.8846 (m-30)
REVERT: H   99 ASP cc_start: 0.9256 (t0) cc_final: 0.8997 (t0)
REVERT: H  104 TYR cc_start: 0.8107 (t80) cc_final: 0.7561 (t80)
REVERT: L   88 TYR cc_start: 0.9417 (m-80) cc_final: 0.9138 (m-80)
REVERT: L  139 PHE cc_start: 0.8581 (p90) cc_final: 0.8362 (p90)
REVERT: L  142 ARG cc_start: 0.8410 (tpt90) cc_final: 0.8165 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1943
  time to fit residues: 32.8524
Evaluate side-chains
  94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 54 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 40 optimal weight:   40.0000
   chunk 63 optimal weight:    5.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 207 ASN
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 138 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.103166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.073783 restraints weight = 13960.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.076808 restraints weight = 6947.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.078795 restraints weight = 4519.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   5769  Z= 0.193
  Angle     :  0.796  12.506   7859  Z= 0.408
  Chirality :  0.051   0.461    875
  Planarity :  0.006   0.071   1000
  Dihedral  :  6.958  56.907    880
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.61 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 12.48 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.30), residues: 706
  helix: -1.77 (1.17), residues: 14
  sheet: -1.03 (0.29), residues: 273
  loop : -2.30 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 258 
 HIS   0.008   0.001   HIS A 146 
 PHE   0.016   0.002   PHE L  72 
 TYR   0.023   0.002   TYR A 144 
 ARG   0.006   0.001   ARG L 108 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00766 (    5)
  link_NAG-ASN         : angle       4.30822 (   15)
  hydrogen bonds       : bond        0.04931 (  169)
  hydrogen bonds       : angle       8.05862 (  429)
  SS BOND              : bond        0.00443 (    6)
  SS BOND              : angle       1.19502 (   12)
  covalent geometry    : bond        0.00422 ( 5758)
  covalent geometry    : angle       0.77330 ( 7832)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.9062 (tp) cc_final: 0.8672 (tp)
REVERT: A   91 TYR cc_start: 0.9286 (t80) cc_final: 0.8894 (t80)
REVERT: A  156 GLU cc_start: 0.8619 (pt0) cc_final: 0.8238 (pt0)
REVERT: A  157 PHE cc_start: 0.8875 (m-80) cc_final: 0.8646 (m-10)
REVERT: H   90 ASP cc_start: 0.8987 (m-30) cc_final: 0.8669 (m-30)
REVERT: L   88 TYR cc_start: 0.9413 (m-80) cc_final: 0.9186 (m-80)
REVERT: L   90 GLN cc_start: 0.8664 (tt0) cc_final: 0.8337 (tt0)
REVERT: L  139 PHE cc_start: 0.8643 (p90) cc_final: 0.8304 (p90)
REVERT: L  142 ARG cc_start: 0.8472 (tpt90) cc_final: 0.8112 (tpt90)
  outliers start: 4
  outliers final: 3
  residues processed: 119
  average time/residue: 0.2102
  time to fit residues: 33.1882
Evaluate side-chains
  98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain H residue  145 THR
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 48 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0870
   chunk 56 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0060
   chunk 5 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   overall best weight:    0.7776

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.106350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.076829 restraints weight = 13834.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.079942 restraints weight = 6851.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.081973 restraints weight = 4412.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5769  Z= 0.134
  Angle     :  0.740  11.514   7859  Z= 0.374
  Chirality :  0.050   0.421    875
  Planarity :  0.006   0.063   1000
  Dihedral  :  6.318  51.893    880
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 15.72 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.30), residues: 706
  helix: -1.32 (1.25), residues: 14
  sheet: -0.86 (0.28), residues: 296
  loop : -2.18 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 258 
 HIS   0.003   0.001   HIS A 146 
 PHE   0.024   0.002   PHE L 209 
 TYR   0.016   0.001   TYR A 145 
 ARG   0.003   0.001   ARG A 214 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00761 (    5)
  link_NAG-ASN         : angle       3.86993 (   15)
  hydrogen bonds       : bond        0.03686 (  169)
  hydrogen bonds       : angle       7.35089 (  429)
  SS BOND              : bond        0.00460 (    6)
  SS BOND              : angle       1.44208 (   12)
  covalent geometry    : bond        0.00295 ( 5758)
  covalent geometry    : angle       0.71915 ( 7832)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.9037 (p)
REVERT: A   56 LEU cc_start: 0.8983 (tp) cc_final: 0.8583 (tp)
REVERT: A  154 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7942 (mt-10)
REVERT: A  156 GLU cc_start: 0.8519 (pt0) cc_final: 0.8158 (pt0)
REVERT: A  157 PHE cc_start: 0.8726 (m-80) cc_final: 0.8460 (m-10)
REVERT: A  253 ASP cc_start: 0.7374 (m-30) cc_final: 0.7141 (m-30)
REVERT: H   74 ASN cc_start: 0.8507 (m-40) cc_final: 0.7784 (m-40)
REVERT: H   90 ASP cc_start: 0.8961 (m-30) cc_final: 0.8581 (m-30)
REVERT: H  161 THR cc_start: 0.8958 (m) cc_final: 0.8655 (p)
REVERT: L   88 TYR cc_start: 0.9382 (m-80) cc_final: 0.9076 (m-80)
REVERT: L   90 GLN cc_start: 0.8661 (tt0) cc_final: 0.8426 (tt0)
REVERT: L  139 PHE cc_start: 0.8587 (p90) cc_final: 0.8323 (p90)
REVERT: L  140 TYR cc_start: 0.7833 (t80) cc_final: 0.7469 (t80)
REVERT: L  142 ARG cc_start: 0.8461 (tpt90) cc_final: 0.8029 (tpt90)
  outliers start: 10
  outliers final: 7
  residues processed: 133
  average time/residue: 0.2341
  time to fit residues: 39.3137
Evaluate side-chains
  108 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain H residue  145 THR
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   chunk 26 optimal weight:    6.9990
   chunk 8 optimal weight:    0.3980
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 207 ASN
** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.106612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.077172 restraints weight = 14240.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.080375 restraints weight = 6823.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.082467 restraints weight = 4338.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5769  Z= 0.146
  Angle     :  0.733  10.538   7859  Z= 0.364
  Chirality :  0.049   0.413    875
  Planarity :  0.006   0.062   1000
  Dihedral  :  5.902  39.215    880
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.49 %
    Favored  : 90.51 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.48 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.30), residues: 706
  helix: -0.99 (1.35), residues: 14
  sheet: -0.88 (0.28), residues: 301
  loop : -2.08 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 258 
 HIS   0.006   0.001   HIS A 146 
 PHE   0.020   0.002   PHE L  72 
 TYR   0.015   0.001   TYR A 144 
 ARG   0.004   0.001   ARG A 214 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00636 (    5)
  link_NAG-ASN         : angle       3.63785 (   15)
  hydrogen bonds       : bond        0.03363 (  169)
  hydrogen bonds       : angle       7.07651 (  429)
  SS BOND              : bond        0.00335 (    6)
  SS BOND              : angle       1.39545 (   12)
  covalent geometry    : bond        0.00330 ( 5758)
  covalent geometry    : angle       0.71454 ( 7832)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 VAL cc_start: 0.9272 (OUTLIER) cc_final: 0.9045 (p)
REVERT: A   56 LEU cc_start: 0.9000 (tp) cc_final: 0.8597 (tp)
REVERT: A  140 PHE cc_start: 0.9614 (p90) cc_final: 0.9035 (p90)
REVERT: A  152 TRP cc_start: 0.7163 (OUTLIER) cc_final: 0.6520 (p90)
REVERT: A  154 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7895 (mt-10)
REVERT: A  156 GLU cc_start: 0.8509 (pt0) cc_final: 0.8126 (pt0)
REVERT: A  157 PHE cc_start: 0.8740 (m-80) cc_final: 0.8483 (m-10)
REVERT: A  191 GLU cc_start: 0.8618 (tt0) cc_final: 0.8384 (mt-10)
REVERT: H   90 ASP cc_start: 0.8958 (m-30) cc_final: 0.8589 (m-30)
REVERT: H  161 THR cc_start: 0.8921 (m) cc_final: 0.8605 (p)
REVERT: L   88 TYR cc_start: 0.9417 (m-80) cc_final: 0.9134 (m-80)
REVERT: L   90 GLN cc_start: 0.8731 (tt0) cc_final: 0.8436 (tt0)
REVERT: L  139 PHE cc_start: 0.8590 (p90) cc_final: 0.8363 (p90)
  outliers start: 15
  outliers final: 10
  residues processed: 127
  average time/residue: 0.1717
  time to fit residues: 28.6528
Evaluate side-chains
  119 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  152 TRP
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  145 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 65 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 17 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  14 GLN
A  52 GLN
A 115 GLN
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 174 HIS
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.106898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.077711 restraints weight = 13944.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.080924 restraints weight = 6783.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.082989 restraints weight = 4319.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5769  Z= 0.146
  Angle     :  0.713  10.111   7859  Z= 0.358
  Chirality :  0.049   0.404    875
  Planarity :  0.005   0.061   1000
  Dihedral  :  5.650  28.974    880
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.20 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 19.77 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.30), residues: 706
  helix: -1.06 (1.39), residues: 14
  sheet: -0.94 (0.27), residues: 323
  loop : -2.11 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 258 
 HIS   0.004   0.001   HIS A 146 
 PHE   0.019   0.002   PHE L  72 
 TYR   0.024   0.001   TYR L 140 
 ARG   0.003   0.000   ARG L 108 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00613 (    5)
  link_NAG-ASN         : angle       3.43175 (   15)
  hydrogen bonds       : bond        0.03039 (  169)
  hydrogen bonds       : angle       6.87901 (  429)
  SS BOND              : bond        0.00354 (    6)
  SS BOND              : angle       1.37885 (   12)
  covalent geometry    : bond        0.00329 ( 5758)
  covalent geometry    : angle       0.69632 ( 7832)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 ASN cc_start: 0.8947 (t0) cc_final: 0.8727 (t0)
REVERT: A   56 LEU cc_start: 0.9000 (tp) cc_final: 0.8621 (tp)
REVERT: A  140 PHE cc_start: 0.9617 (p90) cc_final: 0.9067 (p90)
REVERT: A  152 TRP cc_start: 0.7100 (OUTLIER) cc_final: 0.6448 (p90)
REVERT: A  154 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7886 (mt-10)
REVERT: A  156 GLU cc_start: 0.8534 (pt0) cc_final: 0.8142 (pt0)
REVERT: A  157 PHE cc_start: 0.8738 (m-80) cc_final: 0.8446 (m-10)
REVERT: A  191 GLU cc_start: 0.8633 (tt0) cc_final: 0.8377 (mt-10)
REVERT: H   90 ASP cc_start: 0.8907 (m-30) cc_final: 0.8560 (m-30)
REVERT: H  101 ASP cc_start: 0.8541 (t0) cc_final: 0.8246 (t0)
REVERT: H  161 THR cc_start: 0.8903 (m) cc_final: 0.8603 (p)
REVERT: L   88 TYR cc_start: 0.9422 (m-80) cc_final: 0.9132 (m-80)
REVERT: L   90 GLN cc_start: 0.8740 (tt0) cc_final: 0.8436 (tt0)
REVERT: L  139 PHE cc_start: 0.8529 (p90) cc_final: 0.8305 (p90)
REVERT: L  142 ARG cc_start: 0.8366 (tpt90) cc_final: 0.7886 (tpt90)
REVERT: L  145 LYS cc_start: 0.8991 (mmmm) cc_final: 0.8603 (mmmm)
  outliers start: 17
  outliers final: 11
  residues processed: 130
  average time/residue: 0.1709
  time to fit residues: 29.0701
Evaluate side-chains
  122 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  152 TRP
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   62 ASP
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 68 optimal weight:   20.0000
   chunk 56 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 17 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0980
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.8188

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
L  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.106365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.076622 restraints weight = 14008.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.079795 restraints weight = 6922.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.081861 restraints weight = 4463.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5769  Z= 0.158
  Angle     :  0.707   9.953   7859  Z= 0.357
  Chirality :  0.049   0.394    875
  Planarity :  0.005   0.060   1000
  Dihedral  :  5.558  24.645    880
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.92 %
    Favored  : 90.08 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 20.10 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.30), residues: 706
  helix: -0.85 (1.46), residues: 14
  sheet: -0.93 (0.27), residues: 325
  loop : -2.07 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 258 
 HIS   0.003   0.001   HIS A 146 
 PHE   0.022   0.002   PHE L  72 
 TYR   0.014   0.001   TYR L 140 
 ARG   0.003   0.000   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00562 (    5)
  link_NAG-ASN         : angle       3.35603 (   15)
  hydrogen bonds       : bond        0.02992 (  169)
  hydrogen bonds       : angle       6.76169 (  429)
  SS BOND              : bond        0.00358 (    6)
  SS BOND              : angle       1.24297 (   12)
  covalent geometry    : bond        0.00357 ( 5758)
  covalent geometry    : angle       0.69120 ( 7832)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 ASN cc_start: 0.8956 (t0) cc_final: 0.8724 (t0)
REVERT: A   56 LEU cc_start: 0.9008 (tp) cc_final: 0.8646 (tp)
REVERT: A  140 PHE cc_start: 0.9617 (p90) cc_final: 0.9003 (p90)
REVERT: A  144 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.7372 (p90)
REVERT: A  152 TRP cc_start: 0.7147 (OUTLIER) cc_final: 0.6408 (p90)
REVERT: A  154 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7850 (mt-10)
REVERT: A  156 GLU cc_start: 0.8549 (pt0) cc_final: 0.8133 (pt0)
REVERT: A  157 PHE cc_start: 0.8735 (m-80) cc_final: 0.8465 (m-10)
REVERT: A  191 GLU cc_start: 0.8614 (tt0) cc_final: 0.8398 (mt-10)
REVERT: H   90 ASP cc_start: 0.8920 (m-30) cc_final: 0.8590 (m-30)
REVERT: H  101 ASP cc_start: 0.8553 (t0) cc_final: 0.8259 (t0)
REVERT: L   59 ILE cc_start: 0.9370 (mm) cc_final: 0.9169 (mm)
REVERT: L   88 TYR cc_start: 0.9430 (m-80) cc_final: 0.9108 (m-80)
REVERT: L   90 GLN cc_start: 0.8760 (tt0) cc_final: 0.8443 (tt0)
REVERT: L  139 PHE cc_start: 0.8548 (p90) cc_final: 0.8339 (p90)
REVERT: L  142 ARG cc_start: 0.8379 (tpt90) cc_final: 0.7829 (tpt90)
  outliers start: 22
  outliers final: 13
  residues processed: 129
  average time/residue: 0.1745
  time to fit residues: 29.2679
Evaluate side-chains
  121 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  144 TYR
Chi-restraints excluded: chain A residue  152 TRP
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   62 ASP
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0770
   chunk 3 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 35 optimal weight:    9.9990
   overall best weight:    1.7142

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.106503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.076672 restraints weight = 13997.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.079832 restraints weight = 6888.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.081888 restraints weight = 4423.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   5769  Z= 0.157
  Angle     :  0.717   9.549   7859  Z= 0.363
  Chirality :  0.048   0.379    875
  Planarity :  0.005   0.045   1000
  Dihedral  :  5.527  31.095    880
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.20 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 21.56 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.30), residues: 706
  helix: -0.72 (1.51), residues: 14
  sheet: -0.99 (0.27), residues: 324
  loop : -2.04 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 258 
 HIS   0.002   0.001   HIS A 146 
 PHE   0.017   0.002   PHE L  72 
 TYR   0.028   0.002   TYR L 140 
 ARG   0.004   0.000   ARG H  16 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00693 (    5)
  link_NAG-ASN         : angle       3.23745 (   15)
  hydrogen bonds       : bond        0.03061 (  169)
  hydrogen bonds       : angle       6.71784 (  429)
  SS BOND              : bond        0.00323 (    6)
  SS BOND              : angle       2.70390 (   12)
  covalent geometry    : bond        0.00364 ( 5758)
  covalent geometry    : angle       0.69583 ( 7832)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 ASN cc_start: 0.8946 (t0) cc_final: 0.8735 (t0)
REVERT: A   56 LEU cc_start: 0.8999 (tp) cc_final: 0.8660 (tp)
REVERT: A  140 PHE cc_start: 0.9613 (p90) cc_final: 0.9013 (p90)
REVERT: A  152 TRP cc_start: 0.7175 (OUTLIER) cc_final: 0.6346 (p90)
REVERT: A  154 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7844 (mt-10)
REVERT: A  156 GLU cc_start: 0.8552 (pt0) cc_final: 0.8144 (pt0)
REVERT: A  157 PHE cc_start: 0.8728 (m-80) cc_final: 0.8449 (m-10)
REVERT: H   90 ASP cc_start: 0.8904 (m-30) cc_final: 0.8580 (m-30)
REVERT: H  101 ASP cc_start: 0.8531 (t0) cc_final: 0.8238 (t0)
REVERT: L   88 TYR cc_start: 0.9408 (m-80) cc_final: 0.9133 (m-80)
REVERT: L   90 GLN cc_start: 0.8735 (tt0) cc_final: 0.8381 (tt0)
REVERT: L  139 PHE cc_start: 0.8487 (p90) cc_final: 0.8235 (p90)
REVERT: L  142 ARG cc_start: 0.8357 (tpt90) cc_final: 0.7790 (tpt90)
  outliers start: 19
  outliers final: 16
  residues processed: 133
  average time/residue: 0.1714
  time to fit residues: 30.0678
Evaluate side-chains
  127 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  152 TRP
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   62 ASP
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 46 optimal weight:    7.9990
   chunk 69 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 67 optimal weight:    8.9990
   chunk 60 optimal weight:    0.0870
   overall best weight:    2.8166

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

Flipped N/Q/H residues before XYZ refinement:
A  14 GLN
A 115 GLN
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.104636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.074871 restraints weight = 13960.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.077957 restraints weight = 6900.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.079985 restraints weight = 4431.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.2963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   5769  Z= 0.210
  Angle     :  0.743   9.323   7859  Z= 0.377
  Chirality :  0.050   0.388    875
  Planarity :  0.005   0.048   1000
  Dihedral  :  5.756  30.804    880
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.19 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 21.56 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.30), residues: 706
  helix: -0.76 (1.52), residues: 14
  sheet: -0.93 (0.28), residues: 302
  loop : -1.95 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 258 
 HIS   0.002   0.001   HIS A 146 
 PHE   0.020   0.002   PHE L  72 
 TYR   0.029   0.002   TYR L 140 
 ARG   0.006   0.001   ARG L 108 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00544 (    5)
  link_NAG-ASN         : angle       3.25565 (   15)
  hydrogen bonds       : bond        0.03152 (  169)
  hydrogen bonds       : angle       6.77979 (  429)
  SS BOND              : bond        0.00335 (    6)
  SS BOND              : angle       2.22746 (   12)
  covalent geometry    : bond        0.00477 ( 5758)
  covalent geometry    : angle       0.72512 ( 7832)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.9038 (tp) cc_final: 0.8677 (tp)
REVERT: A  140 PHE cc_start: 0.9622 (p90) cc_final: 0.8965 (p90)
REVERT: A  152 TRP cc_start: 0.7246 (OUTLIER) cc_final: 0.5887 (p90)
REVERT: A  154 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7905 (mt-10)
REVERT: A  156 GLU cc_start: 0.8578 (pt0) cc_final: 0.8152 (pt0)
REVERT: A  157 PHE cc_start: 0.8770 (m-80) cc_final: 0.8491 (m-10)
REVERT: A  190 ARG cc_start: 0.8355 (mtt90) cc_final: 0.8045 (mtt90)
REVERT: A  191 GLU cc_start: 0.8814 (tt0) cc_final: 0.8605 (mt-10)
REVERT: H   90 ASP cc_start: 0.8940 (m-30) cc_final: 0.8633 (m-30)
REVERT: H  101 ASP cc_start: 0.8657 (t0) cc_final: 0.8369 (t0)
REVERT: L   88 TYR cc_start: 0.9438 (m-80) cc_final: 0.9178 (m-80)
REVERT: L   90 GLN cc_start: 0.8779 (tt0) cc_final: 0.8429 (tt0)
REVERT: L  139 PHE cc_start: 0.8521 (p90) cc_final: 0.8304 (p90)
REVERT: L  142 ARG cc_start: 0.8419 (tpt90) cc_final: 0.7816 (tpt90)
  outliers start: 20
  outliers final: 16
  residues processed: 128
  average time/residue: 0.1814
  time to fit residues: 30.0762
Evaluate side-chains
  128 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  152 TRP
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   83 ASP
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 47 optimal weight:    8.9990
   chunk 35 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0970
   chunk 34 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.108574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.079107 restraints weight = 13877.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.082206 restraints weight = 7056.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.084158 restraints weight = 4614.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5769  Z= 0.130
  Angle     :  0.735   9.797   7859  Z= 0.367
  Chirality :  0.049   0.362    875
  Planarity :  0.005   0.049   1000
  Dihedral  :  5.413  25.921    880
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.20 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 22.04 %
    Favored  : 75.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.31), residues: 706
  helix: -0.73 (1.50), residues: 14
  sheet: -0.88 (0.28), residues: 317
  loop : -1.90 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 258 
 HIS   0.002   0.001   HIS A 146 
 PHE   0.013   0.001   PHE H 176 
 TYR   0.032   0.001   TYR L 140 
 ARG   0.006   0.001   ARG L 108 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00645 (    5)
  link_NAG-ASN         : angle       3.09030 (   15)
  hydrogen bonds       : bond        0.02927 (  169)
  hydrogen bonds       : angle       6.55938 (  429)
  SS BOND              : bond        0.00299 (    6)
  SS BOND              : angle       1.72111 (   12)
  covalent geometry    : bond        0.00304 ( 5758)
  covalent geometry    : angle       0.72084 ( 7832)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.8985 (tp) cc_final: 0.8623 (tp)
REVERT: A  140 PHE cc_start: 0.9575 (p90) cc_final: 0.9062 (p90)
REVERT: A  152 TRP cc_start: 0.7198 (OUTLIER) cc_final: 0.6026 (p90)
REVERT: A  154 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7711 (mt-10)
REVERT: A  156 GLU cc_start: 0.8527 (pt0) cc_final: 0.8122 (pt0)
REVERT: A  190 ARG cc_start: 0.8273 (mtt90) cc_final: 0.8003 (mtt90)
REVERT: H   36 TRP cc_start: 0.8516 (m100) cc_final: 0.8255 (m100)
REVERT: H   90 ASP cc_start: 0.8883 (m-30) cc_final: 0.8638 (m-30)
REVERT: H  101 ASP cc_start: 0.8435 (t0) cc_final: 0.8132 (t0)
REVERT: H  161 THR cc_start: 0.8945 (m) cc_final: 0.8643 (p)
REVERT: H  204 TYR cc_start: 0.6011 (m-80) cc_final: 0.5762 (m-10)
REVERT: L   88 TYR cc_start: 0.9364 (m-80) cc_final: 0.9067 (m-80)
REVERT: L   90 GLN cc_start: 0.8693 (tt0) cc_final: 0.8382 (tt0)
REVERT: L  139 PHE cc_start: 0.8466 (p90) cc_final: 0.8144 (p90)
REVERT: L  140 TYR cc_start: 0.7637 (t80) cc_final: 0.7353 (t80)
REVERT: L  142 ARG cc_start: 0.8364 (tpt90) cc_final: 0.7759 (tpt90)
  outliers start: 18
  outliers final: 15
  residues processed: 146
  average time/residue: 0.1911
  time to fit residues: 36.4481
Evaluate side-chains
  130 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  152 TRP
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   62 ASP
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 14 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 63 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 56 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 44 optimal weight:    0.1980
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A  66 HIS
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.107075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.076982 restraints weight = 14260.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.080119 restraints weight = 7024.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.082159 restraints weight = 4532.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.3396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   5769  Z= 0.199
  Angle     :  0.761  10.080   7859  Z= 0.387
  Chirality :  0.050   0.384    875
  Planarity :  0.005   0.051   1000
  Dihedral  :  5.575  27.935    880
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.62 %
    Favored  : 89.38 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 23.18 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.31), residues: 706
  helix: -0.71 (1.52), residues: 14
  sheet: -0.80 (0.28), residues: 324
  loop : -1.94 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H 164 
 HIS   0.005   0.001   HIS A 146 
 PHE   0.027   0.002   PHE L  47 
 TYR   0.029   0.002   TYR L 140 
 ARG   0.005   0.001   ARG A 214 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00521 (    5)
  link_NAG-ASN         : angle       3.16285 (   15)
  hydrogen bonds       : bond        0.03081 (  169)
  hydrogen bonds       : angle       6.63517 (  429)
  SS BOND              : bond        0.00273 (    6)
  SS BOND              : angle       1.84609 (   12)
  covalent geometry    : bond        0.00454 ( 5758)
  covalent geometry    : angle       0.74627 ( 7832)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.9015 (tp) cc_final: 0.8646 (tp)
REVERT: A   91 TYR cc_start: 0.9283 (t80) cc_final: 0.9015 (t80)
REVERT: A  140 PHE cc_start: 0.9614 (p90) cc_final: 0.8975 (p90)
REVERT: A  152 TRP cc_start: 0.7197 (OUTLIER) cc_final: 0.5826 (p90)
REVERT: A  154 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7768 (mt-10)
REVERT: A  156 GLU cc_start: 0.8508 (pt0) cc_final: 0.8053 (pt0)
REVERT: A  191 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8449 (mm-30)
REVERT: H   90 ASP cc_start: 0.8924 (m-30) cc_final: 0.8654 (m-30)
REVERT: H  101 ASP cc_start: 0.8617 (t0) cc_final: 0.8317 (t0)
REVERT: L   88 TYR cc_start: 0.9419 (m-80) cc_final: 0.9159 (m-80)
REVERT: L  139 PHE cc_start: 0.8493 (p90) cc_final: 0.8250 (p90)
REVERT: L  142 ARG cc_start: 0.8389 (tpt90) cc_final: 0.7779 (tpt90)
  outliers start: 17
  outliers final: 15
  residues processed: 125
  average time/residue: 0.1978
  time to fit residues: 32.1270
Evaluate side-chains
  129 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  152 TRP
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 60 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 34 optimal weight:    0.2980
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.6186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.108412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.078213 restraints weight = 13988.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.081402 restraints weight = 6903.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.083483 restraints weight = 4448.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5769  Z= 0.157
  Angle     :  0.749   9.901   7859  Z= 0.377
  Chirality :  0.049   0.369    875
  Planarity :  0.005   0.051   1000
  Dihedral  :  5.471  26.448    880
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.76 %
    Favored  : 89.24 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 23.18 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.06 (0.31), residues: 706
  helix: -0.83 (1.45), residues: 14
  sheet: -0.76 (0.28), residues: 323
  loop : -1.97 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 258 
 HIS   0.003   0.001   HIS A 146 
 PHE   0.025   0.002   PHE L  72 
 TYR   0.031   0.001   TYR L 140 
 ARG   0.003   0.000   ARG H  16 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00579 (    5)
  link_NAG-ASN         : angle       3.10332 (   15)
  hydrogen bonds       : bond        0.03015 (  169)
  hydrogen bonds       : angle       6.52298 (  429)
  SS BOND              : bond        0.00307 (    6)
  SS BOND              : angle       1.72314 (   12)
  covalent geometry    : bond        0.00364 ( 5758)
  covalent geometry    : angle       0.73514 ( 7832)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2367.80 seconds
wall clock time: 42 minutes 44.86 seconds (2564.86 seconds total)