Starting phenix.real_space_refine
on Sat May 10 05:49:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c89_16473/05_2025/8c89_16473_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c89_16473/05_2025/8c89_16473.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c89_16473/05_2025/8c89_16473.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c89_16473/05_2025/8c89_16473.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c89_16473/05_2025/8c89_16473_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c89_16473/05_2025/8c89_16473_neut.cif"
  }
  resolution = 4.41
  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=   0.009
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      25      5.16       5
     C    3227      2.51       5
     N     862      2.21       5
     O     992      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5106
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 1687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1687
          Classifications: {'peptide': 210}
          Link IDs: {'PTRANS': 13, 'TRANS': 196}
    Chain: "H"
      Number of atoms: 1698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1698
          Classifications: {'peptide': 226}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 211}
    Chain: "L"
      Number of atoms: 1665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1665
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.50, per 1000 atoms: 1.08
  Number of scatterers: 5106
  At special positions: 0
  Unit cell: (68.4, 70.965, 145.35, 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      25     16.00
     O     992      8.00
     N     862      7.00
     C    3227      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 101 " - pdb=" SG  CYS H 106 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 150 " - pdb=" SG  CYS H 206 " distance=2.05
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.05
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A   1 " - " ASN C 343 "
      " NAG B   1 " - " ASN H 102 "
  Time building additional restraints: 1.31
  Conformation dependent library (CDL) restraints added in 650.2 milliseconds
  

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1210

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 14 sheets defined
      9.0% alpha, 26.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 385 through 389
      removed outlier: 4.044A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASP C 389 " --> pdb=" O   LYS C 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 385 through 389'
    Processing helix  chain 'C' and resid 403 through 410
      removed outlier: 3.946A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 417 through 422
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 137 through 143
      removed outlier: 4.097A  pdb=" N   SER H 142 " --> pdb=" O   LYS H 139 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   GLY H 143 " --> pdb=" O   SER H 140 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 197 through 199
      No H-bonds generated for 'chain 'H' and resid 197 through 199'
    Processing helix  chain 'L' and resid 80 through 84
    Processing helix  chain 'L' and resid 123 through 129
    Processing helix  chain 'L' and resid 185 through 191
    Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 357
      removed outlier: 3.728A  pdb=" N   ILE C 402 " --> pdb=" O   TYR C 508 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   TYR C 508 " --> pdb=" O   ILE C 402 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU C 513 " --> pdb=" O   CYS C 432 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   CYS C 432 " --> pdb=" O   LEU C 513 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.592A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11
      removed outlier: 7.177A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 120 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL H 119 " --> pdb=" O   ALA H  92 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA H  97 " --> pdb=" O   GLN H  35 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLN H  35 " --> pdb=" O   ALA H  97 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 46 through 47
      removed outlier: 3.682A  pdb=" N   GLN H  35 " --> pdb=" O   ALA H  97 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA H  97 " --> pdb=" O   GLN H  35 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 18 through 19
    Processing sheet with id=AA8, first strand: chain 'H' and resid 130 through 134
      removed outlier: 3.957A  pdb=" N   SER H 130 " --> pdb=" O   LYS H 153 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   VAL H 191 " --> pdb=" O   HIS H 174 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   HIS H 174 " --> pdb=" O   VAL H 191 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 161 through 164
      removed outlier: 3.675A  pdb=" N   THR H 161 " --> pdb=" O   ASN H 209 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 13
      removed outlier: 5.815A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'L' and resid 19 through 22
    Processing sheet with id=AB3, first strand: chain 'L' and resid 46 through 47
    Processing sheet with id=AB4, first strand: chain 'L' and resid 118 through 120
      removed outlier: 3.568A  pdb=" N   VAL L 135 " --> pdb=" O   PHE L 120 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   SER L 176 " --> pdb=" O   THR L 166 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   SER L 178 " --> pdb=" O   SER L 164 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER L 164 " --> pdb=" O   SER L 178 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   THR L 180 " --> pdb=" O   GLN L 162 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 155 through 157
      removed outlier: 3.650A  pdb=" N   TRP L 150 " --> pdb=" O   GLN L 157 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR L 194 " --> pdb=" O   PHE L 211 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   HIS L 200 " --> pdb=" O   SER L 205 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   SER L 205 " --> pdb=" O   HIS L 200 " (cutoff:3.500A)

    128 hydrogen bonds defined for protein.
    294 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: 1.42

  Time building geometry restraints manager: 1.54 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 833
        1.32 -     1.44: 1493
        1.44 -     1.57: 2876
        1.57 -     1.69: 0
        1.69 -     1.82: 30
  Bond restraints: 5232
  Sorted by residual:
  bond pdb=" CZ  ARG L 110 "
       pdb=" NH2 ARG L 110 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.15e+00
  bond pdb=" CD  ARG L 110 "
       pdb=" NE  ARG L 110 "
    ideal  model  delta    sigma   weight residual
    1.458  1.427  0.031 1.40e-02 5.10e+03 4.92e+00
  bond pdb=" CA  SER H 125 "
       pdb=" CB  SER H 125 "
    ideal  model  delta    sigma   weight residual
    1.531  1.496  0.035 1.65e-02 3.67e+03 4.53e+00
  bond pdb=" CA  SER H  55 "
       pdb=" CB  SER H  55 "
    ideal  model  delta    sigma   weight residual
    1.535  1.502  0.033 1.58e-02 4.01e+03 4.29e+00
  bond pdb=" C   GLU H 158 "
       pdb=" N   PRO H 159 "
    ideal  model  delta    sigma   weight residual
    1.332  1.358 -0.027 1.30e-02 5.92e+03 4.24e+00
  ... (remaining 5227 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 6894
        2.57 -     5.14: 210
        5.14 -     7.71: 11
        7.71 -    10.28: 1
       10.28 -    12.85: 1
  Bond angle restraints: 7117
  Sorted by residual:
  angle pdb=" CG  ARG L 110 "
        pdb=" CD  ARG L 110 "
        pdb=" NE  ARG L 110 "
      ideal   model   delta    sigma   weight residual
     112.00  124.85  -12.85 2.20e+00 2.07e-01 3.41e+01
  angle pdb=" C   SER H 123 "
        pdb=" N   ALA H 124 "
        pdb=" CA  ALA H 124 "
      ideal   model   delta    sigma   weight residual
     121.70  128.82   -7.12 1.80e+00 3.09e-01 1.56e+01
  angle pdb=" CA  SER H 123 "
        pdb=" C   SER H 123 "
        pdb=" O   SER H 123 "
      ideal   model   delta    sigma   weight residual
     121.89  117.30    4.59 1.17e+00 7.31e-01 1.54e+01
  angle pdb=" C   THR L 111 "
        pdb=" N   VAL L 112 "
        pdb=" CA  VAL L 112 "
      ideal   model   delta    sigma   weight residual
     122.33  116.29    6.04 1.61e+00 3.86e-01 1.41e+01
  angle pdb=" C   THR C 333 "
        pdb=" CA  THR C 333 "
        pdb=" CB  THR C 333 "
      ideal   model   delta    sigma   weight residual
     110.42  117.77   -7.35 1.99e+00 2.53e-01 1.36e+01
  ... (remaining 7112 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.29: 3013
       24.29 -    48.58: 144
       48.58 -    72.87: 17
       72.87 -    97.16: 4
       97.16 -   121.46: 3
  Dihedral angle restraints: 3181
    sinusoidal: 1288
      harmonic: 1893
  Sorted by residual:
  dihedral pdb=" CB  CYS H 150 "
           pdb=" SG  CYS H 150 "
           pdb=" SG  CYS H 206 "
           pdb=" CB  CYS H 206 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  178.58  -85.58     1      1.00e+01 1.00e-02 8.86e+01
  dihedral pdb=" CA  VAL H  34 "
           pdb=" C   VAL H  34 "
           pdb=" N   GLN H  35 "
           pdb=" CA  GLN H  35 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.04   38.96     0      5.00e+00 4.00e-02 6.07e+01
  dihedral pdb=" CA  CYS H 101 "
           pdb=" C   CYS H 101 "
           pdb=" N   ASN H 102 "
           pdb=" CA  ASN H 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.12   37.88     0      5.00e+00 4.00e-02 5.74e+01
  ... (remaining 3178 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 475
       0.075 -    0.150: 276
       0.150 -    0.224: 39
       0.224 -    0.299: 5
       0.299 -    0.374: 2
  Chirality restraints: 797
  Sorted by residual:
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.34   -0.06 2.00e-02 2.50e+03 8.60e+00
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN H 102 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.03   -0.37 2.00e-01 2.50e+01 3.50e+00
  chirality pdb=" C1  NAG A   1 "
            pdb=" ND2 ASN C 343 "
            pdb=" C2  NAG A   1 "
            pdb=" O5  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.80e+00
  ... (remaining 794 not shown)

  Planarity restraints: 914
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   1 "   -0.181 2.00e-02 2.50e+03   1.50e-01 2.80e+02
        pdb=" C7  NAG A   1 "    0.074 2.00e-02 2.50e+03
        pdb=" C8  NAG A   1 "   -0.140 2.00e-02 2.50e+03
        pdb=" N2  NAG A   1 "    0.232 2.00e-02 2.50e+03
        pdb=" O7  NAG A   1 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   1 "    0.060 2.00e-02 2.50e+03   5.01e-02 3.14e+01
        pdb=" C7  NAG B   1 "   -0.035 2.00e-02 2.50e+03
        pdb=" C8  NAG B   1 "    0.051 2.00e-02 2.50e+03
        pdb=" N2  NAG B   1 "   -0.072 2.00e-02 2.50e+03
        pdb=" O7  NAG B   1 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L 110 "    0.368 9.50e-02 1.11e+02   1.65e-01 1.69e+01
        pdb=" NE  ARG L 110 "   -0.024 2.00e-02 2.50e+03
        pdb=" CZ  ARG L 110 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG L 110 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG L 110 "    0.011 2.00e-02 2.50e+03
  ... (remaining 911 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 207
        2.70 -     3.25: 5278
        3.25 -     3.80: 8452
        3.80 -     4.35: 10929
        4.35 -     4.90: 17257
  Nonbonded interactions: 42123
  Sorted by model distance:
  nonbonded pdb=" OG  SER H  17 "
            pdb=" OE1 GLU H  82 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" NH1 ARG C 357 "
            pdb=" O   ILE C 358 "
     model   vdw
     2.168 3.120
  nonbonded pdb=" O   ALA C 475 "
            pdb=" N   CYS H 106 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" NE2 GLN L  38 "
            pdb=" O   GLU L  82 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" OH  TYR C 473 "
            pdb=" O   THR H 104 "
     model   vdw
     2.245 3.040
  ... (remaining 42118 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             6.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     18.110
  Find NCS groups from input model:        0.080
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
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      :  0.007   0.039   5245  Z= 0.459
  Angle     :  1.132  13.074   7147  Z= 0.682
  Chirality :  0.085   0.374    797
  Planarity :  0.009   0.165    912
  Dihedral  : 14.363 121.455   1944
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 25.75
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 10.37 %
    Favored  : 89.32 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  2.65 %
    Favored  : 96.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 2.70 %
    Twisted General : 0.33 %

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: -2.47 (0.32), residues: 646
  helix: -2.31 (0.83), residues: 28
  sheet: -0.68 (0.36), residues: 217
  loop : -2.25 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.005   TRP C 353 
 HIS   0.007   0.002   HIS L 200 
 PHE   0.032   0.004   PHE H 176 
 TYR   0.030   0.004   TYR L  50 
 ARG   0.007   0.001   ARG L 110 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01708 (    2)
  link_NAG-ASN         : angle       9.00851 (    6)
  link_BETA1-4         : bond        0.00278 (    2)
  link_BETA1-4         : angle       2.16631 (    6)
  hydrogen bonds       : bond        0.29050 (  124)
  hydrogen bonds       : angle      11.87299 (  294)
  SS BOND              : bond        0.01061 (    9)
  SS BOND              : angle       1.15283 (   18)
  covalent geometry    : bond        0.00718 ( 5232)
  covalent geometry    : angle       1.10099 ( 7117)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 143
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  365 TYR cc_start: 0.9052 (m-80) cc_final: 0.8842 (m-80)
REVERT: C  377 PHE cc_start: 0.8966 (t80) cc_final: 0.8669 (t80)
REVERT: C  418 ILE cc_start: 0.9248 (pt) cc_final: 0.9040 (pt)
REVERT: C  429 PHE cc_start: 0.9101 (t80) cc_final: 0.8801 (t80)
REVERT: C  451 TYR cc_start: 0.6961 (m-80) cc_final: 0.6674 (m-80)
REVERT: C  478 LYS cc_start: 0.9190 (tmtt) cc_final: 0.8862 (tmtt)
REVERT: H   10 GLU cc_start: 0.8489 (mp0) cc_final: 0.8243 (pm20)
REVERT: H   73 ASP cc_start: 0.9360 (t0) cc_final: 0.9097 (t0)
REVERT: H   80 TYR cc_start: 0.9387 (m-80) cc_final: 0.9018 (m-80)
REVERT: H   93 MET cc_start: 0.8715 (tpp) cc_final: 0.8322 (tpp)
REVERT: L   37 TYR cc_start: 0.8936 (m-10) cc_final: 0.8720 (m-80)
REVERT: L   88 TYR cc_start: 0.8526 (m-10) cc_final: 0.8064 (m-10)
  outliers start: 4
  outliers final: 3
  residues processed: 147
  average time/residue: 0.2079
  time to fit residues: 37.2921
Evaluate side-chains
  138 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 135
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0970
   chunk 16 optimal weight:    0.0040
   chunk 32 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0980
   chunk 37 optimal weight:    0.6980
   chunk 58 optimal weight:    0.4980
   overall best weight:    0.2790

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

Flipped N/Q/H residues before XYZ refinement:
C 360 ASN
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 ASN
** L  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 126 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.179990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.143944 restraints weight = 10923.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.150328 restraints weight = 6784.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.155214 restraints weight = 4676.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6437
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5245  Z= 0.158
  Angle     :  0.743   9.134   7147  Z= 0.377
  Chirality :  0.049   0.223    797
  Planarity :  0.006   0.055    912
  Dihedral  : 10.813 112.272    796
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 20.58
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.29 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 2.70 %
    Twisted General : 0.16 %

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: -2.21 (0.32), residues: 646
  helix: -1.91 (0.90), residues: 28
  sheet: -0.58 (0.35), residues: 226
  loop : -2.07 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 353 
 HIS   0.006   0.002   HIS L 191 
 PHE   0.017   0.002   PHE H 176 
 TYR   0.020   0.002   TYR C 351 
 ARG   0.007   0.001   ARG C 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00807 (    2)
  link_NAG-ASN         : angle       5.87889 (    6)
  link_BETA1-4         : bond        0.00155 (    2)
  link_BETA1-4         : angle       2.02354 (    6)
  hydrogen bonds       : bond        0.04938 (  124)
  hydrogen bonds       : angle       8.98036 (  294)
  SS BOND              : bond        0.00281 (    9)
  SS BOND              : angle       1.11471 (   18)
  covalent geometry    : bond        0.00334 ( 5232)
  covalent geometry    : angle       0.72066 ( 7117)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  355 ARG cc_start: 0.7871 (mmm160) cc_final: 0.7412 (mmm160)
REVERT: C  357 ARG cc_start: 0.7254 (tpt90) cc_final: 0.6891 (tpt90)
REVERT: C  358 ILE cc_start: 0.7154 (mp) cc_final: 0.6940 (mp)
REVERT: C  392 PHE cc_start: 0.6858 (m-10) cc_final: 0.6558 (m-10)
REVERT: C  398 ASP cc_start: 0.6238 (p0) cc_final: 0.5455 (p0)
REVERT: C  418 ILE cc_start: 0.8658 (pt) cc_final: 0.8348 (pt)
REVERT: C  423 TYR cc_start: 0.7874 (t80) cc_final: 0.7391 (t80)
REVERT: C  429 PHE cc_start: 0.8059 (t80) cc_final: 0.7590 (t80)
REVERT: C  451 TYR cc_start: 0.6302 (m-80) cc_final: 0.5777 (m-80)
REVERT: C  478 LYS cc_start: 0.8909 (tmtt) cc_final: 0.8537 (tmtt)
REVERT: H   10 GLU cc_start: 0.7764 (mp0) cc_final: 0.7457 (mp0)
REVERT: H   38 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7444 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8663 (pm20) cc_final: 0.8258 (pm20)
REVERT: H   64 PHE cc_start: 0.8431 (m-10) cc_final: 0.8163 (m-10)
REVERT: H   73 ASP cc_start: 0.8562 (t0) cc_final: 0.7571 (t0)
REVERT: H   80 TYR cc_start: 0.6679 (m-80) cc_final: 0.6099 (m-80)
REVERT: H   93 MET cc_start: 0.8360 (tpp) cc_final: 0.8126 (tpp)
REVERT: H   94 TYR cc_start: 0.7733 (m-10) cc_final: 0.7465 (m-10)
REVERT: H  187 SER cc_start: 0.8140 (p) cc_final: 0.7821 (t)
REVERT: L   13 LEU cc_start: 0.8488 (tp) cc_final: 0.8206 (tp)
REVERT: L   86 MET cc_start: 0.6683 (tpp) cc_final: 0.6124 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.2006
  time to fit residues: 33.8319
Evaluate side-chains
  130 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 505 HIS
H  39 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  43 GLN
** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 212 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.173101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.138245 restraints weight = 11093.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.144710 restraints weight = 6857.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.149261 restraints weight = 4623.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6621
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   5245  Z= 0.261
  Angle     :  0.793   8.112   7147  Z= 0.414
  Chirality :  0.051   0.231    797
  Planarity :  0.006   0.057    912
  Dihedral  : 10.865 113.483    796
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 27.34
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 11.61 %
    Favored  : 88.08 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  6.55 %
    Favored  : 93.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 2.70 %
    Twisted General : 0.16 %

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: -2.17 (0.33), residues: 646
  helix: -2.46 (0.79), residues: 28
  sheet: -0.34 (0.36), residues: 214
  loop : -2.09 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP C 353 
 HIS   0.005   0.002   HIS L 191 
 PHE   0.018   0.002   PHE C 490 
 TYR   0.023   0.002   TYR L  50 
 ARG   0.011   0.001   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01030 (    2)
  link_NAG-ASN         : angle       5.04729 (    6)
  link_BETA1-4         : bond        0.00731 (    2)
  link_BETA1-4         : angle       2.52627 (    6)
  hydrogen bonds       : bond        0.05216 (  124)
  hydrogen bonds       : angle       8.66899 (  294)
  SS BOND              : bond        0.00506 (    9)
  SS BOND              : angle       1.23228 (   18)
  covalent geometry    : bond        0.00528 ( 5232)
  covalent geometry    : angle       0.77478 ( 7117)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7794 (m110) cc_final: 0.7537 (m110)
REVERT: C  378 LYS cc_start: 0.8958 (tmmt) cc_final: 0.8697 (tmmt)
REVERT: C  392 PHE cc_start: 0.6946 (m-10) cc_final: 0.6502 (m-10)
REVERT: C  418 ILE cc_start: 0.8741 (pt) cc_final: 0.8468 (pt)
REVERT: C  423 TYR cc_start: 0.7854 (t80) cc_final: 0.7336 (t80)
REVERT: C  429 PHE cc_start: 0.8129 (t80) cc_final: 0.7561 (t80)
REVERT: C  451 TYR cc_start: 0.6086 (m-80) cc_final: 0.5681 (m-80)
REVERT: C  457 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7381 (ttp80)
REVERT: C  478 LYS cc_start: 0.8756 (tmtt) cc_final: 0.8537 (tmtt)
REVERT: H   10 GLU cc_start: 0.7868 (mp0) cc_final: 0.7459 (mp0)
REVERT: H   38 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7744 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8768 (pm20) cc_final: 0.8206 (pm20)
REVERT: H   64 PHE cc_start: 0.8553 (m-10) cc_final: 0.8229 (m-10)
REVERT: H   73 ASP cc_start: 0.8655 (t0) cc_final: 0.7477 (t0)
REVERT: H   80 TYR cc_start: 0.6777 (m-80) cc_final: 0.6183 (m-80)
REVERT: H   93 MET cc_start: 0.8507 (tpp) cc_final: 0.8297 (tpp)
REVERT: L   13 LEU cc_start: 0.8745 (tp) cc_final: 0.8352 (tp)
REVERT: L   49 ILE cc_start: 0.4290 (mp) cc_final: 0.4054 (mp)
REVERT: L   86 MET cc_start: 0.7061 (tpp) cc_final: 0.6508 (tpp)
REVERT: L  142 TYR cc_start: 0.7360 (t80) cc_final: 0.7075 (t80)
REVERT: L  174 THR cc_start: 0.7070 (m) cc_final: 0.6725 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2054
  time to fit residues: 37.0785
Evaluate side-chains
  137 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    0.0050
   chunk 25 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0970
   chunk 47 optimal weight:    0.0470
   chunk 3 optimal weight:    0.3980
   chunk 46 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0570
   chunk 14 optimal weight:    0.2980
   chunk 50 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.0808

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

Flipped N/Q/H residues before XYZ refinement:
C 505 HIS
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 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 = 0.4482 r_free = 0.4482 target = 0.181002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.145257 restraints weight = 11364.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.152192 restraints weight = 7109.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.157062 restraints weight = 4806.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6416
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5245  Z= 0.127
  Angle     :  0.717   8.720   7147  Z= 0.361
  Chirality :  0.049   0.229    797
  Planarity :  0.005   0.053    912
  Dihedral  :  9.865 105.780    796
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 18.99
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.05 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 2.70 %
    Twisted General : 0.16 %

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: -1.97 (0.33), residues: 646
  helix: -2.33 (0.84), residues: 28
  sheet: -0.02 (0.37), residues: 211
  loop : -2.07 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.005   0.002   HIS C 519 
 PHE   0.016   0.002   PHE C 464 
 TYR   0.016   0.002   TYR C 380 
 ARG   0.005   0.000   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01043 (    2)
  link_NAG-ASN         : angle       4.67450 (    6)
  link_BETA1-4         : bond        0.00466 (    2)
  link_BETA1-4         : angle       1.89997 (    6)
  hydrogen bonds       : bond        0.03598 (  124)
  hydrogen bonds       : angle       8.05976 (  294)
  SS BOND              : bond        0.00294 (    9)
  SS BOND              : angle       1.21663 (   18)
  covalent geometry    : bond        0.00277 ( 5232)
  covalent geometry    : angle       0.70108 ( 7117)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  355 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7700 (mmm160)
REVERT: C  392 PHE cc_start: 0.6970 (m-10) cc_final: 0.6604 (m-10)
REVERT: C  398 ASP cc_start: 0.6251 (p0) cc_final: 0.5125 (p0)
REVERT: C  414 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7081 (tm-30)
REVERT: C  418 ILE cc_start: 0.8576 (pt) cc_final: 0.8336 (pt)
REVERT: C  425 LEU cc_start: 0.7939 (mp) cc_final: 0.7652 (mp)
REVERT: C  429 PHE cc_start: 0.8114 (t80) cc_final: 0.7600 (t80)
REVERT: C  451 TYR cc_start: 0.6192 (m-80) cc_final: 0.5762 (m-80)
REVERT: C  455 LEU cc_start: 0.5948 (mt) cc_final: 0.5718 (mt)
REVERT: C  457 ARG cc_start: 0.7590 (ttp80) cc_final: 0.7376 (ttp80)
REVERT: H   10 GLU cc_start: 0.7675 (mp0) cc_final: 0.7120 (mp0)
REVERT: H   38 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7716 (tmm-80)
REVERT: H   39 GLN cc_start: 0.7790 (tt0) cc_final: 0.7542 (tt0)
REVERT: H   62 GLN cc_start: 0.8667 (pm20) cc_final: 0.8323 (pm20)
REVERT: H   64 PHE cc_start: 0.8497 (m-10) cc_final: 0.8246 (m-10)
REVERT: H   73 ASP cc_start: 0.8381 (t0) cc_final: 0.7289 (t0)
REVERT: H   80 TYR cc_start: 0.6613 (m-80) cc_final: 0.6144 (m-80)
REVERT: L   13 LEU cc_start: 0.8521 (tp) cc_final: 0.8183 (tp)
REVERT: L  174 THR cc_start: 0.6684 (m) cc_final: 0.6416 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1939
  time to fit residues: 33.0826
Evaluate side-chains
  129 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0170
   chunk 4 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
C 422 ASN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 126 GLN
** L 200 HIS ** 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 = 0.4384 r_free = 0.4384 target = 0.172233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.137275 restraints weight = 11175.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.143717 restraints weight = 7006.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.148437 restraints weight = 4780.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6635
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   5245  Z= 0.247
  Angle     :  0.775   8.787   7147  Z= 0.402
  Chirality :  0.049   0.226    797
  Planarity :  0.006   0.053    912
  Dihedral  : 10.007 106.285    796
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 27.24
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 11.30 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.89 (0.33), residues: 646
  helix: -2.39 (0.82), residues: 28
  sheet: -0.05 (0.37), residues: 210
  loop : -1.94 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  36 
 HIS   0.004   0.001   HIS C 519 
 PHE   0.016   0.002   PHE H  29 
 TYR   0.027   0.002   TYR L 188 
 ARG   0.005   0.001   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00904 (    2)
  link_NAG-ASN         : angle       4.88214 (    6)
  link_BETA1-4         : bond        0.00772 (    2)
  link_BETA1-4         : angle       2.24489 (    6)
  hydrogen bonds       : bond        0.04806 (  124)
  hydrogen bonds       : angle       8.26162 (  294)
  SS BOND              : bond        0.00489 (    9)
  SS BOND              : angle       1.35117 (   18)
  covalent geometry    : bond        0.00499 ( 5232)
  covalent geometry    : angle       0.75783 ( 7117)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7778 (m110) cc_final: 0.7485 (m110)
REVERT: C  392 PHE cc_start: 0.6975 (m-10) cc_final: 0.6600 (m-10)
REVERT: C  418 ILE cc_start: 0.8598 (pt) cc_final: 0.8340 (pt)
REVERT: C  429 PHE cc_start: 0.8192 (t80) cc_final: 0.7629 (t80)
REVERT: C  451 TYR cc_start: 0.6223 (m-80) cc_final: 0.5739 (m-80)
REVERT: C  478 LYS cc_start: 0.8957 (tmtt) cc_final: 0.8568 (tmtt)
REVERT: C  513 LEU cc_start: 0.7755 (mt) cc_final: 0.7553 (mt)
REVERT: H   10 GLU cc_start: 0.7825 (mp0) cc_final: 0.7081 (mp0)
REVERT: H   38 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7923 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8803 (pm20) cc_final: 0.8204 (pm20)
REVERT: H   64 PHE cc_start: 0.8581 (m-10) cc_final: 0.8306 (m-10)
REVERT: H   73 ASP cc_start: 0.8605 (t0) cc_final: 0.7290 (t0)
REVERT: H   74 MET cc_start: 0.7607 (mmt) cc_final: 0.7277 (mmt)
REVERT: H   76 THR cc_start: 0.8291 (t) cc_final: 0.8057 (t)
REVERT: H   80 TYR cc_start: 0.6622 (m-80) cc_final: 0.6187 (m-80)
REVERT: H   94 TYR cc_start: 0.7821 (m-10) cc_final: 0.7508 (m-10)
REVERT: L   13 LEU cc_start: 0.8698 (tp) cc_final: 0.7654 (tp)
REVERT: L   17 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7018 (mt-10)
REVERT: L   37 TYR cc_start: 0.7812 (m-10) cc_final: 0.7548 (m-80)
REVERT: L   92 TYR cc_start: 0.8154 (p90) cc_final: 0.7716 (p90)
REVERT: L  134 VAL cc_start: 0.8280 (t) cc_final: 0.7901 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1949
  time to fit residues: 34.5469
Evaluate side-chains
  136 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 8 optimal weight:    0.4980
   chunk 30 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0470
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.4878

-------------------------------------------------------------------------------
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   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 ASN
** L  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 126 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.173481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.138751 restraints weight = 11287.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.145314 restraints weight = 7122.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.150110 restraints weight = 4860.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6593
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5245  Z= 0.189
  Angle     :  0.752   8.801   7147  Z= 0.385
  Chirality :  0.049   0.228    797
  Planarity :  0.006   0.053    912
  Dihedral  :  9.771 104.577    796
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 22.47
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.37 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.91 (0.33), residues: 646
  helix: -2.32 (0.83), residues: 28
  sheet: -0.11 (0.37), residues: 210
  loop : -1.93 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H 113 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.028   0.002   PHE C 515 
 TYR   0.023   0.002   TYR L  50 
 ARG   0.005   0.001   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01047 (    2)
  link_NAG-ASN         : angle       4.80632 (    6)
  link_BETA1-4         : bond        0.00639 (    2)
  link_BETA1-4         : angle       1.93161 (    6)
  hydrogen bonds       : bond        0.04101 (  124)
  hydrogen bonds       : angle       8.03467 (  294)
  SS BOND              : bond        0.00375 (    9)
  SS BOND              : angle       1.27008 (   18)
  covalent geometry    : bond        0.00389 ( 5232)
  covalent geometry    : angle       0.73522 ( 7117)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7728 (m110) cc_final: 0.7438 (m110)
REVERT: C  377 PHE cc_start: 0.8812 (t80) cc_final: 0.8534 (t80)
REVERT: C  392 PHE cc_start: 0.6939 (m-10) cc_final: 0.6565 (m-10)
REVERT: C  402 ILE cc_start: 0.8478 (tp) cc_final: 0.8270 (tp)
REVERT: C  418 ILE cc_start: 0.8657 (pt) cc_final: 0.8438 (pt)
REVERT: C  422 ASN cc_start: 0.7622 (m110) cc_final: 0.7374 (m110)
REVERT: C  423 TYR cc_start: 0.7754 (t80) cc_final: 0.7240 (t80)
REVERT: C  429 PHE cc_start: 0.8090 (t80) cc_final: 0.7664 (t80)
REVERT: C  451 TYR cc_start: 0.5960 (m-80) cc_final: 0.5527 (m-80)
REVERT: C  478 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8657 (tmtt)
REVERT: C  493 ARG cc_start: 0.6891 (ttp-110) cc_final: 0.6557 (ttp-110)
REVERT: H   10 GLU cc_start: 0.7722 (mp0) cc_final: 0.7104 (mp0)
REVERT: H   38 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7737 (ttp80)
REVERT: H   47 TRP cc_start: 0.8087 (t60) cc_final: 0.6622 (t60)
REVERT: H   62 GLN cc_start: 0.8799 (pm20) cc_final: 0.8206 (pm20)
REVERT: H   73 ASP cc_start: 0.8500 (t0) cc_final: 0.7225 (t0)
REVERT: H   74 MET cc_start: 0.7492 (mmt) cc_final: 0.7145 (mmt)
REVERT: H   76 THR cc_start: 0.8213 (t) cc_final: 0.7979 (t)
REVERT: H   80 TYR cc_start: 0.6649 (m-80) cc_final: 0.6254 (m-80)
REVERT: H   93 MET cc_start: 0.8397 (tpp) cc_final: 0.8100 (tpp)
REVERT: L   13 LEU cc_start: 0.8723 (tp) cc_final: 0.7766 (tp)
REVERT: L   17 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6916 (mt-10)
REVERT: L   37 TYR cc_start: 0.7831 (m-10) cc_final: 0.7620 (m-80)
REVERT: L   92 TYR cc_start: 0.8163 (p90) cc_final: 0.7634 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.2040
  time to fit residues: 37.8097
Evaluate side-chains
  140 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 15 optimal weight:    0.1980
   chunk 58 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0020
   chunk 61 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0470
   chunk 16 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0060
   chunk 13 optimal weight:    0.2980
   overall best weight:    0.1102

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 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 = 0.4447 r_free = 0.4447 target = 0.178520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.143312 restraints weight = 10922.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.149804 restraints weight = 6939.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.154554 restraints weight = 4763.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6463
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5245  Z= 0.127
  Angle     :  0.710   8.725   7147  Z= 0.359
  Chirality :  0.049   0.218    797
  Planarity :  0.005   0.053    912
  Dihedral  :  9.499 104.185    796
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 18.19
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.06 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    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: -1.65 (0.34), residues: 646
  helix: -2.23 (0.84), residues: 28
  sheet:  0.14 (0.38), residues: 222
  loop : -1.84 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 113 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.013   0.002   PHE L 141 
 TYR   0.017   0.001   TYR L  50 
 ARG   0.004   0.001   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00993 (    2)
  link_NAG-ASN         : angle       4.41050 (    6)
  link_BETA1-4         : bond        0.00564 (    2)
  link_BETA1-4         : angle       1.71991 (    6)
  hydrogen bonds       : bond        0.03413 (  124)
  hydrogen bonds       : angle       7.57987 (  294)
  SS BOND              : bond        0.00445 (    9)
  SS BOND              : angle       1.12522 (   18)
  covalent geometry    : bond        0.00282 ( 5232)
  covalent geometry    : angle       0.69529 ( 7117)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7593 (m110) cc_final: 0.7281 (m110)
REVERT: C  377 PHE cc_start: 0.8712 (t80) cc_final: 0.8426 (t80)
REVERT: C  392 PHE cc_start: 0.7009 (m-10) cc_final: 0.6661 (m-10)
REVERT: C  418 ILE cc_start: 0.8522 (pt) cc_final: 0.8247 (pt)
REVERT: C  422 ASN cc_start: 0.7576 (m110) cc_final: 0.7338 (m110)
REVERT: C  429 PHE cc_start: 0.8088 (t80) cc_final: 0.7489 (t80)
REVERT: C  451 TYR cc_start: 0.5981 (m-80) cc_final: 0.5573 (m-80)
REVERT: C  455 LEU cc_start: 0.6276 (mt) cc_final: 0.5738 (mt)
REVERT: C  478 LYS cc_start: 0.8961 (tmtt) cc_final: 0.8693 (tmtt)
REVERT: C  513 LEU cc_start: 0.7797 (mt) cc_final: 0.7568 (mt)
REVERT: H   10 GLU cc_start: 0.7641 (mp0) cc_final: 0.7025 (mp0)
REVERT: H   38 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7784 (ttp80)
REVERT: H   62 GLN cc_start: 0.8816 (pm20) cc_final: 0.8560 (pm20)
REVERT: H   73 ASP cc_start: 0.8387 (t0) cc_final: 0.7164 (t0)
REVERT: H   74 MET cc_start: 0.7408 (mmt) cc_final: 0.7047 (mmt)
REVERT: H   76 THR cc_start: 0.8181 (t) cc_final: 0.7952 (t)
REVERT: H   80 TYR cc_start: 0.6600 (m-80) cc_final: 0.6280 (m-80)
REVERT: H   93 MET cc_start: 0.8424 (tpp) cc_final: 0.8163 (tpp)
REVERT: H  176 PHE cc_start: 0.6868 (t80) cc_final: 0.6508 (t80)
REVERT: L   13 LEU cc_start: 0.8530 (tp) cc_final: 0.7531 (tp)
REVERT: L   17 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6623 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1999
  time to fit residues: 34.9061
Evaluate side-chains
  134 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    0.3980
   chunk 42 optimal weight:    0.1980
   chunk 59 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    0.3980
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 ASN
L 126 GLN
** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.173551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.139213 restraints weight = 10967.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.145496 restraints weight = 6836.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.150219 restraints weight = 4640.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.4123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6568
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   5245  Z= 0.191
  Angle     :  0.770  13.867   7147  Z= 0.392
  Chirality :  0.049   0.220    797
  Planarity :  0.006   0.053    912
  Dihedral  :  9.690 105.105    796
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 23.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.68 %
    Favored  : 89.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.64 (0.34), residues: 646
  helix: -2.17 (0.84), residues: 28
  sheet:  0.23 (0.38), residues: 209
  loop : -1.83 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP L 150 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.014   0.002   PHE C 342 
 TYR   0.021   0.002   TYR L 188 
 ARG   0.005   0.001   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00983 (    2)
  link_NAG-ASN         : angle       4.59938 (    6)
  link_BETA1-4         : bond        0.00532 (    2)
  link_BETA1-4         : angle       1.92383 (    6)
  hydrogen bonds       : bond        0.04085 (  124)
  hydrogen bonds       : angle       7.83196 (  294)
  SS BOND              : bond        0.00428 (    9)
  SS BOND              : angle       1.44730 (   18)
  covalent geometry    : bond        0.00401 ( 5232)
  covalent geometry    : angle       0.75396 ( 7117)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7758 (m110) cc_final: 0.7433 (m110)
REVERT: C  392 PHE cc_start: 0.6997 (m-10) cc_final: 0.6664 (m-10)
REVERT: C  418 ILE cc_start: 0.8622 (pt) cc_final: 0.8379 (pt)
REVERT: C  422 ASN cc_start: 0.7716 (m110) cc_final: 0.7476 (m110)
REVERT: C  429 PHE cc_start: 0.8234 (t80) cc_final: 0.7520 (t80)
REVERT: C  451 TYR cc_start: 0.6113 (m-80) cc_final: 0.5661 (m-80)
REVERT: C  455 LEU cc_start: 0.6419 (mt) cc_final: 0.5750 (mt)
REVERT: C  478 LYS cc_start: 0.8990 (tmtt) cc_final: 0.8662 (tmtt)
REVERT: H   62 GLN cc_start: 0.8859 (pm20) cc_final: 0.8321 (pm20)
REVERT: H   73 ASP cc_start: 0.8525 (t0) cc_final: 0.7318 (t0)
REVERT: H   76 THR cc_start: 0.8233 (t) cc_final: 0.7994 (t)
REVERT: H   80 TYR cc_start: 0.6576 (m-80) cc_final: 0.6270 (m-80)
REVERT: H   94 TYR cc_start: 0.7755 (m-10) cc_final: 0.7452 (m-10)
REVERT: H  176 PHE cc_start: 0.7029 (t80) cc_final: 0.6566 (t80)
REVERT: L   13 LEU cc_start: 0.8691 (tp) cc_final: 0.7714 (tp)
REVERT: L   17 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6726 (mt-10)
REVERT: L   37 TYR cc_start: 0.7860 (m-10) cc_final: 0.7521 (m-80)
REVERT: L   92 TYR cc_start: 0.8205 (p90) cc_final: 0.7716 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1995
  time to fit residues: 34.9821
Evaluate side-chains
  131 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 34 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 57 optimal weight:    0.5980
   chunk 40 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 19 optimal weight:    0.1980
   chunk 38 optimal weight:    0.5980
   chunk 17 optimal weight:    0.4980
   chunk 10 optimal weight:    0.0670
   overall best weight:    0.2918

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

Flipped N/Q/H residues before XYZ refinement:
C 506 GLN
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 126 GLN
** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 200 HIS ** 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 = 0.4420 r_free = 0.4420 target = 0.176318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.142089 restraints weight = 10806.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.148281 restraints weight = 6842.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.152957 restraints weight = 4701.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6509
moved from start:          0.3393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5245  Z= 0.145
  Angle     :  0.735   8.788   7147  Z= 0.373
  Chirality :  0.049   0.216    797
  Planarity :  0.005   0.053    912
  Dihedral  :  9.525 104.163    796
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 19.98
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.91 %
    Favored  : 89.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.61 (0.34), residues: 646
  helix: -2.16 (0.85), residues: 28
  sheet:  0.28 (0.38), residues: 210
  loop : -1.84 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H 113 
 HIS   0.003   0.001   HIS L  91 
 PHE   0.014   0.002   PHE L 141 
 TYR   0.017   0.001   TYR L  50 
 ARG   0.003   0.000   ARG C 493 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00912 (    2)
  link_NAG-ASN         : angle       4.39086 (    6)
  link_BETA1-4         : bond        0.00570 (    2)
  link_BETA1-4         : angle       1.71216 (    6)
  hydrogen bonds       : bond        0.03545 (  124)
  hydrogen bonds       : angle       7.64303 (  294)
  SS BOND              : bond        0.00375 (    9)
  SS BOND              : angle       1.33955 (   18)
  covalent geometry    : bond        0.00311 ( 5232)
  covalent geometry    : angle       0.72105 ( 7117)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7650 (m110) cc_final: 0.7346 (m110)
REVERT: C  392 PHE cc_start: 0.6967 (m-10) cc_final: 0.6657 (m-10)
REVERT: C  418 ILE cc_start: 0.8532 (pt) cc_final: 0.8322 (pt)
REVERT: C  422 ASN cc_start: 0.7624 (m110) cc_final: 0.7398 (m110)
REVERT: C  429 PHE cc_start: 0.8189 (t80) cc_final: 0.7529 (t80)
REVERT: C  451 TYR cc_start: 0.5952 (m-80) cc_final: 0.5568 (m-80)
REVERT: C  455 LEU cc_start: 0.6386 (mt) cc_final: 0.5681 (mt)
REVERT: C  478 LYS cc_start: 0.8996 (tmtt) cc_final: 0.8678 (tmtt)
REVERT: H   10 GLU cc_start: 0.7587 (mp0) cc_final: 0.6768 (mp0)
REVERT: H   38 ARG cc_start: 0.8127 (tmm-80) cc_final: 0.7622 (ttp80)
REVERT: H   62 GLN cc_start: 0.8841 (pm20) cc_final: 0.8308 (pm20)
REVERT: H   73 ASP cc_start: 0.8394 (t0) cc_final: 0.7111 (t0)
REVERT: H   74 MET cc_start: 0.7374 (mmt) cc_final: 0.7073 (mmt)
REVERT: H   76 THR cc_start: 0.8144 (t) cc_final: 0.7928 (t)
REVERT: H   80 TYR cc_start: 0.6439 (m-80) cc_final: 0.6237 (m-80)
REVERT: H   93 MET cc_start: 0.8140 (tpp) cc_final: 0.7749 (tpp)
REVERT: H   94 TYR cc_start: 0.7740 (m-10) cc_final: 0.7506 (m-10)
REVERT: H  176 PHE cc_start: 0.6998 (t80) cc_final: 0.6511 (t80)
REVERT: L   13 LEU cc_start: 0.8642 (tp) cc_final: 0.7627 (tp)
REVERT: L   17 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6592 (mt-10)
REVERT: L   86 MET cc_start: 0.6831 (tpp) cc_final: 0.6617 (tpp)
REVERT: L  142 TYR cc_start: 0.7088 (t80) cc_final: 0.6552 (t80)
REVERT: L  174 THR cc_start: 0.7257 (m) cc_final: 0.6867 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1992
  time to fit residues: 34.5335
Evaluate side-chains
  136 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0070
   chunk 37 optimal weight:    0.3980
   chunk 38 optimal weight:    0.0970
   chunk 23 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 20 optimal weight:    0.4980
   chunk 63 optimal weight:    0.0570
   overall best weight:    0.2114

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 126 GLN
** L 200 HIS ** 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 = 0.4424 r_free = 0.4424 target = 0.177278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.142760 restraints weight = 10888.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.148981 restraints weight = 6850.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.153771 restraints weight = 4712.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.4161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6470
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5245  Z= 0.131
  Angle     :  0.728   9.175   7147  Z= 0.368
  Chirality :  0.048   0.215    797
  Planarity :  0.005   0.053    912
  Dihedral  :  9.414 103.145    796
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 18.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.58 (0.34), residues: 646
  helix: -2.17 (0.86), residues: 28
  sheet:  0.27 (0.37), residues: 215
  loop : -1.82 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP L 150 
 HIS   0.005   0.001   HIS C 519 
 PHE   0.014   0.001   PHE L 141 
 TYR   0.015   0.001   TYR L  50 
 ARG   0.004   0.000   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00889 (    2)
  link_NAG-ASN         : angle       4.36336 (    6)
  link_BETA1-4         : bond        0.00584 (    2)
  link_BETA1-4         : angle       1.64914 (    6)
  hydrogen bonds       : bond        0.03458 (  124)
  hydrogen bonds       : angle       7.46353 (  294)
  SS BOND              : bond        0.00351 (    9)
  SS BOND              : angle       1.28444 (   18)
  covalent geometry    : bond        0.00287 ( 5232)
  covalent geometry    : angle       0.71425 ( 7117)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7685 (m110) cc_final: 0.7419 (m110)
REVERT: C  378 LYS cc_start: 0.8913 (tttm) cc_final: 0.8596 (ttpp)
REVERT: C  392 PHE cc_start: 0.7002 (m-10) cc_final: 0.6672 (m-10)
REVERT: C  418 ILE cc_start: 0.8618 (pt) cc_final: 0.8408 (pt)
REVERT: C  422 ASN cc_start: 0.7682 (m110) cc_final: 0.7402 (m110)
REVERT: C  425 LEU cc_start: 0.7904 (mp) cc_final: 0.7677 (mp)
REVERT: C  429 PHE cc_start: 0.8211 (t80) cc_final: 0.7503 (t80)
REVERT: C  451 TYR cc_start: 0.5905 (m-80) cc_final: 0.5547 (m-80)
REVERT: C  455 LEU cc_start: 0.6305 (mt) cc_final: 0.5577 (mt)
REVERT: C  462 LYS cc_start: 0.9084 (ttpp) cc_final: 0.8830 (ttpp)
REVERT: C  478 LYS cc_start: 0.8978 (tmtt) cc_final: 0.8690 (tmtt)
REVERT: H   10 GLU cc_start: 0.7593 (mp0) cc_final: 0.6845 (mp0)
REVERT: H   38 ARG cc_start: 0.8009 (tmm-80) cc_final: 0.7565 (ttp80)
REVERT: H   62 GLN cc_start: 0.8840 (pm20) cc_final: 0.8290 (pm20)
REVERT: H   73 ASP cc_start: 0.8340 (t0) cc_final: 0.7035 (t0)
REVERT: H   74 MET cc_start: 0.7321 (mmt) cc_final: 0.7007 (mmt)
REVERT: H   76 THR cc_start: 0.8127 (t) cc_final: 0.7912 (t)
REVERT: H   93 MET cc_start: 0.8278 (tpp) cc_final: 0.7845 (tpp)
REVERT: H   94 TYR cc_start: 0.7655 (m-10) cc_final: 0.7426 (m-10)
REVERT: H  176 PHE cc_start: 0.6953 (t80) cc_final: 0.6503 (t80)
REVERT: L   13 LEU cc_start: 0.8578 (tp) cc_final: 0.8171 (tp)
REVERT: L  142 TYR cc_start: 0.7053 (t80) cc_final: 0.6526 (t80)
REVERT: L  174 THR cc_start: 0.7260 (m) cc_final: 0.6832 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.2068
  time to fit residues: 35.3273
Evaluate side-chains
  131 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 0 optimal weight:   40.0000
   chunk 4 optimal weight:    0.1980
   chunk 26 optimal weight:    0.3980
   chunk 24 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 22 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 126 GLN
** L 200 HIS ** 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 = 0.4396 r_free = 0.4396 target = 0.173717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.139699 restraints weight = 11257.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.145858 restraints weight = 7070.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.150525 restraints weight = 4867.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6573
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5245  Z= 0.177
  Angle     :  0.747   8.869   7147  Z= 0.383
  Chirality :  0.048   0.214    797
  Planarity :  0.006   0.053    912
  Dihedral  :  9.515 103.896    796
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 23.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.22 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.68 (0.34), residues: 646
  helix: -2.19 (0.84), residues: 28
  sheet:  0.19 (0.37), residues: 210
  loop : -1.86 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H 113 
 HIS   0.005   0.001   HIS L  91 
 PHE   0.017   0.002   PHE L 211 
 TYR   0.019   0.002   TYR L 188 
 ARG   0.007   0.001   ARG C 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00948 (    2)
  link_NAG-ASN         : angle       4.62297 (    6)
  link_BETA1-4         : bond        0.00506 (    2)
  link_BETA1-4         : angle       1.75168 (    6)
  hydrogen bonds       : bond        0.03833 (  124)
  hydrogen bonds       : angle       7.53142 (  294)
  SS BOND              : bond        0.00414 (    9)
  SS BOND              : angle       1.41280 (   18)
  covalent geometry    : bond        0.00374 ( 5232)
  covalent geometry    : angle       0.73123 ( 7117)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2425.12 seconds
wall clock time: 43 minutes 10.64 seconds (2590.64 seconds total)