Starting phenix.real_space_refine
on Thu Jun  5 05:19:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c89_16473/06_2025/8c89_16473_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c89_16473/06_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_16473/06_2025/8c89_16473.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c89_16473/06_2025/8c89_16473.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c89_16473/06_2025/8c89_16473_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c89_16473/06_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-5710/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: 6.69, per 1000 atoms: 1.31
  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: 1.42
  Conformation dependent library (CDL) restraints added in 645.9 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: 0.64
  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: 1.43

  Time building geometry restraints manager: 1.68 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:             133.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     19.820
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  156.300
-------------------------------------------------------------------------------
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  : 0.573 
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: 0.2142
  time to fit residues: 38.4245
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  : 0.540 
-------------------------------------------------------------------------------
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 = 40)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.143922 restraints weight = 10923.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.150562 restraints weight = 6790.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.155275 restraints weight = 4630.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6435
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       2.02351 (    6)
  hydrogen bonds       : bond        0.04938 (  124)
  hydrogen bonds       : angle       8.98035 (  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  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  355 ARG cc_start: 0.7874 (mmm160) cc_final: 0.7414 (mmm160)
REVERT: C  357 ARG cc_start: 0.7259 (tpt90) cc_final: 0.6894 (tpt90)
REVERT: C  358 ILE cc_start: 0.7155 (mp) cc_final: 0.6941 (mp)
REVERT: C  392 PHE cc_start: 0.6859 (m-10) cc_final: 0.6558 (m-10)
REVERT: C  398 ASP cc_start: 0.6239 (p0) cc_final: 0.5456 (p0)
REVERT: C  418 ILE cc_start: 0.8656 (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: 0.8061 (t80) cc_final: 0.7590 (t80)
REVERT: C  451 TYR cc_start: 0.6306 (m-80) cc_final: 0.5778 (m-80)
REVERT: C  478 LYS cc_start: 0.8909 (tmtt) cc_final: 0.8536 (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: 0.8662 (pm20) cc_final: 0.8258 (pm20)
REVERT: H   64 PHE cc_start: 0.8431 (m-10) cc_final: 0.8164 (m-10)
REVERT: H   73 ASP cc_start: 0.8563 (t0) cc_final: 0.7572 (t0)
REVERT: H   80 TYR cc_start: 0.6676 (m-80) cc_final: 0.6099 (m-80)
REVERT: H   93 MET cc_start: 0.8362 (tpp) cc_final: 0.8126 (tpp)
REVERT: H   94 TYR cc_start: 0.7732 (m-10) cc_final: 0.7465 (m-10)
REVERT: H  187 SER cc_start: 0.8137 (p) cc_final: 0.7817 (t)
REVERT: L   13 LEU cc_start: 0.8489 (tp) cc_final: 0.8206 (tp)
REVERT: L   86 MET cc_start: 0.6685 (tpp) cc_final: 0.6122 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1961
  time to fit residues: 33.1393
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  : 0.556 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 50 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 42 optimal weight:    0.1980
   chunk 11 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 212 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.175368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.140221 restraints weight = 11158.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.146643 restraints weight = 6942.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.151242 restraints weight = 4723.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6569
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   5245  Z= 0.226
  Angle     :  0.759   8.551   7147  Z= 0.392
  Chirality :  0.049   0.231    797
  Planarity :  0.006   0.051    912
  Dihedral  : 10.695 112.348    796
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 25.05
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 11.46 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  5.49 %
    Favored  : 94.34 %
  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: -2.06 (0.33), residues: 646
  helix: -2.38 (0.80), residues: 28
  sheet: -0.20 (0.36), residues: 214
  loop : -2.07 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 353 
 HIS   0.005   0.002   HIS L 191 
 PHE   0.014   0.002   PHE H 110 
 TYR   0.021   0.002   TYR C 380 
 ARG   0.008   0.001   ARG C 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01000 (    2)
  link_NAG-ASN         : angle       5.12310 (    6)
  link_BETA1-4         : bond        0.00616 (    2)
  link_BETA1-4         : angle       2.27225 (    6)
  hydrogen bonds       : bond        0.04834 (  124)
  hydrogen bonds       : angle       8.55143 (  294)
  SS BOND              : bond        0.00451 (    9)
  SS BOND              : angle       1.09585 (   18)
  covalent geometry    : bond        0.00458 ( 5232)
  covalent geometry    : angle       0.74048 ( 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
  149 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  355 ARG cc_start: 0.8298 (mmm160) cc_final: 0.7616 (mmm160)
REVERT: C  357 ARG cc_start: 0.7360 (tpt90) cc_final: 0.7067 (tpt90)
REVERT: C  378 LYS cc_start: 0.8923 (tmmt) cc_final: 0.8651 (tmmt)
REVERT: C  392 PHE cc_start: 0.6977 (m-10) cc_final: 0.6594 (m-10)
REVERT: C  398 ASP cc_start: 0.6474 (p0) cc_final: 0.5102 (p0)
REVERT: C  418 ILE cc_start: 0.8730 (pt) cc_final: 0.8427 (pt)
REVERT: C  423 TYR cc_start: 0.7890 (t80) cc_final: 0.7411 (t80)
REVERT: C  425 LEU cc_start: 0.8192 (mp) cc_final: 0.7940 (mp)
REVERT: C  429 PHE cc_start: 0.8141 (t80) cc_final: 0.7567 (t80)
REVERT: C  451 TYR cc_start: 0.6118 (m-80) cc_final: 0.5725 (m-80)
REVERT: C  457 ARG cc_start: 0.7720 (ttp80) cc_final: 0.7377 (ttp80)
REVERT: C  478 LYS cc_start: 0.8771 (tmtt) cc_final: 0.8545 (tmtt)
REVERT: H   10 GLU cc_start: 0.7850 (mp0) cc_final: 0.7456 (mp0)
REVERT: H   38 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7706 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8714 (pm20) cc_final: 0.8227 (pm20)
REVERT: H   64 PHE cc_start: 0.8524 (m-10) cc_final: 0.8210 (m-10)
REVERT: H   73 ASP cc_start: 0.8622 (t0) cc_final: 0.7507 (t0)
REVERT: H   80 TYR cc_start: 0.6734 (m-80) cc_final: 0.6157 (m-80)
REVERT: H   93 MET cc_start: 0.8452 (tpp) cc_final: 0.8251 (tpp)
REVERT: H   94 TYR cc_start: 0.7780 (m-10) cc_final: 0.7523 (m-10)
REVERT: L   13 LEU cc_start: 0.8672 (tp) cc_final: 0.8304 (tp)
REVERT: L  142 TYR cc_start: 0.7314 (t80) cc_final: 0.7078 (t80)
REVERT: L  174 THR cc_start: 0.7089 (m) cc_final: 0.6722 (t)
REVERT: L  201 GLN cc_start: 0.8424 (mp10) cc_final: 0.8076 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 149
  average time/residue: 0.2040
  time to fit residues: 37.3709
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  : 0.504 
-------------------------------------------------------------------------------
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:    0.0060
   chunk 25 optimal weight:    0.2980
   chunk 6 optimal weight:    0.0170
   chunk 47 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0970
   chunk 50 optimal weight:    0.1980
   chunk 9 optimal weight:    0.8980
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.1032

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

Flipped N/Q/H residues before XYZ refinement:
C 360 ASN
** L   6 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 = 0.4489 r_free = 0.4489 target = 0.181629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.146072 restraints weight = 11218.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.152694 restraints weight = 7024.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.157434 restraints weight = 4766.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6391
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5245  Z= 0.121
  Angle     :  0.716   8.899   7147  Z= 0.359
  Chirality :  0.048   0.224    797
  Planarity :  0.005   0.054    912
  Dihedral  :  9.744 104.562    796
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.05 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  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: -1.84 (0.33), residues: 646
  helix: -2.33 (0.85), residues: 28
  sheet: -0.02 (0.37), residues: 220
  loop : -1.95 (0.30), residues: 398

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   0.012   0.002   PHE C 392 
 TYR   0.015   0.002   TYR C 351 
 ARG   0.004   0.001   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01021 (    2)
  link_NAG-ASN         : angle       4.68642 (    6)
  link_BETA1-4         : bond        0.00562 (    2)
  link_BETA1-4         : angle       1.82650 (    6)
  hydrogen bonds       : bond        0.03548 (  124)
  hydrogen bonds       : angle       7.95007 (  294)
  SS BOND              : bond        0.00337 (    9)
  SS BOND              : angle       1.01236 (   18)
  covalent geometry    : bond        0.00262 ( 5232)
  covalent geometry    : angle       0.70051 ( 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
  139 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.490 
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  355 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7670 (mmm160)
REVERT: C  392 PHE cc_start: 0.6986 (m-10) cc_final: 0.6630 (m-10)
REVERT: C  398 ASP cc_start: 0.6120 (p0) cc_final: 0.5051 (p0)
REVERT: C  418 ILE cc_start: 0.8584 (pt) cc_final: 0.8368 (pt)
REVERT: C  425 LEU cc_start: 0.8139 (mp) cc_final: 0.7855 (mp)
REVERT: C  429 PHE cc_start: 0.8062 (t80) cc_final: 0.7661 (t80)
REVERT: C  451 TYR cc_start: 0.6039 (m-80) cc_final: 0.5623 (m-80)
REVERT: H   10 GLU cc_start: 0.7719 (mp0) cc_final: 0.7236 (mp0)
REVERT: H   38 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7758 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8657 (pm20) cc_final: 0.8352 (pm20)
REVERT: H   64 PHE cc_start: 0.8482 (m-10) cc_final: 0.8217 (m-10)
REVERT: H   73 ASP cc_start: 0.8371 (t0) cc_final: 0.7297 (t0)
REVERT: H   80 TYR cc_start: 0.6587 (m-80) cc_final: 0.6133 (m-80)
REVERT: L   13 LEU cc_start: 0.8503 (tp) cc_final: 0.8175 (tp)
REVERT: L  174 THR cc_start: 0.6715 (m) cc_final: 0.6416 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1849
  time to fit residues: 32.0553
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  : 0.537 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 57 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   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 422 ASN
C 505 HIS
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   6 GLN
** L  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  38 GLN
** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.171460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.136515 restraints weight = 11063.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.142756 restraints weight = 6855.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.147401 restraints weight = 4682.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   5245  Z= 0.261
  Angle     :  0.801   8.947   7147  Z= 0.416
  Chirality :  0.050   0.227    797
  Planarity :  0.006   0.059    912
  Dihedral  : 10.043 106.470    796
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 26.94
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 11.61 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  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: -1.93 (0.33), residues: 646
  helix: -2.37 (0.83), residues: 28
  sheet: -0.23 (0.36), residues: 217
  loop : -1.90 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  36 
 HIS   0.004   0.002   HIS C 519 
 PHE   0.018   0.002   PHE H  29 
 TYR   0.029   0.002   TYR L 188 
 ARG   0.006   0.001   ARG C 493 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00911 (    2)
  link_NAG-ASN         : angle       4.88303 (    6)
  link_BETA1-4         : bond        0.00755 (    2)
  link_BETA1-4         : angle       2.36339 (    6)
  hydrogen bonds       : bond        0.04847 (  124)
  hydrogen bonds       : angle       8.19234 (  294)
  SS BOND              : bond        0.00559 (    9)
  SS BOND              : angle       1.40087 (   18)
  covalent geometry    : bond        0.00528 ( 5232)
  covalent geometry    : angle       0.78378 ( 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
  150 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7898 (m110) cc_final: 0.7681 (m110)
REVERT: C  392 PHE cc_start: 0.6999 (m-10) cc_final: 0.6604 (m-10)
REVERT: C  418 ILE cc_start: 0.8656 (pt) cc_final: 0.8383 (pt)
REVERT: C  429 PHE cc_start: 0.8144 (t80) cc_final: 0.7631 (t80)
REVERT: C  451 TYR cc_start: 0.6174 (m-80) cc_final: 0.5706 (m-80)
REVERT: C  455 LEU cc_start: 0.6117 (mt) cc_final: 0.5672 (mt)
REVERT: C  462 LYS cc_start: 0.9095 (ttpp) cc_final: 0.8870 (ttpp)
REVERT: C  478 LYS cc_start: 0.8942 (tmtt) cc_final: 0.8512 (tmtt)
REVERT: C  513 LEU cc_start: 0.7765 (mt) cc_final: 0.7540 (mt)
REVERT: H   10 GLU cc_start: 0.7768 (mp0) cc_final: 0.7108 (mp0)
REVERT: H   38 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7836 (tmm-80)
REVERT: H   47 TRP cc_start: 0.8165 (t60) cc_final: 0.7671 (t60)
REVERT: H   62 GLN cc_start: 0.8810 (pm20) cc_final: 0.8243 (pm20)
REVERT: H   64 PHE cc_start: 0.8587 (m-10) cc_final: 0.8302 (m-10)
REVERT: H   73 ASP cc_start: 0.8658 (t0) cc_final: 0.7474 (t0)
REVERT: H   76 THR cc_start: 0.8290 (t) cc_final: 0.8068 (t)
REVERT: H   80 TYR cc_start: 0.6658 (m-80) cc_final: 0.6216 (m-80)
REVERT: H   94 TYR cc_start: 0.7815 (m-10) cc_final: 0.7485 (m-10)
REVERT: L   13 LEU cc_start: 0.8682 (tp) cc_final: 0.7656 (tp)
REVERT: L   17 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7037 (mt-10)
REVERT: L   37 TYR cc_start: 0.7783 (m-10) cc_final: 0.7500 (m-80)
REVERT: L   49 ILE cc_start: 0.4492 (mp) cc_final: 0.4281 (mp)
REVERT: L   92 TYR cc_start: 0.8207 (p90) cc_final: 0.7775 (p90)
REVERT: L  134 VAL cc_start: 0.8284 (t) cc_final: 0.7915 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1945
  time to fit residues: 36.2083
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  : 0.497 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 8 optimal weight:    0.0370
   chunk 30 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 10 optimal weight:    0.1980
   chunk 12 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.5260

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

Flipped N/Q/H residues before XYZ refinement:
L  32 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.173497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.138406 restraints weight = 10962.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.144793 restraints weight = 6870.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.149526 restraints weight = 4691.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6591
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5245  Z= 0.198
  Angle     :  0.757   8.864   7147  Z= 0.388
  Chirality :  0.050   0.228    797
  Planarity :  0.006   0.054    912
  Dihedral  :  9.776 104.626    796
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 23.76
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.75 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  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: -1.97 (0.33), residues: 646
  helix: -2.33 (0.87), residues: 28
  sheet: -0.26 (0.36), residues: 220
  loop : -1.94 (0.31), residues: 398

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   0.017   0.002   PHE C 464 
 TYR   0.023   0.002   TYR L  50 
 ARG   0.004   0.001   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00995 (    2)
  link_NAG-ASN         : angle       4.70391 (    6)
  link_BETA1-4         : bond        0.00597 (    2)
  link_BETA1-4         : angle       1.97988 (    6)
  hydrogen bonds       : bond        0.04114 (  124)
  hydrogen bonds       : angle       8.03262 (  294)
  SS BOND              : bond        0.00529 (    9)
  SS BOND              : angle       1.34114 (   18)
  covalent geometry    : bond        0.00412 ( 5232)
  covalent geometry    : angle       0.74045 ( 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
  144 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7894 (m110) cc_final: 0.7676 (m110)
REVERT: C  377 PHE cc_start: 0.8785 (t80) cc_final: 0.8520 (t80)
REVERT: C  392 PHE cc_start: 0.6987 (m-10) cc_final: 0.6612 (m-10)
REVERT: C  418 ILE cc_start: 0.8656 (pt) cc_final: 0.8431 (pt)
REVERT: C  422 ASN cc_start: 0.7628 (m110) cc_final: 0.7370 (m110)
REVERT: C  423 TYR cc_start: 0.7753 (t80) cc_final: 0.7348 (t80)
REVERT: C  429 PHE cc_start: 0.8120 (t80) cc_final: 0.7522 (t80)
REVERT: C  451 TYR cc_start: 0.6400 (m-80) cc_final: 0.5875 (m-80)
REVERT: C  462 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8816 (ttpp)
REVERT: C  464 PHE cc_start: 0.9003 (m-80) cc_final: 0.8721 (m-10)
REVERT: C  478 LYS cc_start: 0.8959 (tmtt) cc_final: 0.8604 (tmtt)
REVERT: H   10 GLU cc_start: 0.7707 (mp0) cc_final: 0.7095 (mp0)
REVERT: H   47 TRP cc_start: 0.8106 (t60) cc_final: 0.6714 (t60)
REVERT: H   62 GLN cc_start: 0.8815 (pm20) cc_final: 0.8245 (pm20)
REVERT: H   73 ASP cc_start: 0.8539 (t0) cc_final: 0.7285 (t0)
REVERT: H   74 MET cc_start: 0.7508 (mmt) cc_final: 0.7201 (mmt)
REVERT: H   76 THR cc_start: 0.8230 (t) cc_final: 0.8000 (t)
REVERT: H   80 TYR cc_start: 0.6608 (m-80) cc_final: 0.6216 (m-80)
REVERT: H   93 MET cc_start: 0.8427 (tpp) cc_final: 0.8121 (tpp)
REVERT: H   94 TYR cc_start: 0.7873 (m-10) cc_final: 0.7631 (m-10)
REVERT: L   13 LEU cc_start: 0.8710 (tp) cc_final: 0.7741 (tp)
REVERT: L   17 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6931 (mt-10)
REVERT: L   37 TYR cc_start: 0.7798 (m-10) cc_final: 0.7592 (m-80)
REVERT: L   40 LYS cc_start: 0.8581 (mmmt) cc_final: 0.8370 (mmpt)
REVERT: L   92 TYR cc_start: 0.8186 (p90) cc_final: 0.7735 (p90)
REVERT: L  134 VAL cc_start: 0.8337 (t) cc_final: 0.7997 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1987
  time to fit residues: 35.5412
Evaluate side-chains
  138 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 57 optimal weight:    0.2980
   chunk 61 optimal weight:    0.1980
   chunk 8 optimal weight:    0.4980
   chunk 43 optimal weight:    4.9990
   chunk 21 optimal weight:    0.1980
   chunk 16 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0670
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.2318

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.176208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.142203 restraints weight = 10849.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.148524 restraints weight = 6833.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.153111 restraints weight = 4654.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.4147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6484
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5245  Z= 0.138
  Angle     :  0.721   8.735   7147  Z= 0.367
  Chirality :  0.048   0.216    797
  Planarity :  0.006   0.053    912
  Dihedral  :  9.599 104.568    796
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 19.28
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.06 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  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: -1.78 (0.33), residues: 646
  helix: -2.32 (0.85), residues: 28
  sheet:  0.01 (0.37), residues: 219
  loop : -1.89 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 113 
 HIS   0.002   0.001   HIS L  91 
 PHE   0.030   0.002   PHE C 515 
 TYR   0.018   0.001   TYR L  50 
 ARG   0.004   0.001   ARG C 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01000 (    2)
  link_NAG-ASN         : angle       4.38186 (    6)
  link_BETA1-4         : bond        0.00585 (    2)
  link_BETA1-4         : angle       1.80809 (    6)
  hydrogen bonds       : bond        0.03701 (  124)
  hydrogen bonds       : angle       7.63061 (  294)
  SS BOND              : bond        0.00339 (    9)
  SS BOND              : angle       1.13629 (   18)
  covalent geometry    : bond        0.00303 ( 5232)
  covalent geometry    : angle       0.70727 ( 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
  140 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.553 
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: 0.7746 (m110) cc_final: 0.7520 (m110)
REVERT: C  377 PHE cc_start: 0.8734 (t80) cc_final: 0.8429 (t80)
REVERT: C  378 LYS cc_start: 0.8937 (tmmt) cc_final: 0.8643 (tmmt)
REVERT: C  392 PHE cc_start: 0.6975 (m-10) cc_final: 0.6636 (m-10)
REVERT: C  418 ILE cc_start: 0.8521 (pt) cc_final: 0.8207 (pt)
REVERT: C  422 ASN cc_start: 0.7506 (m110) cc_final: 0.7281 (m110)
REVERT: C  451 TYR cc_start: 0.6045 (m-80) cc_final: 0.5628 (m-80)
REVERT: C  462 LYS cc_start: 0.9073 (ttpp) cc_final: 0.8794 (ttpp)
REVERT: C  478 LYS cc_start: 0.8972 (tmtt) cc_final: 0.8663 (tmtt)
REVERT: H   10 GLU cc_start: 0.7679 (mp0) cc_final: 0.7076 (mp0)
REVERT: H   62 GLN cc_start: 0.8809 (pm20) cc_final: 0.8547 (pm20)
REVERT: H   73 ASP cc_start: 0.8406 (t0) cc_final: 0.7148 (t0)
REVERT: H   74 MET cc_start: 0.7445 (mmt) cc_final: 0.7105 (mmt)
REVERT: H   80 TYR cc_start: 0.6577 (m-80) cc_final: 0.6211 (m-80)
REVERT: H   93 MET cc_start: 0.8375 (tpp) cc_final: 0.8122 (tpp)
REVERT: H  176 PHE cc_start: 0.6850 (t80) cc_final: 0.6403 (t80)
REVERT: L   13 LEU cc_start: 0.8628 (tp) cc_final: 0.7646 (tp)
REVERT: L   17 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6697 (mt-10)
REVERT: L   40 LYS cc_start: 0.8528 (mmmt) cc_final: 0.8280 (mmpt)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1941
  time to fit residues: 34.0602
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  : 0.583 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0030
   chunk 28 optimal weight:    0.4980
   chunk 45 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    0.5390

-------------------------------------------------------------------------------
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  32 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.172476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.138531 restraints weight = 10944.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.144876 restraints weight = 6813.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.149419 restraints weight = 4625.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.4131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6588
moved from start:          0.3315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5245  Z= 0.206
  Angle     :  0.772  13.702   7147  Z= 0.394
  Chirality :  0.050   0.223    797
  Planarity :  0.006   0.054    912
  Dihedral  :  9.721 105.040    796
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 23.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.84 %
    Favored  : 89.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  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: -1.90 (0.34), residues: 646
  helix: -2.31 (0.85), residues: 28
  sheet: -0.14 (0.37), residues: 226
  loop : -1.96 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP H  36 
 HIS   0.005   0.001   HIS C 519 
 PHE   0.014   0.002   PHE C 464 
 TYR   0.022   0.002   TYR L  50 
 ARG   0.005   0.001   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00884 (    2)
  link_NAG-ASN         : angle       4.62444 (    6)
  link_BETA1-4         : bond        0.00576 (    2)
  link_BETA1-4         : angle       1.93215 (    6)
  hydrogen bonds       : bond        0.04165 (  124)
  hydrogen bonds       : angle       7.84218 (  294)
  SS BOND              : bond        0.00404 (    9)
  SS BOND              : angle       1.37135 (   18)
  covalent geometry    : bond        0.00430 ( 5232)
  covalent geometry    : angle       0.75685 ( 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
  145 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7878 (m110) cc_final: 0.7654 (m110)
REVERT: C  392 PHE cc_start: 0.6971 (m-10) cc_final: 0.6623 (m-10)
REVERT: C  418 ILE cc_start: 0.8594 (pt) cc_final: 0.8289 (pt)
REVERT: C  422 ASN cc_start: 0.7614 (m110) cc_final: 0.7353 (m110)
REVERT: C  425 LEU cc_start: 0.8027 (tp) cc_final: 0.7774 (tp)
REVERT: C  451 TYR cc_start: 0.6230 (m-80) cc_final: 0.5755 (m-80)
REVERT: C  455 LEU cc_start: 0.6468 (mt) cc_final: 0.5988 (mt)
REVERT: C  462 LYS cc_start: 0.9080 (ttpp) cc_final: 0.8774 (ttpp)
REVERT: H   62 GLN cc_start: 0.8867 (pm20) cc_final: 0.8312 (pm20)
REVERT: H   73 ASP cc_start: 0.8528 (t0) cc_final: 0.7193 (t0)
REVERT: H   74 MET cc_start: 0.7525 (mmt) cc_final: 0.7164 (mmt)
REVERT: H   76 THR cc_start: 0.8256 (t) cc_final: 0.7993 (t)
REVERT: H   80 TYR cc_start: 0.6578 (m-80) cc_final: 0.6276 (m-80)
REVERT: H   94 TYR cc_start: 0.7725 (m-10) cc_final: 0.7496 (m-10)
REVERT: L   13 LEU cc_start: 0.8740 (tp) cc_final: 0.7739 (tp)
REVERT: L   17 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6785 (mt-10)
REVERT: L   37 TYR cc_start: 0.7811 (m-10) cc_final: 0.7546 (m-80)
REVERT: L   40 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8330 (mmpt)
REVERT: L   92 TYR cc_start: 0.8092 (p90) cc_final: 0.7519 (p90)
REVERT: L  134 VAL cc_start: 0.8293 (t) cc_final: 0.7972 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1997
  time to fit residues: 35.5893
Evaluate side-chains
  133 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 13 optimal weight:    0.0970
   chunk 24 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 57 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0870
   chunk 53 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.3956

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

Flipped N/Q/H residues before XYZ refinement:
C 360 ASN
C 506 GLN
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 ASN
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.174147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.140394 restraints weight = 10867.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.146569 restraints weight = 6839.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.150885 restraints weight = 4687.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6550
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5245  Z= 0.164
  Angle     :  0.754   8.859   7147  Z= 0.385
  Chirality :  0.049   0.217    797
  Planarity :  0.006   0.053    912
  Dihedral  :  9.610 104.170    796
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 23.16
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.22 %
    Favored  : 89.63 %
  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: -1.85 (0.34), residues: 646
  helix: -2.30 (0.84), residues: 28
  sheet: -0.04 (0.37), residues: 225
  loop : -1.97 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP H 113 
 HIS   0.005   0.001   HIS C 519 
 PHE   0.016   0.002   PHE L 141 
 TYR   0.025   0.002   TYR L  50 
 ARG   0.006   0.001   ARG C 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00886 (    2)
  link_NAG-ASN         : angle       4.48828 (    6)
  link_BETA1-4         : bond        0.00583 (    2)
  link_BETA1-4         : angle       1.81788 (    6)
  hydrogen bonds       : bond        0.03851 (  124)
  hydrogen bonds       : angle       7.70539 (  294)
  SS BOND              : bond        0.00337 (    9)
  SS BOND              : angle       1.38880 (   18)
  covalent geometry    : bond        0.00349 ( 5232)
  covalent geometry    : angle       0.73956 ( 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  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7788 (m110) cc_final: 0.7559 (m110)
REVERT: C  355 ARG cc_start: 0.8344 (mmm160) cc_final: 0.7966 (mmm160)
REVERT: C  392 PHE cc_start: 0.6919 (m-10) cc_final: 0.6592 (m-10)
REVERT: C  418 ILE cc_start: 0.8567 (pt) cc_final: 0.8301 (pt)
REVERT: C  422 ASN cc_start: 0.7521 (m110) cc_final: 0.7274 (m110)
REVERT: C  436 TRP cc_start: 0.9057 (p90) cc_final: 0.7632 (p90)
REVERT: C  451 TYR cc_start: 0.6089 (m-80) cc_final: 0.5635 (m-80)
REVERT: C  455 LEU cc_start: 0.6508 (mt) cc_final: 0.5969 (mt)
REVERT: C  462 LYS cc_start: 0.9083 (ttpp) cc_final: 0.8744 (ttpp)
REVERT: C  529 LYS cc_start: 0.7966 (mtpp) cc_final: 0.7619 (mtpp)
REVERT: H   10 GLU cc_start: 0.7510 (mp0) cc_final: 0.6674 (mp0)
REVERT: H   62 GLN cc_start: 0.8865 (pm20) cc_final: 0.8290 (pm20)
REVERT: H   73 ASP cc_start: 0.8448 (t0) cc_final: 0.7146 (t0)
REVERT: H   74 MET cc_start: 0.7498 (mmt) cc_final: 0.7158 (mmt)
REVERT: H   76 THR cc_start: 0.8223 (t) cc_final: 0.7975 (t)
REVERT: H   80 TYR cc_start: 0.6528 (m-80) cc_final: 0.6233 (m-80)
REVERT: H   93 MET cc_start: 0.8155 (tpp) cc_final: 0.7799 (tpp)
REVERT: H   94 TYR cc_start: 0.7769 (m-10) cc_final: 0.7002 (m-10)
REVERT: L   13 LEU cc_start: 0.8710 (tp) cc_final: 0.7675 (tp)
REVERT: L   17 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6641 (mt-10)
REVERT: L   37 TYR cc_start: 0.7781 (m-10) cc_final: 0.7502 (m-80)
REVERT: L   92 TYR cc_start: 0.8017 (p90) cc_final: 0.7398 (p90)
REVERT: L  134 VAL cc_start: 0.8259 (t) cc_final: 0.7996 (p)
REVERT: L  142 TYR cc_start: 0.7150 (t80) cc_final: 0.6645 (t80)
REVERT: L  174 THR cc_start: 0.7188 (m) cc_final: 0.6837 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1887
  time to fit residues: 33.6608
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  : 0.540 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 26 optimal weight:    0.0870
   chunk 37 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.1980
   chunk 48 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0980
   chunk 39 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0870
   chunk 20 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.2136

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

Flipped N/Q/H residues before XYZ refinement:
C 360 ASN
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
L  32 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4425 r_free = 0.4425 target = 0.176285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.142545 restraints weight = 11050.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.149004 restraints weight = 6850.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.153902 restraints weight = 4640.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6486
moved from start:          0.3602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5245  Z= 0.146
  Angle     :  0.789  10.704   7147  Z= 0.402
  Chirality :  0.051   0.216    797
  Planarity :  0.006   0.053    912
  Dihedral  :  9.696 103.526    796
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 21.87
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.44 %
    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 : 0.33 %

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: -1.91 (0.33), residues: 646
  helix: -2.65 (0.74), residues: 34
  sheet: -0.05 (0.36), residues: 226
  loop : -2.00 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H 113 
 HIS   0.004   0.001   HIS C 519 
 PHE   0.017   0.002   PHE C 464 
 TYR   0.020   0.002   TYR L  50 
 ARG   0.008   0.001   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00904 (    2)
  link_NAG-ASN         : angle       4.39561 (    6)
  link_BETA1-4         : bond        0.00507 (    2)
  link_BETA1-4         : angle       1.69969 (    6)
  hydrogen bonds       : bond        0.03787 (  124)
  hydrogen bonds       : angle       7.53361 (  294)
  SS BOND              : bond        0.00375 (    9)
  SS BOND              : angle       3.13780 (   18)
  covalent geometry    : bond        0.00327 ( 5232)
  covalent geometry    : angle       0.76257 ( 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
  140 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.496 
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  346 ARG cc_start: 0.7710 (mtp-110) cc_final: 0.7503 (mtp-110)
REVERT: C  354 ASN cc_start: 0.7740 (m110) cc_final: 0.7498 (m110)
REVERT: C  392 PHE cc_start: 0.6976 (m-10) cc_final: 0.6609 (m-10)
REVERT: C  418 ILE cc_start: 0.8635 (pt) cc_final: 0.8320 (pt)
REVERT: C  422 ASN cc_start: 0.7590 (m110) cc_final: 0.7312 (m110)
REVERT: C  429 PHE cc_start: 0.7859 (t80) cc_final: 0.7632 (t80)
REVERT: C  434 ILE cc_start: 0.7759 (mp) cc_final: 0.7514 (mp)
REVERT: C  436 TRP cc_start: 0.9041 (p90) cc_final: 0.7646 (p90)
REVERT: C  451 TYR cc_start: 0.6049 (m-80) cc_final: 0.5629 (m-80)
REVERT: C  455 LEU cc_start: 0.6339 (mt) cc_final: 0.5663 (mt)
REVERT: C  462 LYS cc_start: 0.9071 (ttpp) cc_final: 0.8725 (ttpp)
REVERT: C  478 LYS cc_start: 0.9008 (tmmt) cc_final: 0.8772 (tmtt)
REVERT: H   10 GLU cc_start: 0.7469 (mp0) cc_final: 0.6649 (mp0)
REVERT: H   47 TRP cc_start: 0.8071 (t60) cc_final: 0.7107 (t60)
REVERT: H   62 GLN cc_start: 0.8850 (pm20) cc_final: 0.8459 (pm20)
REVERT: H   73 ASP cc_start: 0.8399 (t0) cc_final: 0.7158 (t0)
REVERT: H   74 MET cc_start: 0.7402 (mmt) cc_final: 0.7011 (mmt)
REVERT: H   76 THR cc_start: 0.8173 (t) cc_final: 0.7936 (t)
REVERT: H   94 TYR cc_start: 0.7677 (m-10) cc_final: 0.7056 (m-10)
REVERT: H  176 PHE cc_start: 0.6957 (t80) cc_final: 0.6496 (t80)
REVERT: L   13 LEU cc_start: 0.8633 (tp) cc_final: 0.8220 (tp)
REVERT: L   40 LYS cc_start: 0.8206 (mmpt) cc_final: 0.7923 (mmpt)
REVERT: L   86 MET cc_start: 0.6809 (tpp) cc_final: 0.5894 (tpp)
REVERT: L  134 VAL cc_start: 0.8027 (t) cc_final: 0.7720 (p)
REVERT: L  142 TYR cc_start: 0.7133 (t80) cc_final: 0.6593 (t80)
REVERT: L  174 THR cc_start: 0.7160 (m) cc_final: 0.6743 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2014
  time to fit residues: 34.9665
Evaluate side-chains
  135 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
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:   50.0000
   chunk 4 optimal weight:    0.0470
   chunk 26 optimal weight:    0.0870
   chunk 24 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 22 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 ASN
** 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 = 0.4411 r_free = 0.4411 target = 0.174580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.140256 restraints weight = 11284.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.146892 restraints weight = 7037.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.151598 restraints weight = 4786.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6559
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5245  Z= 0.159
  Angle     :  0.764   9.460   7147  Z= 0.392
  Chirality :  0.050   0.215    797
  Planarity :  0.006   0.053    912
  Dihedral  :  9.644 103.741    796
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 22.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  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 : 0.33 %

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: -1.99 (0.33), residues: 646
  helix: -2.66 (0.79), residues: 34
  sheet: -0.02 (0.37), residues: 218
  loop : -2.08 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  36 
 HIS   0.004   0.001   HIS C 519 
 PHE   0.016   0.002   PHE L 211 
 TYR   0.021   0.002   TYR L  50 
 ARG   0.007   0.001   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00847 (    2)
  link_NAG-ASN         : angle       4.43790 (    6)
  link_BETA1-4         : bond        0.00535 (    2)
  link_BETA1-4         : angle       1.72662 (    6)
  hydrogen bonds       : bond        0.03919 (  124)
  hydrogen bonds       : angle       7.49100 (  294)
  SS BOND              : bond        0.00487 (    9)
  SS BOND              : angle       2.81181 (   18)
  covalent geometry    : bond        0.00345 ( 5232)
  covalent geometry    : angle       0.73998 ( 7117)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2691.15 seconds
wall clock time: 47 minutes 27.25 seconds (2847.25 seconds total)