Starting phenix.real_space_refine
on Fri Aug 22 15:46:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c89_16473/08_2025/8c89_16473_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c89_16473/08_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_16473/08_2025/8c89_16473.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c89_16473/08_2025/8c89_16473.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c89_16473/08_2025/8c89_16473_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c89_16473/08_2025/8c89_16473_neut.cif"
  }
  resolution = 4.41
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.44, per 1000 atoms: 0.28
  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: 0.39
  Conformation dependent library (CDL) restraints added in 253.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.21
  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: 0.85

  Time building geometry restraints manager: 0.59 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:             10.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.640
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.870
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.007   0.001   ARG L 110 
 TYR   0.030   0.004   TYR L  50 
 PHE   0.032   0.004   PHE H 176 
 TRP   0.017   0.005   TRP C 353 
 HIS   0.007   0.002   HIS L 200 

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

*********************** 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  : 0.185 
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: 0.9096 (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: 0.8323 (tpp)
REVERT: L   37 TYR cc_start: 0.8936 (m-10) cc_final: 0.8721 (m-80)
REVERT: L   88 TYR cc_start: 0.8526 (m-10) cc_final: 0.8065 (m-10)
  outliers start: 4
  outliers final: 3
  residues processed: 147
  average time/residue: 0.0866
  time to fit residues: 15.6982
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  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    0.0010
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0470
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    0.4980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.3084

-------------------------------------------------------------------------------
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 = 0.4455 r_free = 0.4455 target = 0.179394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.143311 restraints weight = 11066.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.149917 restraints weight = 6852.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.154664 restraints weight = 4665.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.158276 restraints weight = 3388.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.160831 restraints weight = 2569.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.4231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6342
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5245  Z= 0.161
  Angle     :  0.747   8.951   7147  Z= 0.380
  Chirality :  0.049   0.224    797
  Planarity :  0.006   0.055    912
  Dihedral  : 10.827 112.107    796
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 20.97
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.75 %
    Favored  : 89.94 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.20 (0.32), residues: 646
  helix: -1.93 (0.89), residues: 28
  sheet: -0.56 (0.35), residues: 226
  loop : -2.07 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 466 
 TYR   0.021   0.002   TYR C 351 
 PHE   0.017   0.002   PHE H 176 
 TRP   0.012   0.002   TRP C 353 
 HIS   0.006   0.002   HIS L 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 5232)
  covalent geometry    : angle       0.72371 ( 7117)
  SS BOND              : bond        0.00301 (    9)
  SS BOND              : angle       1.13177 (   18)
  hydrogen bonds       : bond        0.05055 (  124)
  hydrogen bonds       : angle       8.95643 (  294)
  link_BETA1-4         : bond        0.00310 (    2)
  link_BETA1-4         : angle       1.96783 (    6)
  link_NAG-ASN         : bond        0.00985 (    2)
  link_NAG-ASN         : angle       5.94538 (    6)

*********************** 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
  139 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  355 ARG cc_start: 0.7900 (mmm160) cc_final: 0.7396 (mmm160)
REVERT: C  357 ARG cc_start: 0.7264 (tpt90) cc_final: 0.6906 (tpt90)
REVERT: C  358 ILE cc_start: 0.7178 (mp) cc_final: 0.6973 (mp)
REVERT: C  392 PHE cc_start: 0.6897 (m-10) cc_final: 0.6588 (m-10)
REVERT: C  398 ASP cc_start: 0.6173 (p0) cc_final: 0.5358 (p0)
REVERT: C  418 ILE cc_start: 0.8621 (pt) cc_final: 0.8323 (pt)
REVERT: C  423 TYR cc_start: 0.7875 (t80) cc_final: 0.7397 (t80)
REVERT: C  429 PHE cc_start: 0.8045 (t80) cc_final: 0.7595 (t80)
REVERT: C  451 TYR cc_start: 0.6205 (m-80) cc_final: 0.5722 (m-80)
REVERT: C  478 LYS cc_start: 0.8882 (tmtt) cc_final: 0.8513 (tmtt)
REVERT: H   10 GLU cc_start: 0.7817 (mp0) cc_final: 0.7515 (mp0)
REVERT: H   38 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7421 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8665 (pm20) cc_final: 0.8290 (pm20)
REVERT: H   64 PHE cc_start: 0.8399 (m-10) cc_final: 0.8139 (m-10)
REVERT: H   73 ASP cc_start: 0.8554 (t0) cc_final: 0.7586 (t0)
REVERT: H   80 TYR cc_start: 0.6731 (m-80) cc_final: 0.6166 (m-80)
REVERT: H   94 TYR cc_start: 0.7707 (m-10) cc_final: 0.7393 (m-10)
REVERT: L   13 LEU cc_start: 0.8493 (tp) cc_final: 0.8208 (tp)
REVERT: L   86 MET cc_start: 0.6576 (tpp) cc_final: 0.6019 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0759
  time to fit residues: 13.1158
Evaluate side-chains
  134 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 0 optimal weight:   50.0000
   chunk 42 optimal weight:    0.0970
   chunk 39 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0570
   chunk 52 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.4496

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

Flipped N/Q/H residues before XYZ refinement:
C 505 HIS
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
L   6 GLN
L 212 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.177041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.141437 restraints weight = 11160.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.148100 restraints weight = 6889.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.152885 restraints weight = 4666.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.156189 restraints weight = 3372.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.158864 restraints weight = 2591.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.4206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6414
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5245  Z= 0.181
  Angle     :  0.734   8.954   7147  Z= 0.376
  Chirality :  0.049   0.232    797
  Planarity :  0.005   0.049    912
  Dihedral  : 10.521 111.201    796
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 21.97
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 10.84 %
    Favored  : 88.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 2.70 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.07 (0.32), residues: 646
  helix: -2.39 (0.81), residues: 28
  sheet: -0.19 (0.36), residues: 217
  loop : -2.10 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  62 
 TYR   0.019   0.002   TYR C 380 
 PHE   0.013   0.002   PHE C 456 
 TRP   0.013   0.002   TRP C 353 
 HIS   0.005   0.001   HIS L 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 5232)
  covalent geometry    : angle       0.71589 ( 7117)
  SS BOND              : bond        0.00379 (    9)
  SS BOND              : angle       0.98830 (   18)
  hydrogen bonds       : bond        0.04475 (  124)
  hydrogen bonds       : angle       8.37763 (  294)
  link_BETA1-4         : bond        0.00411 (    2)
  link_BETA1-4         : angle       2.15249 (    6)
  link_NAG-ASN         : bond        0.00967 (    2)
  link_NAG-ASN         : angle       5.17148 (    6)

*********************** 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
  137 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  355 ARG cc_start: 0.8199 (mmm160) cc_final: 0.7533 (mmm160)
REVERT: C  378 LYS cc_start: 0.8893 (tmmt) cc_final: 0.8666 (tmmt)
REVERT: C  392 PHE cc_start: 0.6929 (m-10) cc_final: 0.6581 (m-10)
REVERT: C  398 ASP cc_start: 0.6263 (p0) cc_final: 0.4903 (p0)
REVERT: C  418 ILE cc_start: 0.8685 (pt) cc_final: 0.8389 (pt)
REVERT: C  423 TYR cc_start: 0.7863 (t80) cc_final: 0.7357 (t80)
REVERT: C  425 LEU cc_start: 0.8154 (mp) cc_final: 0.7918 (mp)
REVERT: C  429 PHE cc_start: 0.8117 (t80) cc_final: 0.7558 (t80)
REVERT: C  451 TYR cc_start: 0.5957 (m-80) cc_final: 0.5591 (m-80)
REVERT: C  457 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7335 (ttp80)
REVERT: H   10 GLU cc_start: 0.7817 (mp0) cc_final: 0.7383 (mp0)
REVERT: H   38 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7719 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8722 (pm20) cc_final: 0.8322 (pm20)
REVERT: H   64 PHE cc_start: 0.8466 (m-10) cc_final: 0.8202 (m-10)
REVERT: H   73 ASP cc_start: 0.8568 (t0) cc_final: 0.7496 (t0)
REVERT: H   80 TYR cc_start: 0.6737 (m-80) cc_final: 0.6198 (m-80)
REVERT: H   93 MET cc_start: 0.8410 (tpp) cc_final: 0.8089 (tpp)
REVERT: H   94 TYR cc_start: 0.7798 (m-10) cc_final: 0.7586 (m-10)
REVERT: L   13 LEU cc_start: 0.8554 (tp) cc_final: 0.8231 (tp)
REVERT: L  149 GLN cc_start: 0.7997 (tp40) cc_final: 0.7792 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0725
  time to fit residues: 12.3064
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  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 57 optimal weight:    0.0000
   chunk 61 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0270
   chunk 58 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0670
   chunk 10 optimal weight:    0.0470
   overall best weight:    0.1278

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

Flipped N/Q/H residues before XYZ refinement:
C 505 HIS
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 ASN
L 126 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.181338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.145400 restraints weight = 11301.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.152114 restraints weight = 7103.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.156927 restraints weight = 4854.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.160575 restraints weight = 3518.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.163042 restraints weight = 2648.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6305
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5245  Z= 0.125
  Angle     :  0.713   8.805   7147  Z= 0.358
  Chirality :  0.049   0.224    797
  Planarity :  0.005   0.053    912
  Dihedral  :  9.755 105.499    796
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 18.59
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.51 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 2.70 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.80 (0.33), residues: 646
  helix: -2.33 (0.85), residues: 28
  sheet:  0.06 (0.37), residues: 220
  loop : -1.96 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  55 
 TYR   0.014   0.001   TYR C 351 
 PHE   0.012   0.001   PHE C 392 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.005   0.002   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 5232)
  covalent geometry    : angle       0.69568 ( 7117)
  SS BOND              : bond        0.00815 (    9)
  SS BOND              : angle       1.25451 (   18)
  hydrogen bonds       : bond        0.03654 (  124)
  hydrogen bonds       : angle       7.75580 (  294)
  link_BETA1-4         : bond        0.00597 (    2)
  link_BETA1-4         : angle       1.85486 (    6)
  link_NAG-ASN         : bond        0.01003 (    2)
  link_NAG-ASN         : angle       4.74377 (    6)

*********************** 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
  136 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  355 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7590 (mmm160)
REVERT: C  392 PHE cc_start: 0.6981 (m-10) cc_final: 0.6600 (m-10)
REVERT: C  398 ASP cc_start: 0.6077 (p0) cc_final: 0.5052 (p0)
REVERT: C  418 ILE cc_start: 0.8555 (pt) cc_final: 0.8316 (pt)
REVERT: C  425 LEU cc_start: 0.8086 (mp) cc_final: 0.7840 (mp)
REVERT: C  429 PHE cc_start: 0.8042 (t80) cc_final: 0.7629 (t80)
REVERT: C  451 TYR cc_start: 0.5948 (m-80) cc_final: 0.5583 (m-80)
REVERT: C  457 ARG cc_start: 0.7705 (ttp80) cc_final: 0.7371 (ttp80)
REVERT: C  478 LYS cc_start: 0.8777 (tmtt) cc_final: 0.8426 (tmtt)
REVERT: H   10 GLU cc_start: 0.7760 (mp0) cc_final: 0.7307 (mp0)
REVERT: H   38 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7722 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8681 (pm20) cc_final: 0.8391 (pm20)
REVERT: H   73 ASP cc_start: 0.8387 (t0) cc_final: 0.7334 (t0)
REVERT: H   80 TYR cc_start: 0.6629 (m-80) cc_final: 0.6176 (m-80)
REVERT: H   93 MET cc_start: 0.8519 (tpp) cc_final: 0.8219 (tpp)
REVERT: L   13 LEU cc_start: 0.8428 (tp) cc_final: 0.8115 (tp)
REVERT: L   86 MET cc_start: 0.6819 (tpp) cc_final: 0.6260 (tpp)
REVERT: L  134 VAL cc_start: 0.8172 (t) cc_final: 0.7828 (p)
REVERT: L  174 THR cc_start: 0.6804 (m) cc_final: 0.6579 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0868
  time to fit residues: 14.7199
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  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 33 optimal weight:    0.0060
   chunk 48 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 51 optimal weight:    0.4980
   chunk 26 optimal weight:    0.0770
   chunk 39 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.3754

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  39 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.177144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.140822 restraints weight = 11195.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.147388 restraints weight = 6975.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.152091 restraints weight = 4761.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.155858 restraints weight = 3463.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.158471 restraints weight = 2623.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.4218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6406
moved from start:          0.2426

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= 0.161
  Angle     :  0.728   9.431   7147  Z= 0.370
  Chirality :  0.048   0.223    797
  Planarity :  0.005   0.052    912
  Dihedral  :  9.687 105.239    796
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 20.48
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.53 %
    Favored  : 89.32 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.33), residues: 646
  helix: -2.32 (0.84), residues: 28
  sheet:  0.22 (0.38), residues: 210
  loop : -1.93 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  38 
 TYR   0.017   0.002   TYR L  50 
 PHE   0.014   0.002   PHE H 176 
 TRP   0.009   0.002   TRP C 353 
 HIS   0.004   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 5232)
  covalent geometry    : angle       0.71180 ( 7117)
  SS BOND              : bond        0.00601 (    9)
  SS BOND              : angle       1.11169 (   18)
  hydrogen bonds       : bond        0.03805 (  124)
  hydrogen bonds       : angle       7.59552 (  294)
  link_BETA1-4         : bond        0.00602 (    2)
  link_BETA1-4         : angle       1.98653 (    6)
  link_NAG-ASN         : bond        0.00848 (    2)
  link_NAG-ASN         : angle       4.74848 (    6)

*********************** 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
  137 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.123 
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  378 LYS cc_start: 0.8904 (tmmt) cc_final: 0.8654 (tmmt)
REVERT: C  392 PHE cc_start: 0.6943 (m-10) cc_final: 0.6589 (m-10)
REVERT: C  400 PHE cc_start: 0.7952 (p90) cc_final: 0.7746 (p90)
REVERT: C  418 ILE cc_start: 0.8613 (pt) cc_final: 0.8340 (pt)
REVERT: C  429 PHE cc_start: 0.8074 (t80) cc_final: 0.7537 (t80)
REVERT: C  451 TYR cc_start: 0.5840 (m-80) cc_final: 0.5527 (m-80)
REVERT: C  455 LEU cc_start: 0.5749 (mt) cc_final: 0.5302 (mt)
REVERT: C  457 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7322 (ttp80)
REVERT: C  462 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8830 (ttpp)
REVERT: C  478 LYS cc_start: 0.8778 (tmtt) cc_final: 0.8481 (tmtt)
REVERT: H   10 GLU cc_start: 0.7762 (mp0) cc_final: 0.7328 (mp0)
REVERT: H   38 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7730 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8723 (pm20) cc_final: 0.8378 (pm20)
REVERT: H   73 ASP cc_start: 0.8493 (t0) cc_final: 0.7399 (t0)
REVERT: H   80 TYR cc_start: 0.6544 (m-80) cc_final: 0.6157 (m-80)
REVERT: H   93 MET cc_start: 0.8388 (tpp) cc_final: 0.8150 (tpp)
REVERT: H   94 TYR cc_start: 0.7713 (m-10) cc_final: 0.7478 (m-10)
REVERT: H  176 PHE cc_start: 0.6765 (t80) cc_final: 0.6432 (t80)
REVERT: L   13 LEU cc_start: 0.8530 (tp) cc_final: 0.8169 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0827
  time to fit residues: 14.2125
Evaluate side-chains
  132 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0270
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
C 422 ASN
L  38 GLN
L 126 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.173202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.137992 restraints weight = 11211.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.144491 restraints weight = 6989.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.149148 restraints weight = 4754.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.152748 restraints weight = 3445.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.155312 restraints weight = 2602.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6476
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5245  Z= 0.195
  Angle     :  0.752   8.740   7147  Z= 0.386
  Chirality :  0.050   0.227    797
  Planarity :  0.006   0.053    912
  Dihedral  :  9.670 104.735    796
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 23.76
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.84 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.88 (0.33), residues: 646
  helix: -2.32 (0.80), residues: 28
  sheet: -0.23 (0.36), residues: 226
  loop : -1.87 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  55 
 TYR   0.021   0.002   TYR L  50 
 PHE   0.015   0.002   PHE C 429 
 TRP   0.014   0.002   TRP H 113 
 HIS   0.003   0.001   HIS L 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 5232)
  covalent geometry    : angle       0.73581 ( 7117)
  SS BOND              : bond        0.00613 (    9)
  SS BOND              : angle       1.24973 (   18)
  hydrogen bonds       : bond        0.04211 (  124)
  hydrogen bonds       : angle       7.60350 (  294)
  link_BETA1-4         : bond        0.00580 (    2)
  link_BETA1-4         : angle       1.98628 (    6)
  link_NAG-ASN         : bond        0.01034 (    2)
  link_NAG-ASN         : angle       4.79968 (    6)

*********************** 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
  143 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7722 (m110) cc_final: 0.7426 (m110)
REVERT: C  392 PHE cc_start: 0.7042 (m-10) cc_final: 0.6635 (m-10)
REVERT: C  418 ILE cc_start: 0.8548 (pt) cc_final: 0.8291 (pt)
REVERT: C  429 PHE cc_start: 0.8146 (t80) cc_final: 0.7583 (t80)
REVERT: C  451 TYR cc_start: 0.6096 (m-80) cc_final: 0.5710 (m-80)
REVERT: C  462 LYS cc_start: 0.9046 (ttpp) cc_final: 0.8769 (ttpp)
REVERT: H   10 GLU cc_start: 0.7750 (mp0) cc_final: 0.7209 (mp0)
REVERT: H   38 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7883 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8803 (pm20) cc_final: 0.8306 (pm20)
REVERT: H   73 ASP cc_start: 0.8502 (t0) cc_final: 0.7377 (t0)
REVERT: H   76 THR cc_start: 0.8141 (t) cc_final: 0.7937 (t)
REVERT: H   80 TYR cc_start: 0.6561 (m-80) cc_final: 0.6251 (m-80)
REVERT: H   94 TYR cc_start: 0.7787 (m-10) cc_final: 0.7495 (m-10)
REVERT: H  176 PHE cc_start: 0.6912 (t80) cc_final: 0.6536 (t80)
REVERT: L   13 LEU cc_start: 0.8707 (tp) cc_final: 0.7726 (tp)
REVERT: L   17 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6853 (mt-10)
REVERT: L   37 TYR cc_start: 0.7771 (m-10) cc_final: 0.7437 (m-80)
REVERT: L   92 TYR cc_start: 0.8146 (p90) cc_final: 0.7574 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.0761
  time to fit residues: 13.7463
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  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 49 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0050
   chunk 8 optimal weight:    0.1980
   overall best weight:    0.3794

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
L  32 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 126 GLN
** L 149 GLN ** 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 = 0.4405 r_free = 0.4405 target = 0.174510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.139955 restraints weight = 11063.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.146173 restraints weight = 6886.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.150838 restraints weight = 4683.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.154101 restraints weight = 3376.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.156603 restraints weight = 2574.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.4192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6440
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5245  Z= 0.162
  Angle     :  0.751  12.126   7147  Z= 0.379
  Chirality :  0.049   0.217    797
  Planarity :  0.006   0.053    912
  Dihedral  :  9.623 105.387    796
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 20.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.22 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.33), residues: 646
  helix: -2.41 (0.78), residues: 28
  sheet:  0.06 (0.37), residues: 219
  loop : -1.90 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 355 
 TYR   0.020   0.002   TYR L  50 
 PHE   0.015   0.002   PHE L 141 
 TRP   0.014   0.002   TRP L 150 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 5232)
  covalent geometry    : angle       0.73658 ( 7117)
  SS BOND              : bond        0.00468 (    9)
  SS BOND              : angle       1.18157 (   18)
  hydrogen bonds       : bond        0.03775 (  124)
  hydrogen bonds       : angle       7.61639 (  294)
  link_BETA1-4         : bond        0.00645 (    2)
  link_BETA1-4         : angle       1.91146 (    6)
  link_NAG-ASN         : bond        0.00960 (    2)
  link_NAG-ASN         : angle       4.44340 (    6)

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

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.151 
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: 0.7668 (m110) cc_final: 0.7357 (m110)
REVERT: C  377 PHE cc_start: 0.8666 (t80) cc_final: 0.8325 (t80)
REVERT: C  378 LYS cc_start: 0.8957 (tmmt) cc_final: 0.8621 (tmmt)
REVERT: C  392 PHE cc_start: 0.6966 (m-10) cc_final: 0.6567 (m-10)
REVERT: C  418 ILE cc_start: 0.8646 (pt) cc_final: 0.8407 (pt)
REVERT: C  422 ASN cc_start: 0.7567 (m110) cc_final: 0.7308 (m110)
REVERT: C  429 PHE cc_start: 0.8165 (t80) cc_final: 0.7556 (t80)
REVERT: C  451 TYR cc_start: 0.6143 (m-80) cc_final: 0.5759 (m-80)
REVERT: C  462 LYS cc_start: 0.9066 (ttpp) cc_final: 0.8777 (ttpp)
REVERT: C  478 LYS cc_start: 0.8926 (tmtt) cc_final: 0.8656 (tmtt)
REVERT: H   10 GLU cc_start: 0.7720 (mp0) cc_final: 0.7130 (mp0)
REVERT: H   47 TRP cc_start: 0.8081 (t60) cc_final: 0.7132 (t60)
REVERT: H   62 GLN cc_start: 0.8836 (pm20) cc_final: 0.8542 (pm20)
REVERT: H   73 ASP cc_start: 0.8441 (t0) cc_final: 0.7203 (t0)
REVERT: H   74 MET cc_start: 0.7355 (mmt) cc_final: 0.6993 (mmt)
REVERT: H   80 TYR cc_start: 0.6598 (m-80) cc_final: 0.6272 (m-80)
REVERT: H   94 TYR cc_start: 0.7738 (m-10) cc_final: 0.7493 (m-10)
REVERT: H  176 PHE cc_start: 0.7050 (t80) cc_final: 0.6592 (t80)
REVERT: L   13 LEU cc_start: 0.8676 (tp) cc_final: 0.7711 (tp)
REVERT: L   17 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6738 (mt-10)
REVERT: L   37 TYR cc_start: 0.7799 (m-10) cc_final: 0.7477 (m-80)
REVERT: L  174 THR cc_start: 0.7185 (m) cc_final: 0.6949 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0718
  time to fit residues: 12.7706
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  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 47 optimal weight:    0.4980
   chunk 37 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0980
   chunk 26 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
L  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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.172876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.138044 restraints weight = 11140.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.144448 restraints weight = 6948.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.149207 restraints weight = 4717.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.152612 restraints weight = 3407.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.155045 restraints weight = 2580.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.4178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6488
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   5245  Z= 0.186
  Angle     :  0.762   8.816   7147  Z= 0.392
  Chirality :  0.050   0.221    797
  Planarity :  0.006   0.053    912
  Dihedral  :  9.644 104.876    796
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 22.37
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.22 %
    Favored  : 89.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.33), residues: 646
  helix: -2.32 (0.85), residues: 28
  sheet:  0.12 (0.37), residues: 219
  loop : -1.96 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  55 
 TYR   0.020   0.002   TYR L  50 
 PHE   0.014   0.002   PHE L 141 
 TRP   0.019   0.002   TRP H  36 
 HIS   0.005   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 5232)
  covalent geometry    : angle       0.74711 ( 7117)
  SS BOND              : bond        0.00508 (    9)
  SS BOND              : angle       1.30329 (   18)
  hydrogen bonds       : bond        0.04036 (  124)
  hydrogen bonds       : angle       7.69872 (  294)
  link_BETA1-4         : bond        0.00729 (    2)
  link_BETA1-4         : angle       1.84963 (    6)
  link_NAG-ASN         : bond        0.00877 (    2)
  link_NAG-ASN         : angle       4.60035 (    6)

*********************** 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
  143 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7747 (m110) cc_final: 0.7461 (m110)
REVERT: C  377 PHE cc_start: 0.8690 (t80) cc_final: 0.8464 (t80)
REVERT: C  392 PHE cc_start: 0.7011 (m-10) cc_final: 0.6666 (m-10)
REVERT: C  418 ILE cc_start: 0.8581 (pt) cc_final: 0.8374 (pt)
REVERT: C  422 ASN cc_start: 0.7602 (m110) cc_final: 0.7347 (m110)
REVERT: C  429 PHE cc_start: 0.8219 (t80) cc_final: 0.7533 (t80)
REVERT: C  451 TYR cc_start: 0.6070 (m-80) cc_final: 0.5634 (m-80)
REVERT: C  462 LYS cc_start: 0.9063 (ttpp) cc_final: 0.8764 (ttpp)
REVERT: C  478 LYS cc_start: 0.8988 (tmtt) cc_final: 0.8701 (tmtt)
REVERT: H   47 TRP cc_start: 0.8120 (t60) cc_final: 0.7194 (t60)
REVERT: H   62 GLN cc_start: 0.8851 (pm20) cc_final: 0.8322 (pm20)
REVERT: H   73 ASP cc_start: 0.8437 (t0) cc_final: 0.7152 (t0)
REVERT: H   74 MET cc_start: 0.7419 (mmt) cc_final: 0.7125 (mmt)
REVERT: H   76 THR cc_start: 0.8203 (t) cc_final: 0.7988 (t)
REVERT: H   80 TYR cc_start: 0.6586 (m-80) cc_final: 0.6296 (m-80)
REVERT: H   93 MET cc_start: 0.8349 (tpp) cc_final: 0.7994 (tpp)
REVERT: L   13 LEU cc_start: 0.8740 (tp) cc_final: 0.7750 (tp)
REVERT: L   17 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6736 (mt-10)
REVERT: L   37 TYR cc_start: 0.7809 (m-10) cc_final: 0.7525 (m-80)
REVERT: L   92 TYR cc_start: 0.8032 (p90) cc_final: 0.7447 (p90)
REVERT: L  134 VAL cc_start: 0.8268 (t) cc_final: 0.7948 (p)
REVERT: L  174 THR cc_start: 0.7220 (m) cc_final: 0.7007 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.0780
  time to fit residues: 14.1102
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  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0270
   chunk 4 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0870
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.4616

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
L  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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.172689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.137979 restraints weight = 11056.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.144403 restraints weight = 6888.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.149140 restraints weight = 4684.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.152395 restraints weight = 3378.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.154976 restraints weight = 2570.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.4180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6488
moved from start:          0.3491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5245  Z= 0.181
  Angle     :  0.781   8.924   7147  Z= 0.401
  Chirality :  0.051   0.217    797
  Planarity :  0.006   0.053    912
  Dihedral  :  9.700 104.744    796
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 21.87
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.92 (0.33), residues: 646
  helix: -2.80 (0.72), residues: 34
  sheet: -0.01 (0.36), residues: 226
  loop : -2.01 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  38 
 TYR   0.022   0.002   TYR L 188 
 PHE   0.017   0.002   PHE C 515 
 TRP   0.014   0.002   TRP L 150 
 HIS   0.005   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 5232)
  covalent geometry    : angle       0.75714 ( 7117)
  SS BOND              : bond        0.00516 (    9)
  SS BOND              : angle       2.74517 (   18)
  hydrogen bonds       : bond        0.03923 (  124)
  hydrogen bonds       : angle       7.63274 (  294)
  link_BETA1-4         : bond        0.00660 (    2)
  link_BETA1-4         : angle       1.97254 (    6)
  link_NAG-ASN         : bond        0.00864 (    2)
  link_NAG-ASN         : angle       4.51127 (    6)

*********************** 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
  142 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7755 (m110) cc_final: 0.7427 (m110)
REVERT: C  377 PHE cc_start: 0.8701 (t80) cc_final: 0.8424 (t80)
REVERT: C  392 PHE cc_start: 0.7000 (m-10) cc_final: 0.6634 (m-10)
REVERT: C  418 ILE cc_start: 0.8635 (pt) cc_final: 0.8421 (pt)
REVERT: C  422 ASN cc_start: 0.7635 (m110) cc_final: 0.7403 (m110)
REVERT: C  429 PHE cc_start: 0.8210 (t80) cc_final: 0.7585 (t80)
REVERT: C  451 TYR cc_start: 0.6004 (m-80) cc_final: 0.5568 (m-80)
REVERT: C  455 LEU cc_start: 0.6249 (mt) cc_final: 0.5681 (mt)
REVERT: C  462 LYS cc_start: 0.9066 (ttpp) cc_final: 0.8771 (ttpp)
REVERT: C  478 LYS cc_start: 0.9015 (tmtt) cc_final: 0.8731 (tmtt)
REVERT: H   47 TRP cc_start: 0.8148 (t60) cc_final: 0.7246 (t60)
REVERT: H   62 GLN cc_start: 0.8863 (pm20) cc_final: 0.8373 (pm20)
REVERT: H   73 ASP cc_start: 0.8440 (t0) cc_final: 0.7133 (t0)
REVERT: H   74 MET cc_start: 0.7348 (mmt) cc_final: 0.7074 (mmt)
REVERT: H   76 THR cc_start: 0.8217 (t) cc_final: 0.7998 (t)
REVERT: H   80 TYR cc_start: 0.6540 (m-80) cc_final: 0.6256 (m-80)
REVERT: H   93 MET cc_start: 0.8361 (tpp) cc_final: 0.8033 (tpp)
REVERT: H   94 TYR cc_start: 0.7809 (m-10) cc_final: 0.7038 (m-10)
REVERT: L   13 LEU cc_start: 0.8756 (tp) cc_final: 0.7772 (tp)
REVERT: L   17 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6710 (mt-10)
REVERT: L   37 TYR cc_start: 0.7843 (m-10) cc_final: 0.7554 (m-80)
REVERT: L   92 TYR cc_start: 0.8032 (p90) cc_final: 0.7440 (p90)
REVERT: L  142 TYR cc_start: 0.7221 (t80) cc_final: 0.6739 (t80)
REVERT: L  174 THR cc_start: 0.7183 (m) cc_final: 0.6810 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0827
  time to fit residues: 14.6703
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  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 3 optimal weight:    0.2980
   chunk 6 optimal weight:    0.0670
   chunk 34 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 55 optimal weight:    0.6980
   chunk 15 optimal weight:    0.3980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.3918

-------------------------------------------------------------------------------
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 126 GLN
** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.173873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.138693 restraints weight = 11098.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.145287 restraints weight = 6935.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.150101 restraints weight = 4710.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.153688 restraints weight = 3394.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.156081 restraints weight = 2550.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6470
moved from start:          0.3610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5245  Z= 0.167
  Angle     :  0.776   9.634   7147  Z= 0.400
  Chirality :  0.051   0.217    797
  Planarity :  0.006   0.053    912
  Dihedral  :  9.693 104.338    796
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 23.06
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.60 %
    Favored  : 90.25 %
  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 : 0.33 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.94 (0.33), residues: 646
  helix: -2.79 (0.76), residues: 34
  sheet: -0.04 (0.36), residues: 226
  loop : -2.01 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  38 
 TYR   0.020   0.002   TYR L  50 
 PHE   0.015   0.002   PHE L 141 
 TRP   0.017   0.002   TRP H  36 
 HIS   0.004   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 5232)
  covalent geometry    : angle       0.75140 ( 7117)
  SS BOND              : bond        0.00631 (    9)
  SS BOND              : angle       2.87309 (   18)
  hydrogen bonds       : bond        0.03824 (  124)
  hydrogen bonds       : angle       7.54779 (  294)
  link_BETA1-4         : bond        0.00619 (    2)
  link_BETA1-4         : angle       1.82006 (    6)
  link_NAG-ASN         : bond        0.00875 (    2)
  link_NAG-ASN         : angle       4.51456 (    6)

********************** 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
  145 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.190 
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: C  355 ARG cc_start: 0.8330 (mmm160) cc_final: 0.7980 (mmm160)
REVERT: C  377 PHE cc_start: 0.8702 (t80) cc_final: 0.8492 (t80)
REVERT: C  392 PHE cc_start: 0.7046 (m-10) cc_final: 0.6662 (m-10)
REVERT: C  418 ILE cc_start: 0.8630 (pt) cc_final: 0.8430 (pt)
REVERT: C  422 ASN cc_start: 0.7654 (m110) cc_final: 0.7387 (m110)
REVERT: C  429 PHE cc_start: 0.8232 (t80) cc_final: 0.7559 (t80)
REVERT: C  436 TRP cc_start: 0.9049 (p90) cc_final: 0.7583 (p90)
REVERT: C  451 TYR cc_start: 0.5990 (m-80) cc_final: 0.5548 (m-80)
REVERT: C  455 LEU cc_start: 0.6177 (mt) cc_final: 0.5463 (mt)
REVERT: C  462 LYS cc_start: 0.9066 (ttpp) cc_final: 0.8757 (ttpp)
REVERT: C  478 LYS cc_start: 0.9020 (tmtt) cc_final: 0.8742 (tmtt)
REVERT: H   10 GLU cc_start: 0.7607 (mp0) cc_final: 0.6748 (mp0)
REVERT: H   47 TRP cc_start: 0.8112 (t60) cc_final: 0.7208 (t60)
REVERT: H   62 GLN cc_start: 0.8873 (pm20) cc_final: 0.8337 (pm20)
REVERT: H   65 GLN cc_start: 0.8619 (pt0) cc_final: 0.8414 (pt0)
REVERT: H   73 ASP cc_start: 0.8406 (t0) cc_final: 0.7105 (t0)
REVERT: H   74 MET cc_start: 0.7327 (mmt) cc_final: 0.7040 (mmt)
REVERT: H   76 THR cc_start: 0.8186 (t) cc_final: 0.7972 (t)
REVERT: H   80 TYR cc_start: 0.6511 (m-80) cc_final: 0.6249 (m-80)
REVERT: H   94 TYR cc_start: 0.7809 (m-10) cc_final: 0.7159 (m-10)
REVERT: L   13 LEU cc_start: 0.8715 (tp) cc_final: 0.8303 (tp)
REVERT: L   37 TYR cc_start: 0.7863 (m-10) cc_final: 0.7534 (m-80)
REVERT: L   92 TYR cc_start: 0.8029 (p90) cc_final: 0.7408 (p90)
REVERT: L  134 VAL cc_start: 0.8286 (t) cc_final: 0.7989 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.0734
  time to fit residues: 13.4214
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  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0060
   chunk 51 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0970
   chunk 19 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 32 optimal weight:    0.2980
   chunk 26 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0870
   chunk 2 optimal weight:    0.0020
   overall best weight:    0.0980

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

Flipped N/Q/H residues before XYZ refinement:
C 506 GLN
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.179243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.144376 restraints weight = 11351.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.150653 restraints weight = 7163.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.155648 restraints weight = 4956.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.159160 restraints weight = 3585.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.161678 restraints weight = 2708.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6352
moved from start:          0.3682

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= 0.128
  Angle     :  0.747   9.012   7147  Z= 0.381
  Chirality :  0.050   0.213    797
  Planarity :  0.005   0.053    912
  Dihedral  :  9.391 102.082    796
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 18.79
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.05 %
    Favored  : 91.80 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.33), residues: 646
  helix: -2.82 (0.76), residues: 34
  sheet:  0.18 (0.37), residues: 218
  loop : -1.93 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  38 
 TYR   0.021   0.001   TYR L  50 
 PHE   0.013   0.002   PHE L 141 
 TRP   0.014   0.002   TRP H 113 
 HIS   0.004   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 5232)
  covalent geometry    : angle       0.72803 ( 7117)
  SS BOND              : bond        0.00531 (    9)
  SS BOND              : angle       2.23389 (   18)
  hydrogen bonds       : bond        0.03507 (  124)
  hydrogen bonds       : angle       7.30212 (  294)
  link_BETA1-4         : bond        0.00568 (    2)
  link_BETA1-4         : angle       1.58397 (    6)
  link_NAG-ASN         : bond        0.00997 (    2)
  link_NAG-ASN         : angle       4.24762 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1253.21 seconds
wall clock time: 22 minutes 22.11 seconds (1342.11 seconds total)