Starting phenix.real_space_refine
on Thu Jul  2 05:23:20 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8fbl_28964/07_2026/8fbl_28964.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fbl_28964/07_2026/8fbl_28964.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fbl_28964/07_2026/8fbl_28964.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fbl_28964/07_2026/8fbl_28964.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fbl_28964/07_2026/8fbl_28964.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fbl_28964/07_2026/8fbl_28964.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8fbl_28964/07_2026/8fbl_28964.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8fbl_28964/07_2026/8fbl_28964.cif"
  }
  resolution = 2.7
  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=   0.002 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      30      5.16       5
     C    4440      2.51       5
     N    1104      2.21       5
     O    1245      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2190
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 13, 'TRANS': 264}
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 84
          Unusual residues: {'NAG': 4, 'PIO': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 10
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.63, per 1000 atoms: 0.24
  Number of scatterers: 6822
  At special positions: 0
  Unit cell: (80.122, 81.774, 124.726, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       3     15.00
     O    1245      8.00
     N    1104      7.00
     C    4440      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 128 " - pdb=" SG  CYS B 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 128 " - pdb=" SG  CYS C 149 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 401 " - " ASN A 148 "
      " NAG A 402 " - " ASN A 162 "
      " NAG A 403 " - " ASN A 190 "
      " NAG A 404 " - " ASN A 155 "
      " NAG B 401 " - " ASN B 148 "
      " NAG B 402 " - " ASN B 162 "
      " NAG B 403 " - " ASN B 190 "
      " NAG B 404 " - " ASN B 155 "
      " NAG C 401 " - " ASN C 148 "
      " NAG C 402 " - " ASN C 162 "
      " NAG C 403 " - " ASN C 190 "
      " NAG C 404 " - " ASN C 155 "
  Time building additional restraints: 0.39
  Conformation dependent library (CDL) restraints added in 402.7 milliseconds
  

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1608

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 4 sheets defined
      36.5% alpha, 15.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 94
    Processing helix  chain 'A' and resid 206 through 212
      removed outlier: 3.676A  pdb=" N   PHE A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 226
    Processing helix  chain 'A' and resid 272 through 278
      removed outlier: 4.191A  pdb=" N   SER A 277 " --> pdb=" O   ALA A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 302
      removed outlier: 3.817A  pdb=" N   ASN A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 298 through 302'
    Processing helix  chain 'A' and resid 302 through 339
      removed outlier: 4.148A  pdb=" N   THR A 306 " --> pdb=" O   ASN A 302 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS A 329 " --> pdb=" O   LYS A 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 94
    Processing helix  chain 'B' and resid 206 through 212
      removed outlier: 3.676A  pdb=" N   PHE B 210 " --> pdb=" O   SER B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 226
    Processing helix  chain 'B' and resid 272 through 278
      removed outlier: 4.191A  pdb=" N   SER B 277 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 302
      removed outlier: 3.818A  pdb=" N   ASN B 302 " --> pdb=" O   ILE B 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 298 through 302'
    Processing helix  chain 'B' and resid 302 through 339
      removed outlier: 4.147A  pdb=" N   THR B 306 " --> pdb=" O   ASN B 302 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS B 329 " --> pdb=" O   LYS B 325 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 94
    Processing helix  chain 'C' and resid 206 through 212
      removed outlier: 3.677A  pdb=" N   PHE C 210 " --> pdb=" O   SER C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 226
    Processing helix  chain 'C' and resid 272 through 278
      removed outlier: 4.190A  pdb=" N   SER C 277 " --> pdb=" O   ALA C 274 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 302
      removed outlier: 3.817A  pdb=" N   ASN C 302 " --> pdb=" O   ILE C 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 298 through 302'
    Processing helix  chain 'C' and resid 302 through 339
      removed outlier: 4.148A  pdb=" N   THR C 306 " --> pdb=" O   ASN C 302 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS C 329 " --> pdb=" O   LYS C 325 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 100 through 107
    current: chain 'A' and resid 181 through 189
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 181 through 189
    current: chain 'A' and resid 254 through 259
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 254 through 259
    current: chain 'B' and resid 181 through 189
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 181 through 189
    current: chain 'B' and resid 254 through 259
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 254 through 259
    current: chain 'C' and resid 181 through 189
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 181 through 189
    current: chain 'C' and resid 254 through 259
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 157
      removed outlier: 3.644A  pdb=" N   GLY A 115 " --> pdb=" O   PHE A 204 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   ASP A 200 " --> pdb=" O   TYR A 119 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE A 199 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE A 232 " --> pdb=" O   ILE A 199 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 151 through 157
      removed outlier: 3.643A  pdb=" N   GLY B 115 " --> pdb=" O   PHE B 204 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   ASP B 200 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE B 199 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE B 232 " --> pdb=" O   ILE B 199 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 151 through 157
      removed outlier: 3.643A  pdb=" N   GLY C 115 " --> pdb=" O   PHE C 204 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   ASP C 200 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE C 199 " --> pdb=" O   PHE C 232 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE C 232 " --> pdb=" O   ILE C 199 " (cutoff:3.500A)

    268 hydrogen bonds defined for protein.
    777 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: 0.90

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1066
        1.32 -     1.44: 1969
        1.44 -     1.56: 3901
        1.56 -     1.69: 6
        1.69 -     1.81: 48
  Bond restraints: 6990
  Sorted by residual:
  bond pdb=" O1  PIO C 405 "
       pdb=" P1  PIO C 405 "
    ideal  model  delta    sigma   weight residual
    1.633  1.478  0.155 2.00e-02 2.50e+03 6.00e+01
  bond pdb=" O1  PIO B 405 "
       pdb=" P1  PIO B 405 "
    ideal  model  delta    sigma   weight residual
    1.633  1.478  0.155 2.00e-02 2.50e+03 5.99e+01
  bond pdb=" O1  PIO A 405 "
       pdb=" P1  PIO A 405 "
    ideal  model  delta    sigma   weight residual
    1.633  1.479  0.154 2.00e-02 2.50e+03 5.96e+01
  bond pdb=" O11 PIO C 405 "
       pdb=" P1  PIO C 405 "
    ideal  model  delta    sigma   weight residual
    1.495  1.566 -0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" O11 PIO A 405 "
       pdb=" P1  PIO A 405 "
    ideal  model  delta    sigma   weight residual
    1.495  1.566 -0.071 2.00e-02 2.50e+03 1.26e+01
  ... (remaining 6985 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.06: 9447
        4.06 -     8.12: 15
        8.12 -    12.18: 6
       12.18 -    16.25: 3
       16.25 -    20.31: 3
  Bond angle restraints: 9474
  Sorted by residual:
  angle pdb=" O11 PIO C 405 "
        pdb=" P1  PIO C 405 "
        pdb=" O12 PIO C 405 "
      ideal   model   delta    sigma   weight residual
     121.09  100.78   20.31 3.00e+00 1.11e-01 4.58e+01
  angle pdb=" O11 PIO B 405 "
        pdb=" P1  PIO B 405 "
        pdb=" O12 PIO B 405 "
      ideal   model   delta    sigma   weight residual
     121.09  100.83   20.26 3.00e+00 1.11e-01 4.56e+01
  angle pdb=" O11 PIO A 405 "
        pdb=" P1  PIO A 405 "
        pdb=" O12 PIO A 405 "
      ideal   model   delta    sigma   weight residual
     121.09  100.84   20.25 3.00e+00 1.11e-01 4.56e+01
  angle pdb=" C   ARG B  93 "
        pdb=" CA  ARG B  93 "
        pdb=" CB  ARG B  93 "
      ideal   model   delta    sigma   weight residual
     110.90  104.03    6.87 1.58e+00 4.01e-01 1.89e+01
  angle pdb=" C   ARG C  93 "
        pdb=" CA  ARG C  93 "
        pdb=" CB  ARG C  93 "
      ideal   model   delta    sigma   weight residual
     110.90  104.04    6.86 1.58e+00 4.01e-01 1.89e+01
  ... (remaining 9469 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.69: 3694
       15.69 -    31.38: 275
       31.38 -    47.07: 72
       47.07 -    62.76: 9
       62.76 -    78.45: 9
  Dihedral angle restraints: 4059
    sinusoidal: 1590
      harmonic: 2469
  Sorted by residual:
  dihedral pdb=" CA  PHE A 204 "
           pdb=" C   PHE A 204 "
           pdb=" N   SER A 205 "
           pdb=" CA  SER A 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.36  -15.64     0      5.00e+00 4.00e-02 9.79e+00
  dihedral pdb=" CA  PHE C 204 "
           pdb=" C   PHE C 204 "
           pdb=" N   SER C 205 "
           pdb=" CA  SER C 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.37  -15.63     0      5.00e+00 4.00e-02 9.78e+00
  dihedral pdb=" CA  PHE B 204 "
           pdb=" C   PHE B 204 "
           pdb=" N   SER B 205 "
           pdb=" CA  SER B 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.37  -15.63     0      5.00e+00 4.00e-02 9.77e+00
  ... (remaining 4056 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 922
       0.058 -    0.116: 146
       0.116 -    0.175: 9
       0.175 -    0.233: 0
       0.233 -    0.291: 6
  Chirality restraints: 1083
  Sorted by residual:
  chirality pdb=" C1  NAG C 401 "
            pdb=" ND2 ASN C 148 "
            pdb=" C2  NAG C 401 "
            pdb=" O5  NAG C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" C1  NAG B 401 "
            pdb=" ND2 ASN B 148 "
            pdb=" C2  NAG B 401 "
            pdb=" O5  NAG B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" C1  NAG A 401 "
            pdb=" ND2 ASN A 148 "
            pdb=" C2  NAG A 401 "
            pdb=" O5  NAG A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.09e+00
  ... (remaining 1080 not shown)

  Planarity restraints: 1188
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 403 "    0.304 2.00e-02 2.50e+03   2.57e-01 8.29e+02
        pdb=" C7  NAG A 403 "   -0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG A 403 "    0.184 2.00e-02 2.50e+03
        pdb=" N2  NAG A 403 "   -0.445 2.00e-02 2.50e+03
        pdb=" O7  NAG A 403 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 403 "   -0.304 2.00e-02 2.50e+03   2.57e-01 8.28e+02
        pdb=" C7  NAG C 403 "    0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG C 403 "   -0.184 2.00e-02 2.50e+03
        pdb=" N2  NAG C 403 "    0.445 2.00e-02 2.50e+03
        pdb=" O7  NAG C 403 "   -0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 403 "   -0.303 2.00e-02 2.50e+03   2.57e-01 8.27e+02
        pdb=" C7  NAG B 403 "    0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG B 403 "   -0.184 2.00e-02 2.50e+03
        pdb=" N2  NAG B 403 "    0.445 2.00e-02 2.50e+03
        pdb=" O7  NAG B 403 "   -0.035 2.00e-02 2.50e+03
  ... (remaining 1185 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1092
        2.77 -     3.30: 6602
        3.30 -     3.83: 11111
        3.83 -     4.37: 12845
        4.37 -     4.90: 22656
  Nonbonded interactions: 54306
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 119 "
            pdb=" OE2 GLU B 224 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OH  TYR A 119 "
            pdb=" OE2 GLU A 224 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OH  TYR C 119 "
            pdb=" OE2 GLU C 224 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" ND2 ASN C 302 "
            pdb=" OD1 ASN C 305 "
     model   vdw
     2.363 3.120
  nonbonded pdb=" ND2 ASN A 302 "
            pdb=" OD1 ASN A 305 "
     model   vdw
     2.364 3.120
  ... (remaining 54301 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.820
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.350
  Find NCS groups from input model:        0.060
  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:6.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.155   7005  Z= 0.286
  Angle     :  0.798  20.307   9516  Z= 0.340
  Chirality :  0.047   0.291   1083
  Planarity :  0.020   0.257   1176
  Dihedral  : 12.467  78.450   2442
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.30), residues: 828
  helix:  2.89 (0.27), residues: 300
  sheet: -0.31 (0.29), residues: 330
  loop : -0.66 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 253 
 TYR   0.008   0.001   TYR C  86 
 PHE   0.011   0.001   PHE A 204 
 TRP   0.014   0.001   TRP A 330 
 HIS   0.003   0.001   HIS A 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00562 /  0.29 ( 6990)
  covalent geometry    : angle       0.74898 /  0.33 ( 9474)
  SS BOND              : bond        0.00130 /  0.07 (    3)
  SS BOND              : angle       0.14306 /  0.08 (    6)
  hydrogen bonds       : bond        0.14217 /  9.62 (  268)
  hydrogen bonds       : angle       5.31186 /  3.90 (  777)
  link_NAG-ASN         : bond        0.01063 /  0.76 (   12)
  link_NAG-ASN         : angle       4.55903 /  3.63 (   36)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ILE cc_start: 0.6960 (mm) cc_final: 0.6757 (mp)
REVERT: A  106 LYS cc_start: 0.7924 (tttt) cc_final: 0.7547 (tttm)
REVERT: A  107 GLU cc_start: 0.8165 (tt0) cc_final: 0.7754 (tt0)
REVERT: A  110 ARG cc_start: 0.6724 (ttm110) cc_final: 0.6511 (ttm110)
REVERT: A  124 GLN cc_start: 0.6408 (mm-40) cc_final: 0.5714 (pm20)
REVERT: A  176 GLU cc_start: 0.6895 (mp0) cc_final: 0.6563 (mp0)
REVERT: A  179 LYS cc_start: 0.7208 (mttt) cc_final: 0.6944 (mttm)
REVERT: A  188 ARG cc_start: 0.7334 (ttt90) cc_final: 0.6793 (ttt90)
REVERT: A  236 PHE cc_start: 0.7087 (m-80) cc_final: 0.6842 (m-80)
REVERT: A  257 GLU cc_start: 0.8013 (pt0) cc_final: 0.7589 (pt0)
REVERT: A  259 ARG cc_start: 0.6633 (mtt-85) cc_final: 0.6195 (mtm-85)
REVERT: A  262 THR cc_start: 0.7652 (p) cc_final: 0.7431 (m)
REVERT: A  294 LYS cc_start: 0.6829 (tttt) cc_final: 0.5930 (ttmm)
REVERT: B  106 LYS cc_start: 0.7958 (tttt) cc_final: 0.7468 (tttt)
REVERT: B  107 GLU cc_start: 0.8196 (tt0) cc_final: 0.7865 (tt0)
REVERT: B  124 GLN cc_start: 0.6431 (mm-40) cc_final: 0.5733 (pm20)
REVERT: B  157 THR cc_start: 0.7841 (p) cc_final: 0.7605 (t)
REVERT: B  179 LYS cc_start: 0.7427 (mttt) cc_final: 0.7109 (mtpt)
REVERT: B  188 ARG cc_start: 0.7483 (ttt90) cc_final: 0.7024 (ttt90)
REVERT: B  236 PHE cc_start: 0.7234 (m-80) cc_final: 0.6945 (m-80)
REVERT: B  248 LYS cc_start: 0.6888 (ttmt) cc_final: 0.6521 (ttpp)
REVERT: B  257 GLU cc_start: 0.8090 (pt0) cc_final: 0.7682 (pt0)
REVERT: B  259 ARG cc_start: 0.6543 (mtt-85) cc_final: 0.6224 (mtt-85)
REVERT: B  262 THR cc_start: 0.7693 (p) cc_final: 0.7450 (m)
REVERT: B  263 SER cc_start: 0.7717 (m) cc_final: 0.7460 (t)
REVERT: C  106 LYS cc_start: 0.7767 (tttt) cc_final: 0.7352 (ttmm)
REVERT: C  107 GLU cc_start: 0.8123 (tt0) cc_final: 0.7719 (tt0)
REVERT: C  124 GLN cc_start: 0.6335 (mm-40) cc_final: 0.5678 (pt0)
REVERT: C  132 TYR cc_start: 0.8116 (m-80) cc_final: 0.7766 (m-80)
REVERT: C  179 LYS cc_start: 0.7430 (mttt) cc_final: 0.7030 (mtpt)
REVERT: C  188 ARG cc_start: 0.7413 (ttt90) cc_final: 0.7005 (ttt90)
REVERT: C  209 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7197 (mt-10)
REVERT: C  225 SER cc_start: 0.6793 (t) cc_final: 0.6587 (m)
REVERT: C  249 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6500 (mm-30)
REVERT: C  257 GLU cc_start: 0.8004 (pt0) cc_final: 0.7638 (pt0)
REVERT: C  259 ARG cc_start: 0.6621 (mtt-85) cc_final: 0.6268 (mtt-85)
REVERT: C  263 SER cc_start: 0.7820 (m) cc_final: 0.7598 (t)
  outliers start: 0
  outliers final: 1
  residues processed: 167
  average time/residue: 0.6102
  time to fit residues: 106.2925
Evaluate side-chains
  124 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  122 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0870
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.161668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.130416 restraints weight = 8038.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.86
r_work: 0.3370 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3223
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.1302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7005  Z= 0.147
  Angle     :  0.618  11.773   9516  Z= 0.288
  Chirality :  0.047   0.321   1083
  Planarity :  0.003   0.038   1176
  Dihedral  :  8.127  73.763    942
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 10.33 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.29), residues: 828
  helix:  3.09 (0.26), residues: 276
  sheet: -0.39 (0.28), residues: 339
  loop :  0.12 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 110 
 TYR   0.010   0.001   TYR A  74 
 PHE   0.018   0.001   PHE C 204 
 TRP   0.007   0.001   TRP A 330 
 HIS   0.002   0.001   HIS A 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 ( 6990)
  covalent geometry    : angle       0.53796 /  0.27 ( 9474)
  SS BOND              : bond        0.00127 /  0.06 (    3)
  SS BOND              : angle       0.26573 /  0.14 (    6)
  hydrogen bonds       : bond        0.03346 /  2.23 (  268)
  hydrogen bonds       : angle       4.22225 /  3.07 (  777)
  link_NAG-ASN         : bond        0.01044 /  0.75 (   12)
  link_NAG-ASN         : angle       4.96829 /  3.89 (   36)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 129
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 PHE cc_start: 0.8324 (m-80) cc_final: 0.8122 (m-80)
REVERT: A  294 LYS cc_start: 0.8584 (tttt) cc_final: 0.8199 (ttmm)
REVERT: B  134 VAL cc_start: 0.8341 (p) cc_final: 0.8141 (t)
REVERT: B  195 ASP cc_start: 0.7425 (m-30) cc_final: 0.6923 (m-30)
REVERT: B  236 PHE cc_start: 0.8487 (m-80) cc_final: 0.8261 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 131
  average time/residue: 0.6750
  time to fit residues: 92.1672
Evaluate side-chains
  106 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain C residue  103 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 61 optimal weight:    0.0060
   chunk 46 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0570
   chunk 17 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0000
   chunk 36 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.2918

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 266 ASN
** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.162493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.131253 restraints weight = 8021.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 1.83
r_work: 0.3387 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7005  Z= 0.101
  Angle     :  0.576  11.621   9516  Z= 0.262
  Chirality :  0.045   0.308   1083
  Planarity :  0.003   0.029   1176
  Dihedral  :  7.245  59.780    939
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.72 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.29), residues: 828
  helix:  3.14 (0.26), residues: 279
  sheet: -0.52 (0.28), residues: 333
  loop :  0.37 (0.44), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 110 
 TYR   0.008   0.001   TYR B  74 
 PHE   0.016   0.001   PHE B 204 
 TRP   0.006   0.001   TRP A 330 
 HIS   0.002   0.001   HIS A 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00218 /  0.10 ( 6990)
  covalent geometry    : angle       0.49327 /  0.24 ( 9474)
  SS BOND              : bond        0.00043 /  0.02 (    3)
  SS BOND              : angle       0.29157 /  0.16 (    6)
  hydrogen bonds       : bond        0.03032 /  2.00 (  268)
  hydrogen bonds       : angle       3.93857 /  2.86 (  777)
  link_NAG-ASN         : bond        0.00986 /  0.71 (   12)
  link_NAG-ASN         : angle       4.86287 /  3.84 (   36)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7716 (mp)
REVERT: A  294 LYS cc_start: 0.8500 (tttt) cc_final: 0.8153 (ttmm)
REVERT: B   77 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7271 (mp)
REVERT: B  134 VAL cc_start: 0.8354 (p) cc_final: 0.8153 (t)
REVERT: B  195 ASP cc_start: 0.7334 (m-30) cc_final: 0.6819 (m-30)
REVERT: B  253 ARG cc_start: 0.6944 (ptt90) cc_final: 0.6703 (ttp-110)
REVERT: C  294 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8128 (ttmm)
  outliers start: 18
  outliers final: 8
  residues processed: 118
  average time/residue: 0.5946
  time to fit residues: 73.4724
Evaluate side-chains
  118 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  122 GLN
Chi-restraints excluded: chain C residue  167 SER
Chi-restraints excluded: chain C residue  294 LYS
Chi-restraints excluded: chain C residue  300 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.158439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.125962 restraints weight = 8007.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.89
r_work: 0.3313 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8707
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7005  Z= 0.148
  Angle     :  0.585  11.028   9516  Z= 0.274
  Chirality :  0.046   0.333   1083
  Planarity :  0.003   0.027   1176
  Dihedral  :  7.245  59.722    939
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.59 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.29), residues: 828
  helix:  3.03 (0.26), residues: 279
  sheet: -0.54 (0.28), residues: 333
  loop :  0.54 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  93 
 TYR   0.009   0.001   TYR B  74 
 PHE   0.016   0.002   PHE B 204 
 TRP   0.007   0.001   TRP B 304 
 HIS   0.002   0.001   HIS C  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.15 ( 6990)
  covalent geometry    : angle       0.51184 /  0.26 ( 9474)
  SS BOND              : bond        0.00046 /  0.02 (    3)
  SS BOND              : angle       0.43634 /  0.24 (    6)
  hydrogen bonds       : bond        0.03149 /  2.10 (  268)
  hydrogen bonds       : angle       3.77321 /  2.70 (  777)
  link_NAG-ASN         : bond        0.01025 /  0.74 (   12)
  link_NAG-ASN         : angle       4.61929 /  3.67 (   36)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7629 (mp)
REVERT: A  294 LYS cc_start: 0.8591 (tttt) cc_final: 0.8227 (ttmm)
REVERT: B  124 GLN cc_start: 0.8030 (pm20) cc_final: 0.7766 (mp10)
REVERT: B  134 VAL cc_start: 0.8507 (p) cc_final: 0.8295 (t)
REVERT: B  195 ASP cc_start: 0.7469 (m-30) cc_final: 0.6913 (m-30)
REVERT: B  225 SER cc_start: 0.8335 (t) cc_final: 0.7922 (m)
REVERT: B  253 ARG cc_start: 0.7007 (ptt90) cc_final: 0.6708 (ttp-110)
REVERT: C  167 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8680 (p)
REVERT: C  188 ARG cc_start: 0.8565 (ttt90) cc_final: 0.8050 (ttp-170)
REVERT: C  294 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8169 (ttmm)
  outliers start: 14
  outliers final: 7
  residues processed: 99
  average time/residue: 0.5258
  time to fit residues: 54.7714
Evaluate side-chains
  94 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  167 SER
Chi-restraints excluded: chain C residue  294 LYS
Chi-restraints excluded: chain C residue  300 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0270
   chunk 78 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.7240

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 279 GLN
** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 ASN
C 279 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.159519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.127348 restraints weight = 8015.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.87
r_work: 0.3320 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7005  Z= 0.126
  Angle     :  0.558  10.228   9516  Z= 0.259
  Chirality :  0.045   0.323   1083
  Planarity :  0.003   0.028   1176
  Dihedral  :  6.968  55.258    939
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.32 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.29), residues: 828
  helix:  3.00 (0.26), residues: 279
  sheet: -0.64 (0.27), residues: 333
  loop :  0.58 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 110 
 TYR   0.013   0.001   TYR C 227 
 PHE   0.018   0.001   PHE B 204 
 TRP   0.006   0.001   TRP B 304 
 HIS   0.001   0.001   HIS C  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.12 ( 6990)
  covalent geometry    : angle       0.48731 /  0.24 ( 9474)
  SS BOND              : bond        0.00074 /  0.04 (    3)
  SS BOND              : angle       0.37166 /  0.21 (    6)
  hydrogen bonds       : bond        0.02958 /  1.96 (  268)
  hydrogen bonds       : angle       3.65157 /  2.63 (  777)
  link_NAG-ASN         : bond        0.00970 /  0.70 (   12)
  link_NAG-ASN         : angle       4.44795 /  3.55 (   36)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7617 (mp)
REVERT: A  176 GLU cc_start: 0.8013 (mp0) cc_final: 0.7769 (mm-30)
REVERT: A  253 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.5865 (ttt90)
REVERT: A  294 LYS cc_start: 0.8612 (tttt) cc_final: 0.8255 (ttmm)
REVERT: B  134 VAL cc_start: 0.8529 (p) cc_final: 0.8314 (t)
REVERT: B  195 ASP cc_start: 0.7463 (m-30) cc_final: 0.6889 (m-30)
REVERT: B  225 SER cc_start: 0.8306 (t) cc_final: 0.7907 (m)
REVERT: B  253 ARG cc_start: 0.7022 (ptt90) cc_final: 0.6740 (ttp-110)
REVERT: B  300 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8534 (p)
REVERT: C  161 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7264 (t)
REVERT: C  188 ARG cc_start: 0.8516 (ttt90) cc_final: 0.8010 (ttp-170)
REVERT: C  294 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8204 (ttmm)
  outliers start: 20
  outliers final: 11
  residues processed: 111
  average time/residue: 0.5629
  time to fit residues: 65.6894
Evaluate side-chains
  106 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  253 ARG
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  294 LYS
Chi-restraints excluded: chain C residue  300 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0570
   chunk 61 optimal weight:    0.0970
   chunk 74 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0030
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.2706

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.161503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.130125 restraints weight = 8014.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 1.86
r_work: 0.3345 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3196
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3196
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7005  Z= 0.092
  Angle     :  0.533   9.776   9516  Z= 0.245
  Chirality :  0.044   0.313   1083
  Planarity :  0.003   0.025   1176
  Dihedral  :  6.593  51.093    939
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.47 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.29), residues: 828
  helix:  3.11 (0.26), residues: 279
  sheet: -0.64 (0.27), residues: 333
  loop :  0.57 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 110 
 TYR   0.015   0.001   TYR C 227 
 PHE   0.016   0.001   PHE A 204 
 TRP   0.005   0.001   TRP B 304 
 HIS   0.002   0.001   HIS C 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00201 /  0.09 ( 6990)
  covalent geometry    : angle       0.46301 /  0.23 ( 9474)
  SS BOND              : bond        0.00025 /  0.01 (    3)
  SS BOND              : angle       0.35076 /  0.19 (    6)
  hydrogen bonds       : bond        0.02797 /  1.84 (  268)
  hydrogen bonds       : angle       3.50710 /  2.53 (  777)
  link_NAG-ASN         : bond        0.00921 /  0.67 (   12)
  link_NAG-ASN         : angle       4.32915 /  3.47 (   36)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7632 (mp)
REVERT: A  294 LYS cc_start: 0.8605 (tttt) cc_final: 0.8227 (ttmm)
REVERT: B   77 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7307 (mp)
REVERT: B  134 VAL cc_start: 0.8501 (p) cc_final: 0.8282 (t)
REVERT: B  195 ASP cc_start: 0.7422 (m-30) cc_final: 0.6861 (m-30)
REVERT: B  253 ARG cc_start: 0.6983 (ptt90) cc_final: 0.6730 (ttp-110)
REVERT: C  188 ARG cc_start: 0.8462 (ttt90) cc_final: 0.7984 (ttp-170)
  outliers start: 20
  outliers final: 10
  residues processed: 112
  average time/residue: 0.5136
  time to fit residues: 60.5872
Evaluate side-chains
  98 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  300 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.9182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.158183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.126096 restraints weight = 7967.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 1.86
r_work: 0.3289 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7005  Z= 0.149
  Angle     :  0.561   9.379   9516  Z= 0.264
  Chirality :  0.045   0.330   1083
  Planarity :  0.003   0.027   1176
  Dihedral  :  6.663  50.164    939
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 16.89 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.29), residues: 828
  helix:  2.95 (0.26), residues: 279
  sheet: -0.79 (0.26), residues: 342
  loop :  0.56 (0.46), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  93 
 TYR   0.013   0.001   TYR C 227 
 PHE   0.016   0.001   PHE A 204 
 TRP   0.007   0.001   TRP B 304 
 HIS   0.001   0.001   HIS C  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 ( 6990)
  covalent geometry    : angle       0.50131 /  0.25 ( 9474)
  SS BOND              : bond        0.00089 /  0.04 (    3)
  SS BOND              : angle       0.46256 /  0.24 (    6)
  hydrogen bonds       : bond        0.02985 /  1.98 (  268)
  hydrogen bonds       : angle       3.59038 /  2.57 (  777)
  link_NAG-ASN         : bond        0.00937 /  0.68 (   12)
  link_NAG-ASN         : angle       4.13238 /  3.32 (   36)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7659 (mp)
REVERT: A  294 LYS cc_start: 0.8663 (tttt) cc_final: 0.8276 (ttmm)
REVERT: B  134 VAL cc_start: 0.8507 (p) cc_final: 0.8295 (t)
REVERT: B  225 SER cc_start: 0.8435 (t) cc_final: 0.8034 (m)
REVERT: B  253 ARG cc_start: 0.7036 (ptt90) cc_final: 0.6790 (ttp-110)
REVERT: C  161 SER cc_start: 0.7760 (OUTLIER) cc_final: 0.7258 (t)
REVERT: C  188 ARG cc_start: 0.8551 (ttt90) cc_final: 0.8068 (ttp-170)
REVERT: C  294 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8199 (ttmm)
  outliers start: 23
  outliers final: 14
  residues processed: 112
  average time/residue: 0.5267
  time to fit residues: 62.2744
Evaluate side-chains
  103 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  225 SER
Chi-restraints excluded: chain C residue  294 LYS
Chi-restraints excluded: chain C residue  300 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0570
   chunk 72 optimal weight:    0.7980
   chunk 7 optimal weight:    0.2980
   chunk 69 optimal weight:    0.1980
   chunk 37 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.4098

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.160190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.128146 restraints weight = 8067.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.90
r_work: 0.3323 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3167
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8695
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7005  Z= 0.101
  Angle     :  0.534   9.231   9516  Z= 0.248
  Chirality :  0.044   0.316   1083
  Planarity :  0.003   0.026   1176
  Dihedral  :  6.421  48.922    939
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.90 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.29), residues: 828
  helix:  3.40 (0.25), residues: 264
  sheet: -0.73 (0.27), residues: 333
  loop :  0.54 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 110 
 TYR   0.014   0.001   TYR C 227 
 PHE   0.016   0.001   PHE A 204 
 TRP   0.006   0.001   TRP B 304 
 HIS   0.001   0.001   HIS C 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00225 /  0.10 ( 6990)
  covalent geometry    : angle       0.46969 /  0.23 ( 9474)
  SS BOND              : bond        0.00029 /  0.01 (    3)
  SS BOND              : angle       0.30535 /  0.17 (    6)
  hydrogen bonds       : bond        0.02777 /  1.82 (  268)
  hydrogen bonds       : angle       3.48310 /  2.51 (  777)
  link_NAG-ASN         : bond        0.00906 /  0.66 (   12)
  link_NAG-ASN         : angle       4.15235 /  3.34 (   36)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7617 (mp)
REVERT: A  294 LYS cc_start: 0.8648 (tttt) cc_final: 0.8272 (ttmm)
REVERT: B   77 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7325 (mp)
REVERT: B  134 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8276 (t)
REVERT: B  195 ASP cc_start: 0.7416 (m-30) cc_final: 0.6827 (m-30)
REVERT: B  225 SER cc_start: 0.8206 (t) cc_final: 0.7812 (m)
REVERT: B  253 ARG cc_start: 0.6973 (ptt90) cc_final: 0.6720 (ttp-110)
REVERT: C  188 ARG cc_start: 0.8522 (ttt90) cc_final: 0.8029 (ttp-170)
  outliers start: 21
  outliers final: 12
  residues processed: 109
  average time/residue: 0.4652
  time to fit residues: 53.6817
Evaluate side-chains
  105 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  155 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0670
   chunk 26 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.6520

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.158876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.126753 restraints weight = 8048.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.88
r_work: 0.3306 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3157
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3157
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7005  Z= 0.119
  Angle     :  0.541   9.530   9516  Z= 0.252
  Chirality :  0.044   0.323   1083
  Planarity :  0.003   0.028   1176
  Dihedral  :  6.381  48.315    939
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.61 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.29), residues: 828
  helix:  3.35 (0.26), residues: 264
  sheet: -0.78 (0.26), residues: 342
  loop :  0.61 (0.44), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  93 
 TYR   0.016   0.001   TYR C 227 
 PHE   0.016   0.001   PHE A 204 
 TRP   0.006   0.001   TRP B 304 
 HIS   0.001   0.001   HIS C 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 ( 6990)
  covalent geometry    : angle       0.48157 /  0.24 ( 9474)
  SS BOND              : bond        0.00056 /  0.03 (    3)
  SS BOND              : angle       0.32253 /  0.17 (    6)
  hydrogen bonds       : bond        0.02829 /  1.85 (  268)
  hydrogen bonds       : angle       3.49985 /  2.51 (  777)
  link_NAG-ASN         : bond        0.00907 /  0.66 (   12)
  link_NAG-ASN         : angle       4.03001 /  3.24 (   36)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7634 (mp)
REVERT: A  253 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.5581 (ttt90)
REVERT: A  294 LYS cc_start: 0.8680 (tttt) cc_final: 0.8291 (ttmm)
REVERT: B  134 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8314 (t)
REVERT: B  225 SER cc_start: 0.8313 (t) cc_final: 0.7908 (m)
REVERT: B  253 ARG cc_start: 0.7016 (ptt90) cc_final: 0.6747 (ttp-110)
REVERT: C  161 SER cc_start: 0.7693 (OUTLIER) cc_final: 0.7225 (t)
REVERT: C  188 ARG cc_start: 0.8534 (ttt90) cc_final: 0.8044 (ttp-170)
  outliers start: 21
  outliers final: 13
  residues processed: 108
  average time/residue: 0.4901
  time to fit residues: 55.8955
Evaluate side-chains
  105 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  253 ARG
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  161 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0060
   chunk 65 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0980
   chunk 49 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 8 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.5396

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.159352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.127419 restraints weight = 8009.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.86
r_work: 0.3314 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3158
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3158
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7005  Z= 0.107
  Angle     :  0.533   9.331   9516  Z= 0.247
  Chirality :  0.044   0.318   1083
  Planarity :  0.003   0.030   1176
  Dihedral  :  6.301  47.310    939
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.05 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.29), residues: 828
  helix:  3.38 (0.26), residues: 264
  sheet: -0.79 (0.27), residues: 342
  loop :  0.60 (0.44), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  93 
 TYR   0.015   0.001   TYR C 227 
 PHE   0.016   0.001   PHE B 204 
 TRP   0.006   0.001   TRP B 304 
 HIS   0.001   0.001   HIS C 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 ( 6990)
  covalent geometry    : angle       0.47333 /  0.23 ( 9474)
  SS BOND              : bond        0.00034 /  0.02 (    3)
  SS BOND              : angle       0.28355 /  0.16 (    6)
  hydrogen bonds       : bond        0.02766 /  1.82 (  268)
  hydrogen bonds       : angle       3.43106 /  2.46 (  777)
  link_NAG-ASN         : bond        0.00882 /  0.64 (   12)
  link_NAG-ASN         : angle       4.01179 /  3.24 (   36)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7616 (mp)
REVERT: A  294 LYS cc_start: 0.8679 (tttt) cc_final: 0.8288 (ttmm)
REVERT: B  134 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8307 (t)
REVERT: B  225 SER cc_start: 0.8222 (t) cc_final: 0.7843 (m)
REVERT: B  253 ARG cc_start: 0.7041 (ptt90) cc_final: 0.6758 (ttp-110)
REVERT: C  188 ARG cc_start: 0.8512 (ttt90) cc_final: 0.8039 (ttp-170)
  outliers start: 16
  outliers final: 11
  residues processed: 100
  average time/residue: 0.5210
  time to fit residues: 55.0703
Evaluate side-chains
  101 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  155 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0470
   chunk 79 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.6278

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 266 ASN
B 302 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.158587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.126652 restraints weight = 7968.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 1.85
r_work: 0.3291 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3147
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (5 function evaluations)
r_final: 0.3147
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7005  Z= 0.117
  Angle     :  0.536   9.314   9516  Z= 0.250
  Chirality :  0.044   0.322   1083
  Planarity :  0.003   0.030   1176
  Dihedral  :  6.284  46.541    939
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.34 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.29), residues: 828
  helix:  3.37 (0.26), residues: 264
  sheet: -0.79 (0.27), residues: 342
  loop :  0.62 (0.44), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  93 
 TYR   0.015   0.001   TYR C 227 
 PHE   0.017   0.001   PHE B 236 
 TRP   0.006   0.001   TRP B 304 
 HIS   0.001   0.001   HIS C 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 ( 6990)
  covalent geometry    : angle       0.47961 /  0.24 ( 9474)
  SS BOND              : bond        0.00061 /  0.03 (    3)
  SS BOND              : angle       0.31682 /  0.17 (    6)
  hydrogen bonds       : bond        0.02787 /  1.83 (  268)
  hydrogen bonds       : angle       3.43004 /  2.45 (  777)
  link_NAG-ASN         : bond        0.00885 /  0.64 (   12)
  link_NAG-ASN         : angle       3.92771 /  3.17 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2803.46 seconds
wall clock time: 48 minutes 26.18 seconds (2906.18 seconds total)