Starting phenix.real_space_refine
on Tue Mar  3 14:44:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p54_13194/03_2026/7p54_13194.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p54_13194/03_2026/7p54_13194.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p54_13194/03_2026/7p54_13194.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p54_13194/03_2026/7p54_13194.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p54_13194/03_2026/7p54_13194.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p54_13194/03_2026/7p54_13194.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    4030      2.51       5
     N     986      2.21       5
     O    1182      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6248
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3040
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 397, 3040
          Classifications: {'peptide': 397}
          Link IDs: {'PTRANS': 9, 'TRANS': 387}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3040
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 397, 3040
          Classifications: {'peptide': 397}
          Link IDs: {'PTRANS': 9, 'TRANS': 387}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.51, per 1000 atoms: 0.24
  Number of scatterers: 6248
  At special positions: 0
  Unit cell: (93.744, 70.308, 128.898, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1182      8.00
     N     986      7.00
     C    4030      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 382 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 300 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 274 " - pdb=" SG  CYS B 382 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 300 " - pdb=" SG  CYS B 367 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 601 " - " ASN A 283 "
      " NAG A 602 " - " ASN A  31 "
      " NAG B 601 " - " ASN B 283 "
      " NAG B 602 " - " ASN B  31 "
      " NAG C   1 " - " ASN A 352 "
      " NAG D   1 " - " ASN A 129 "
      " NAG E   1 " - " ASN B 352 "
      " NAG F   1 " - " ASN B 129 "
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 256.2 milliseconds
  

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1480

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 0 sheets defined
      89.3% alpha, 0.0% 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 11 through 19
    Processing helix  chain 'A' and resid 38 through 72
    Processing helix  chain 'A' and resid 89 through 161
      removed outlier: 4.269A  pdb=" N   LEU A 150 " --> pdb=" O   MET A 146 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLU A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE A 160 " --> pdb=" O   ARG A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 187
      removed outlier: 3.744A  pdb=" N   LEU A 171 " --> pdb=" O   TYR A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 237
    Processing helix  chain 'A' and resid 238 through 276
      removed outlier: 3.560A  pdb=" N   SER A 244 " --> pdb=" O   CYS A 240 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ALA A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 285
    Processing helix  chain 'A' and resid 290 through 299
    Processing helix  chain 'A' and resid 308 through 337
      removed outlier: 3.580A  pdb=" N   VAL A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
      Proline residue:  A 335  - end of helix
    Processing helix  chain 'A' and resid 341 through 365
    Processing helix  chain 'A' and resid 366 through 383
      removed outlier: 4.482A  pdb=" N   LEU A 370 " --> pdb=" O   ASP A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 409
    Processing helix  chain 'A' and resid 409 through 416
      removed outlier: 3.614A  pdb=" N   ALA A 413 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 19
    Processing helix  chain 'B' and resid 38 through 72
    Processing helix  chain 'B' and resid 89 through 161
      removed outlier: 4.283A  pdb=" N   LEU B 150 " --> pdb=" O   MET B 146 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   GLU B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE B 160 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 187
      removed outlier: 3.773A  pdb=" N   LEU B 171 " --> pdb=" O   TYR B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 237
    Processing helix  chain 'B' and resid 239 through 276
      removed outlier: 4.272A  pdb=" N   ALA B 276 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 285
    Processing helix  chain 'B' and resid 290 through 300
    Processing helix  chain 'B' and resid 308 through 337
      removed outlier: 3.597A  pdb=" N   VAL B 334 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
      Proline residue:  B 335  - end of helix
    Processing helix  chain 'B' and resid 340 through 365
      removed outlier: 3.772A  pdb=" N   LEU B 344 " --> pdb=" O   ALA B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 383
      removed outlier: 4.559A  pdb=" N   LEU B 370 " --> pdb=" O   ASP B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 409
    Processing helix  chain 'B' and resid 409 through 416
      removed outlier: 3.647A  pdb=" N   ALA B 413 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)

    581 hydrogen bonds defined for protein.
    1743 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1935
        1.34 -     1.46: 1538
        1.46 -     1.58: 2839
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 6378
  Sorted by residual:
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.53e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.43e+00
  bond pdb=" C1  NAG B 602 "
       pdb=" O5  NAG B 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.33e+00
  bond pdb=" C1  NAG A 602 "
       pdb=" O5  NAG A 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.82e+00
  bond pdb=" C1  NAG B 601 "
       pdb=" O5  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.61e+00
  ... (remaining 6373 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 8390
        1.38 -     2.76: 254
        2.76 -     4.13: 34
        4.13 -     5.51: 11
        5.51 -     6.89: 3
  Bond angle restraints: 8692
  Sorted by residual:
  angle pdb=" C   VAL B  23 "
        pdb=" N   GLY B  24 "
        pdb=" CA  GLY B  24 "
      ideal   model   delta    sigma   weight residual
     121.44  117.03    4.41 1.45e+00 4.76e-01 9.25e+00
  angle pdb=" N   GLN A 325 "
        pdb=" CA  GLN A 325 "
        pdb=" CB  GLN A 325 "
      ideal   model   delta    sigma   weight residual
     110.16  114.31   -4.15 1.48e+00 4.57e-01 7.87e+00
  angle pdb=" N   ARG B 368 "
        pdb=" CA  ARG B 368 "
        pdb=" C   ARG B 368 "
      ideal   model   delta    sigma   weight residual
     111.11  114.34   -3.23 1.20e+00 6.94e-01 7.25e+00
  angle pdb=" N   GLY B  37 "
        pdb=" CA  GLY B  37 "
        pdb=" C   GLY B  37 "
      ideal   model   delta    sigma   weight residual
     114.25  111.02    3.23 1.30e+00 5.92e-01 6.18e+00
  angle pdb=" C   CYS B 367 "
        pdb=" N   ARG B 368 "
        pdb=" CA  ARG B 368 "
      ideal   model   delta    sigma   weight residual
     120.54  123.89   -3.35 1.35e+00 5.49e-01 6.16e+00
  ... (remaining 8687 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 3460
       16.06 -    32.12: 290
       32.12 -    48.18: 91
       48.18 -    64.23: 25
       64.23 -    80.29: 8
  Dihedral angle restraints: 3874
    sinusoidal: 1570
      harmonic: 2304
  Sorted by residual:
  dihedral pdb=" CB  CYS A 300 "
           pdb=" SG  CYS A 300 "
           pdb=" SG  CYS A 367 "
           pdb=" CB  CYS A 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -162.49   76.49     1      1.00e+01 1.00e-02 7.36e+01
  dihedral pdb=" CB  CYS B 300 "
           pdb=" SG  CYS B 300 "
           pdb=" SG  CYS B 367 "
           pdb=" CB  CYS B 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.61   55.61     1      1.00e+01 1.00e-02 4.18e+01
  dihedral pdb=" CB  CYS A 274 "
           pdb=" SG  CYS A 274 "
           pdb=" SG  CYS A 382 "
           pdb=" CB  CYS A 382 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  128.88  -35.88     1      1.00e+01 1.00e-02 1.82e+01
  ... (remaining 3871 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 985
       0.063 -    0.126: 84
       0.126 -    0.188: 1
       0.188 -    0.251: 0
       0.251 -    0.314: 2
  Chirality restraints: 1072
  Sorted by residual:
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN B 129 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 129 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CA  GLN A 325 "
            pdb=" N   GLN A 325 "
            pdb=" C   GLN A 325 "
            pdb=" CB  GLN A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.29e-01
  ... (remaining 1069 not shown)

  Planarity restraints: 1066
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  20 "   -0.055 5.00e-02 4.00e+02   8.28e-02 1.10e+01
        pdb=" N   PRO A  21 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO A  21 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A  21 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  20 "   -0.053 5.00e-02 4.00e+02   8.04e-02 1.03e+01
        pdb=" N   PRO B  21 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO B  21 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO B  21 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 147 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.66e+00
        pdb=" C   LYS B 147 "    0.028 2.00e-02 2.50e+03
        pdb=" O   LYS B 147 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   VAL B 148 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1063 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 737
        2.74 -     3.28: 6440
        3.28 -     3.82: 11254
        3.82 -     4.36: 11217
        4.36 -     4.90: 20634
  Nonbonded interactions: 50282
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 278 "
            pdb=" OH  TYR A 374 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OD1 ASN B 111 "
            pdb=" NH1 ARG B 212 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" OD2 ASP A  38 "
            pdb=" OG  SER A  40 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   ILE B 281 "
            pdb=" OG1 THR B 285 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OD1 ASN A 111 "
            pdb=" NH1 ARG A 212 "
     model   vdw
     2.243 3.120
  ... (remaining 50277 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.770
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
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      :  0.004   0.038   6394  Z= 0.173
  Angle     :  0.586   7.623   8736  Z= 0.302
  Chirality :  0.038   0.314   1072
  Planarity :  0.005   0.083   1058
  Dihedral  : 13.935  80.293   2382
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  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:  4.08 (0.29), residues: 786
  helix:  3.32 (0.18), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.34 (0.49), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 192 
 TYR   0.010   0.001   TYR A   8 
 PHE   0.012   0.002   PHE B 395 
 TRP   0.007   0.001   TRP B 213 
 HIS   0.002   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6378)
  covalent geometry    : angle       0.55278 ( 8692)
  SS BOND              : bond        0.00444 (    4)
  SS BOND              : angle       3.15677 (    8)
  hydrogen bonds       : bond        0.09394 (  581)
  hydrogen bonds       : angle       4.11908 ( 1743)
  link_BETA1-4         : bond        0.01212 (    4)
  link_BETA1-4         : angle       4.04926 (   12)
  link_NAG-ASN         : bond        0.00337 (    8)
  link_NAG-ASN         : angle       1.63199 (   24)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A   16 TRP cc_start: 0.6870 (m100) cc_final: 0.6646 (m100)
REVERT: A  207 TYR cc_start: 0.7719 (t80) cc_final: 0.7392 (t80)
REVERT: A  213 TRP cc_start: 0.8415 (t60) cc_final: 0.7703 (t-100)
REVERT: A  245 MET cc_start: 0.6533 (mmp) cc_final: 0.6259 (mmp)
REVERT: A  353 SER cc_start: 0.8925 (t) cc_final: 0.8714 (t)
REVERT: B   12 TRP cc_start: 0.8176 (p-90) cc_final: 0.7966 (p-90)
REVERT: B  213 TRP cc_start: 0.8324 (t60) cc_final: 0.7643 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0895
  time to fit residues: 15.8095
Evaluate side-chains
  116 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0470
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.9080

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
B  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.161163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.131284 restraints weight = 6775.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.34
r_work: 0.3236 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.0898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6394  Z= 0.163
  Angle     :  0.539   6.788   8736  Z= 0.271
  Chirality :  0.039   0.240   1072
  Planarity :  0.004   0.053   1058
  Dihedral  :  7.335  59.364   1096
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  8.18 %
    Favored  : 90.30 %
  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:  4.12 (0.29), residues: 786
  helix:  3.42 (0.18), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.82 (0.51), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 295 
 TYR   0.020   0.001   TYR A   8 
 PHE   0.017   0.002   PHE A  62 
 TRP   0.017   0.001   TRP A  16 
 HIS   0.003   0.001   HIS A  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6378)
  covalent geometry    : angle       0.51111 ( 8692)
  SS BOND              : bond        0.00821 (    4)
  SS BOND              : angle       1.97716 (    8)
  hydrogen bonds       : bond        0.04082 (  581)
  hydrogen bonds       : angle       3.60992 ( 1743)
  link_BETA1-4         : bond        0.01198 (    4)
  link_BETA1-4         : angle       3.43399 (   12)
  link_NAG-ASN         : bond        0.00276 (    8)
  link_NAG-ASN         : angle       1.94703 (   24)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8222 (t80) cc_final: 0.7801 (t80)
REVERT: A  213 TRP cc_start: 0.8578 (t60) cc_final: 0.7724 (t-100)
REVERT: A  245 MET cc_start: 0.6536 (mmp) cc_final: 0.5946 (mmp)
REVERT: A  332 PHE cc_start: 0.7907 (m-10) cc_final: 0.7688 (m-10)
REVERT: A  336 LEU cc_start: 0.8900 (mp) cc_final: 0.8686 (mp)
REVERT: B   16 TRP cc_start: 0.8049 (m100) cc_final: 0.7830 (m100)
REVERT: B  213 TRP cc_start: 0.8576 (t60) cc_final: 0.7649 (t-100)
REVERT: B  283 ASN cc_start: 0.8236 (t0) cc_final: 0.7901 (t0)
  outliers start: 10
  outliers final: 7
  residues processed: 125
  average time/residue: 0.0851
  time to fit residues: 13.7583
Evaluate side-chains
  122 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 115
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.157256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.128080 restraints weight = 6956.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.28
r_work: 0.3238 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.1103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6394  Z= 0.151
  Angle     :  0.523   6.823   8736  Z= 0.258
  Chirality :  0.038   0.242   1072
  Planarity :  0.004   0.042   1058
  Dihedral  :  6.829  58.505   1096
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.73 %
    Favored  : 85.76 %
  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:  4.13 (0.29), residues: 786
  helix:  3.44 (0.18), residues: 668
  sheet:  None (None), residues: 0
  loop : -2.05 (0.49), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  26 
 TYR   0.018   0.001   TYR A   8 
 PHE   0.022   0.002   PHE A  62 
 TRP   0.007   0.001   TRP A  16 
 HIS   0.002   0.001   HIS A  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6378)
  covalent geometry    : angle       0.49764 ( 8692)
  SS BOND              : bond        0.00827 (    4)
  SS BOND              : angle       1.57053 (    8)
  hydrogen bonds       : bond        0.03932 (  581)
  hydrogen bonds       : angle       3.56393 ( 1743)
  link_BETA1-4         : bond        0.01212 (    4)
  link_BETA1-4         : angle       3.41801 (   12)
  link_NAG-ASN         : bond        0.00236 (    8)
  link_NAG-ASN         : angle       1.81146 (   24)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8317 (t80) cc_final: 0.7873 (t80)
REVERT: A  213 TRP cc_start: 0.8586 (t60) cc_final: 0.7712 (t-100)
REVERT: A  245 MET cc_start: 0.6576 (mmp) cc_final: 0.5949 (mmt)
REVERT: A  283 ASN cc_start: 0.7986 (t0) cc_final: 0.7726 (t0)
REVERT: A  332 PHE cc_start: 0.7951 (m-10) cc_final: 0.7621 (m-10)
REVERT: A  336 LEU cc_start: 0.8940 (mp) cc_final: 0.8704 (mp)
REVERT: B    8 TYR cc_start: 0.7581 (t80) cc_final: 0.7195 (t80)
REVERT: B   16 TRP cc_start: 0.7995 (m100) cc_final: 0.7775 (m100)
REVERT: B  213 TRP cc_start: 0.8572 (t60) cc_final: 0.7593 (t-100)
REVERT: B  283 ASN cc_start: 0.8395 (t0) cc_final: 0.8056 (t0)
  outliers start: 10
  outliers final: 9
  residues processed: 130
  average time/residue: 0.0815
  time to fit residues: 13.7977
Evaluate side-chains
  128 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    1.1784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.154212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.124847 restraints weight = 7084.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 2.30
r_work: 0.3216 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6394  Z= 0.189
  Angle     :  0.563   6.764   8736  Z= 0.279
  Chirality :  0.040   0.237   1072
  Planarity :  0.004   0.039   1058
  Dihedral  :  6.466  58.913   1096
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.91 %
    Favored  : 81.82 %
  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:  3.90 (0.29), residues: 786
  helix:  3.23 (0.18), residues: 678
  sheet:  None (None), residues: 0
  loop : -2.22 (0.52), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 295 
 TYR   0.017   0.002   TYR A   8 
 PHE   0.026   0.002   PHE B  62 
 TRP   0.007   0.001   TRP A 414 
 HIS   0.003   0.001   HIS A  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 6378)
  covalent geometry    : angle       0.53748 ( 8692)
  SS BOND              : bond        0.01087 (    4)
  SS BOND              : angle       1.82887 (    8)
  hydrogen bonds       : bond        0.04041 (  581)
  hydrogen bonds       : angle       3.58921 ( 1743)
  link_BETA1-4         : bond        0.01117 (    4)
  link_BETA1-4         : angle       3.47801 (   12)
  link_NAG-ASN         : bond        0.00246 (    8)
  link_NAG-ASN         : angle       1.89923 (   24)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  176 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7312 (tt0)
REVERT: A  207 TYR cc_start: 0.8452 (t80) cc_final: 0.7934 (t80)
REVERT: A  213 TRP cc_start: 0.8640 (t60) cc_final: 0.7680 (t-100)
REVERT: A  283 ASN cc_start: 0.8166 (t0) cc_final: 0.7852 (t0)
REVERT: A  332 PHE cc_start: 0.8101 (m-10) cc_final: 0.7792 (m-10)
REVERT: A  336 LEU cc_start: 0.8889 (mp) cc_final: 0.8645 (mp)
REVERT: B   16 TRP cc_start: 0.7980 (m100) cc_final: 0.7722 (m100)
REVERT: B  213 TRP cc_start: 0.8655 (t60) cc_final: 0.7616 (t-100)
REVERT: B  283 ASN cc_start: 0.8447 (t0) cc_final: 0.8169 (t0)
  outliers start: 15
  outliers final: 13
  residues processed: 124
  average time/residue: 0.0834
  time to fit residues: 13.3972
Evaluate side-chains
  129 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.155080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.125554 restraints weight = 7063.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.30
r_work: 0.3187 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6394  Z= 0.158
  Angle     :  0.523   7.042   8736  Z= 0.261
  Chirality :  0.038   0.243   1072
  Planarity :  0.004   0.035   1058
  Dihedral  :  6.260  59.663   1096
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.12 %
    Favored  : 80.30 %
  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:  4.01 (0.29), residues: 786
  helix:  3.24 (0.18), residues: 686
  sheet:  None (None), residues: 0
  loop : -2.11 (0.55), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 164 
 TYR   0.017   0.001   TYR A   8 
 PHE   0.027   0.002   PHE B  62 
 TRP   0.006   0.001   TRP A 414 
 HIS   0.003   0.001   HIS A 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6378)
  covalent geometry    : angle       0.49753 ( 8692)
  SS BOND              : bond        0.00906 (    4)
  SS BOND              : angle       1.66958 (    8)
  hydrogen bonds       : bond        0.03911 (  581)
  hydrogen bonds       : angle       3.52220 ( 1743)
  link_BETA1-4         : bond        0.01180 (    4)
  link_BETA1-4         : angle       3.43385 (   12)
  link_NAG-ASN         : bond        0.00203 (    8)
  link_NAG-ASN         : angle       1.75252 (   24)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A  176 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7359 (tt0)
REVERT: A  207 TYR cc_start: 0.8436 (t80) cc_final: 0.7932 (t80)
REVERT: A  213 TRP cc_start: 0.8620 (t60) cc_final: 0.7642 (t-100)
REVERT: A  283 ASN cc_start: 0.8184 (t0) cc_final: 0.7856 (t0)
REVERT: A  325 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.6547 (mp10)
REVERT: A  332 PHE cc_start: 0.8105 (m-10) cc_final: 0.7699 (m-10)
REVERT: A  336 LEU cc_start: 0.8861 (mp) cc_final: 0.8661 (mp)
REVERT: B    8 TYR cc_start: 0.7738 (t80) cc_final: 0.7398 (t80)
REVERT: B   16 TRP cc_start: 0.7937 (m100) cc_final: 0.7590 (m100)
REVERT: B  213 TRP cc_start: 0.8619 (t60) cc_final: 0.7522 (t-100)
REVERT: B  283 ASN cc_start: 0.8504 (t0) cc_final: 0.8232 (t0)
REVERT: B  332 PHE cc_start: 0.8127 (m-10) cc_final: 0.7855 (m-10)
  outliers start: 17
  outliers final: 14
  residues processed: 128
  average time/residue: 0.0885
  time to fit residues: 14.6955
Evaluate side-chains
  128 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  378 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 40 optimal weight:    0.2980
   chunk 57 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.156435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.126963 restraints weight = 6925.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.29
r_work: 0.3206 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6394  Z= 0.133
  Angle     :  0.506   7.706   8736  Z= 0.252
  Chirality :  0.038   0.244   1072
  Planarity :  0.003   0.032   1058
  Dihedral  :  6.122  59.822   1096
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 17.42 %
    Favored  : 79.39 %
  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:  4.21 (0.29), residues: 786
  helix:  3.36 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -2.07 (0.56), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 295 
 TYR   0.016   0.001   TYR A   8 
 PHE   0.028   0.002   PHE B  62 
 TRP   0.007   0.001   TRP A  16 
 HIS   0.002   0.001   HIS A 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6378)
  covalent geometry    : angle       0.48144 ( 8692)
  SS BOND              : bond        0.00750 (    4)
  SS BOND              : angle       1.54263 (    8)
  hydrogen bonds       : bond        0.03780 (  581)
  hydrogen bonds       : angle       3.51124 ( 1743)
  link_BETA1-4         : bond        0.01222 (    4)
  link_BETA1-4         : angle       3.38343 (   12)
  link_NAG-ASN         : bond        0.00197 (    8)
  link_NAG-ASN         : angle       1.62125 (   24)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7313 (tt0)
REVERT: A  207 TYR cc_start: 0.8390 (t80) cc_final: 0.7893 (t80)
REVERT: A  213 TRP cc_start: 0.8601 (t60) cc_final: 0.7623 (t-100)
REVERT: A  283 ASN cc_start: 0.8190 (t0) cc_final: 0.7844 (t0)
REVERT: A  325 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.6509 (mp10)
REVERT: A  332 PHE cc_start: 0.8212 (m-10) cc_final: 0.7819 (m-10)
REVERT: B    8 TYR cc_start: 0.7636 (t80) cc_final: 0.7377 (t80)
REVERT: B   16 TRP cc_start: 0.7925 (m100) cc_final: 0.7569 (m100)
REVERT: B  213 TRP cc_start: 0.8634 (t60) cc_final: 0.7582 (t-100)
REVERT: B  283 ASN cc_start: 0.8495 (t0) cc_final: 0.8212 (t0)
REVERT: B  332 PHE cc_start: 0.8129 (m-10) cc_final: 0.7836 (m-10)
  outliers start: 21
  outliers final: 18
  residues processed: 129
  average time/residue: 0.0840
  time to fit residues: 14.1125
Evaluate side-chains
  135 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain B residue  378 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 32 optimal weight:    0.1980
   chunk 7 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0470
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.5878

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.157087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.127521 restraints weight = 6914.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.29
r_work: 0.3266 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6394  Z= 0.128
  Angle     :  0.500   7.425   8736  Z= 0.248
  Chirality :  0.038   0.242   1072
  Planarity :  0.003   0.032   1058
  Dihedral  :  5.994  59.630   1096
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.64 %
    Favored  : 78.33 %
  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:  4.31 (0.29), residues: 786
  helix:  3.42 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -2.07 (0.57), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 295 
 TYR   0.016   0.001   TYR A   8 
 PHE   0.029   0.002   PHE A  62 
 TRP   0.007   0.001   TRP A  16 
 HIS   0.003   0.001   HIS B  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6378)
  covalent geometry    : angle       0.47575 ( 8692)
  SS BOND              : bond        0.00711 (    4)
  SS BOND              : angle       1.49458 (    8)
  hydrogen bonds       : bond        0.03702 (  581)
  hydrogen bonds       : angle       3.49320 ( 1743)
  link_BETA1-4         : bond        0.01195 (    4)
  link_BETA1-4         : angle       3.38510 (   12)
  link_NAG-ASN         : bond        0.00204 (    8)
  link_NAG-ASN         : angle       1.58020 (   24)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.8107 (mtm110) cc_final: 0.7841 (mpp80)
REVERT: A  176 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7281 (tt0)
REVERT: A  207 TYR cc_start: 0.8359 (t80) cc_final: 0.7868 (t80)
REVERT: A  213 TRP cc_start: 0.8593 (t60) cc_final: 0.7577 (t-100)
REVERT: A  283 ASN cc_start: 0.8219 (t0) cc_final: 0.7876 (t0)
REVERT: A  325 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.6492 (mp10)
REVERT: A  332 PHE cc_start: 0.8273 (m-10) cc_final: 0.8021 (m-10)
REVERT: B    8 TYR cc_start: 0.7630 (t80) cc_final: 0.7399 (t80)
REVERT: B   16 TRP cc_start: 0.7914 (m100) cc_final: 0.7544 (m100)
REVERT: B   26 ARG cc_start: 0.7681 (mpp80) cc_final: 0.7347 (mpp80)
REVERT: B  176 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7283 (tt0)
REVERT: B  213 TRP cc_start: 0.8622 (t60) cc_final: 0.7533 (t-100)
REVERT: B  283 ASN cc_start: 0.8496 (t0) cc_final: 0.8208 (t0)
REVERT: B  325 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.6892 (mp10)
REVERT: B  332 PHE cc_start: 0.8161 (m-10) cc_final: 0.7857 (m-10)
  outliers start: 20
  outliers final: 17
  residues processed: 133
  average time/residue: 0.0810
  time to fit residues: 14.0285
Evaluate side-chains
  137 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain B residue  378 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 41 optimal weight:    0.3980
   chunk 59 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.156008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.126912 restraints weight = 7005.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 2.28
r_work: 0.3251 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6394  Z= 0.140
  Angle     :  0.519   7.562   8736  Z= 0.257
  Chirality :  0.038   0.238   1072
  Planarity :  0.003   0.031   1058
  Dihedral  :  5.933  59.373   1096
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 18.79 %
    Favored  : 77.73 %
  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:  4.28 (0.29), residues: 786
  helix:  3.40 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -2.04 (0.57), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 295 
 TYR   0.015   0.001   TYR A   8 
 PHE   0.030   0.002   PHE B  62 
 TRP   0.007   0.001   TRP A  16 
 HIS   0.002   0.001   HIS B 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6378)
  covalent geometry    : angle       0.49549 ( 8692)
  SS BOND              : bond        0.00789 (    4)
  SS BOND              : angle       1.59735 (    8)
  hydrogen bonds       : bond        0.03718 (  581)
  hydrogen bonds       : angle       3.50811 ( 1743)
  link_BETA1-4         : bond        0.01170 (    4)
  link_BETA1-4         : angle       3.39971 (   12)
  link_NAG-ASN         : bond        0.00207 (    8)
  link_NAG-ASN         : angle       1.60592 (   24)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.8085 (mtm110) cc_final: 0.7823 (mpp80)
REVERT: A  176 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7337 (tt0)
REVERT: A  207 TYR cc_start: 0.8398 (t80) cc_final: 0.7888 (t80)
REVERT: A  213 TRP cc_start: 0.8604 (t60) cc_final: 0.7604 (t-100)
REVERT: A  283 ASN cc_start: 0.8285 (t0) cc_final: 0.7950 (t0)
REVERT: A  325 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.6530 (mp10)
REVERT: B   16 TRP cc_start: 0.7925 (m100) cc_final: 0.7566 (m100)
REVERT: B   26 ARG cc_start: 0.7779 (mpp80) cc_final: 0.7466 (mpp80)
REVERT: B  176 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7337 (tt0)
REVERT: B  213 TRP cc_start: 0.8609 (t60) cc_final: 0.7555 (t-100)
REVERT: B  283 ASN cc_start: 0.8539 (t0) cc_final: 0.8240 (t0)
REVERT: B  325 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.6912 (mp10)
REVERT: B  332 PHE cc_start: 0.8173 (m-10) cc_final: 0.7870 (m-10)
  outliers start: 23
  outliers final: 20
  residues processed: 132
  average time/residue: 0.0793
  time to fit residues: 13.8121
Evaluate side-chains
  138 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  378 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.156071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.126509 restraints weight = 6992.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 2.30
r_work: 0.3254 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6394  Z= 0.143
  Angle     :  0.524   7.752   8736  Z= 0.260
  Chirality :  0.038   0.240   1072
  Planarity :  0.003   0.031   1058
  Dihedral  :  5.901  59.340   1096
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.09 %
    Favored  : 77.58 %
  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:  4.30 (0.29), residues: 786
  helix:  3.41 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -2.01 (0.56), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 295 
 TYR   0.022   0.002   TYR B   8 
 PHE   0.030   0.002   PHE A  62 
 TRP   0.008   0.001   TRP A  16 
 HIS   0.003   0.001   HIS B  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6378)
  covalent geometry    : angle       0.50092 ( 8692)
  SS BOND              : bond        0.00812 (    4)
  SS BOND              : angle       1.58748 (    8)
  hydrogen bonds       : bond        0.03711 (  581)
  hydrogen bonds       : angle       3.51823 ( 1743)
  link_BETA1-4         : bond        0.01155 (    4)
  link_BETA1-4         : angle       3.39274 (   12)
  link_NAG-ASN         : bond        0.00205 (    8)
  link_NAG-ASN         : angle       1.58038 (   24)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7832 (mpp80)
REVERT: A  164 ARG cc_start: 0.7129 (mtp-110) cc_final: 0.6777 (mtp-110)
REVERT: A  176 GLN cc_start: 0.7402 (mm-40) cc_final: 0.7177 (tt0)
REVERT: A  207 TYR cc_start: 0.8392 (t80) cc_final: 0.7908 (t80)
REVERT: A  213 TRP cc_start: 0.8606 (t60) cc_final: 0.7613 (t-100)
REVERT: A  283 ASN cc_start: 0.8310 (t0) cc_final: 0.7980 (t0)
REVERT: A  325 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.6522 (mp10)
REVERT: A  332 PHE cc_start: 0.8411 (m-80) cc_final: 0.8192 (m-10)
REVERT: B    8 TYR cc_start: 0.7290 (t80) cc_final: 0.6948 (t80)
REVERT: B   16 TRP cc_start: 0.7967 (m100) cc_final: 0.7583 (m100)
REVERT: B   26 ARG cc_start: 0.7784 (mpp80) cc_final: 0.7476 (mpp80)
REVERT: B  176 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7343 (tt0)
REVERT: B  213 TRP cc_start: 0.8608 (t60) cc_final: 0.7567 (t-100)
REVERT: B  283 ASN cc_start: 0.8529 (t0) cc_final: 0.8252 (t0)
REVERT: B  325 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.6896 (mp10)
REVERT: B  332 PHE cc_start: 0.8190 (m-10) cc_final: 0.7893 (m-10)
  outliers start: 22
  outliers final: 19
  residues processed: 133
  average time/residue: 0.0760
  time to fit residues: 13.1863
Evaluate side-chains
  139 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  378 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 68 optimal weight:    0.5980
   chunk 63 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.157543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.128741 restraints weight = 6941.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.26
r_work: 0.3203 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6394  Z= 0.138
  Angle     :  0.520   7.682   8736  Z= 0.258
  Chirality :  0.038   0.240   1072
  Planarity :  0.003   0.038   1058
  Dihedral  :  5.821  59.222   1096
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.70 %
    Favored  : 77.42 %
  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:  4.34 (0.29), residues: 786
  helix:  3.44 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -2.00 (0.56), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 295 
 TYR   0.019   0.001   TYR B   8 
 PHE   0.030   0.002   PHE B  62 
 TRP   0.009   0.001   TRP A  16 
 HIS   0.002   0.001   HIS B 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6378)
  covalent geometry    : angle       0.49770 ( 8692)
  SS BOND              : bond        0.00756 (    4)
  SS BOND              : angle       1.54240 (    8)
  hydrogen bonds       : bond        0.03674 (  581)
  hydrogen bonds       : angle       3.50109 ( 1743)
  link_BETA1-4         : bond        0.01187 (    4)
  link_BETA1-4         : angle       3.39301 (   12)
  link_NAG-ASN         : bond        0.00203 (    8)
  link_NAG-ASN         : angle       1.53294 (   24)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.8143 (mtm110) cc_final: 0.7894 (mpp80)
REVERT: A  164 ARG cc_start: 0.7037 (mtp-110) cc_final: 0.6818 (mtp-110)
REVERT: A  176 GLN cc_start: 0.7324 (mm-40) cc_final: 0.7074 (tt0)
REVERT: A  207 TYR cc_start: 0.8305 (t80) cc_final: 0.7799 (t80)
REVERT: A  213 TRP cc_start: 0.8599 (t60) cc_final: 0.7525 (t-100)
REVERT: A  283 ASN cc_start: 0.8211 (t0) cc_final: 0.7866 (t0)
REVERT: A  325 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.6399 (mp10)
REVERT: A  332 PHE cc_start: 0.8522 (m-80) cc_final: 0.8206 (m-10)
REVERT: B    8 TYR cc_start: 0.7078 (t80) cc_final: 0.6782 (t80)
REVERT: B   16 TRP cc_start: 0.7958 (m100) cc_final: 0.7549 (m100)
REVERT: B   26 ARG cc_start: 0.7744 (mpp80) cc_final: 0.7446 (mpp80)
REVERT: B  156 ARG cc_start: 0.8001 (ttp-110) cc_final: 0.7712 (ttp-110)
REVERT: B  176 GLN cc_start: 0.7438 (mm-40) cc_final: 0.7130 (tt0)
REVERT: B  213 TRP cc_start: 0.8607 (t60) cc_final: 0.7493 (t-100)
REVERT: B  283 ASN cc_start: 0.8431 (t0) cc_final: 0.8155 (t0)
REVERT: B  325 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.6840 (mp10)
REVERT: B  332 PHE cc_start: 0.8227 (m-10) cc_final: 0.7941 (m-10)
  outliers start: 19
  outliers final: 17
  residues processed: 131
  average time/residue: 0.0755
  time to fit residues: 12.8746
Evaluate side-chains
  134 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  378 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.155924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.127161 restraints weight = 7024.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.28
r_work: 0.3225 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6394  Z= 0.160
  Angle     :  0.546   7.817   8736  Z= 0.270
  Chirality :  0.039   0.241   1072
  Planarity :  0.003   0.035   1058
  Dihedral  :  5.771  59.554   1096
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 20.00 %
    Favored  : 76.97 %
  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:  4.21 (0.29), residues: 786
  helix:  3.33 (0.18), residues: 690
  sheet:  None (None), residues: 0
  loop : -1.96 (0.57), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 295 
 TYR   0.020   0.002   TYR B   8 
 PHE   0.031   0.002   PHE B  62 
 TRP   0.007   0.001   TRP A  16 
 HIS   0.003   0.001   HIS B 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6378)
  covalent geometry    : angle       0.52297 ( 8692)
  SS BOND              : bond        0.00889 (    4)
  SS BOND              : angle       1.72103 (    8)
  hydrogen bonds       : bond        0.03763 (  581)
  hydrogen bonds       : angle       3.54210 ( 1743)
  link_BETA1-4         : bond        0.01097 (    4)
  link_BETA1-4         : angle       3.41365 (   12)
  link_NAG-ASN         : bond        0.00212 (    8)
  link_NAG-ASN         : angle       1.63600 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1530.71 seconds
wall clock time: 26 minutes 51.85 seconds (1611.85 seconds total)