Starting phenix.real_space_refine
on Wed Sep 17 04:37:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9elg_48148/09_2025/9elg_48148.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9elg_48148/09_2025/9elg_48148.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9elg_48148/09_2025/9elg_48148.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9elg_48148/09_2025/9elg_48148.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9elg_48148/09_2025/9elg_48148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9elg_48148/09_2025/9elg_48148.map"
  }
  resolution = 3.71
  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=   0.013
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      15      5.16       5
     C    2742      2.51       5
     N     688      2.21       5
     O     810      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4255
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1928
          Classifications: {'peptide': 238}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 226}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 2173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2173
          Classifications: {'peptide': 272}
          Link IDs: {'PTRANS': 18, 'TRANS': 253}
    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
    Chain: "A"
      Number of atoms: 98
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 98
          Unusual residues: {'NAG': 7}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
    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
  Time building chain proxies: 1.36, per 1000 atoms: 0.32
  Number of scatterers: 4255
  At special positions: 0
  Unit cell: (83.288, 89.75, 84.724, 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      15     16.00
     O     810      8.00
     N     688      7.00
     C    2742      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 129 " - pdb=" SG  CYS A 163 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 538 " - pdb=" SG  CYS C 590 " 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 B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A 301 " - " ASN A  30 "
      " NAG A 302 " - " ASN A  61 "
      " NAG A 303 " - " ASN A 230 "
      " NAG A 304 " - " ASN A 120 "
      " NAG A 305 " - " ASN A 162 "
      " NAG A 306 " - " ASN A 241 "
      " NAG A 307 " - " ASN A 278 "
      " NAG B   1 " - " ASN C 354 "
      " NAG C 601 " - " ASN C 331 "
      " NAG C 602 " - " ASN C 343 "
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 161.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  958

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 7 sheets defined
      8.8% alpha, 33.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 152 through 155
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.505A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 349 through 353
      removed outlier: 3.586A  pdb=" N   TRP C 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 366 through 372
      removed outlier: 3.515A  pdb=" N   ASN C 370 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 386 through 389
      removed outlier: 4.242A  pdb=" N   ASP C 389 " --> pdb=" O   LYS C 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 386 through 389'
    Processing helix  chain 'C' and resid 405 through 411
      removed outlier: 4.795A  pdb=" N   SER C 408 " --> pdb=" O   ASN C 405 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA C 411 " --> pdb=" O   SER C 408 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28
      removed outlier: 6.336A  pdb=" N   PHE A 198 " --> pdb=" O   ASP A 224 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ASP A 224 " --> pdb=" O   PHE A 198 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ILE A 200 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43
      removed outlier: 6.566A  pdb=" N   PHE A  43 " --> pdb=" O   ARG C 567 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   GLY C 566 " --> pdb=" O   ASP C 574 " (cutoff:3.500A)
      removed outlier: 5.379A  pdb=" N   ASP C 574 " --> pdb=" O   ILE C 587 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55
      removed outlier: 4.022A  pdb=" N   ASP A 283 " --> pdb=" O   LYS A 274 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83
      removed outlier: 3.568A  pdb=" N   LEU A 240 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   VAL A 141 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83
      removed outlier: 4.070A  pdb=" N   GLY A 101 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ALA A 239 " --> pdb=" O   ILE A  99 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   ILE A  99 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 5.622A  pdb=" N   ARG A 100 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   GLU A 130 " --> pdb=" O   CYS A 163 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   CYS A 163 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   GLN A 132 " --> pdb=" O   ASN A 161 " (cutoff:3.500A)
      removed outlier: 8.824A  pdb=" N   ASN A 161 " --> pdb=" O   GLN A 132 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358
    Processing sheet with id=AA7, first strand: chain 'C' and resid 391 through 392

    124 hydrogen bonds defined for protein.
    306 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: 0.52

  Time building geometry restraints manager: 0.58 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 667
        1.31 -     1.44: 1307
        1.44 -     1.56: 2377
        1.56 -     1.69: 3
        1.69 -     1.82: 16
  Bond restraints: 4370
  Sorted by residual:
  bond pdb=" CA  THR A  29 "
       pdb=" C   THR A  29 "
    ideal  model  delta    sigma   weight residual
    1.523  1.432  0.092 1.28e-02 6.10e+03 5.12e+01
  bond pdb=" CA  PHE A  32 "
       pdb=" C   PHE A  32 "
    ideal  model  delta    sigma   weight residual
    1.521  1.452  0.069 1.17e-02 7.31e+03 3.52e+01
  bond pdb=" C   PHE A  32 "
       pdb=" O   PHE A  32 "
    ideal  model  delta    sigma   weight residual
    1.236  1.186  0.050 1.14e-02 7.69e+03 1.92e+01
  bond pdb=" C   THR A  29 "
       pdb=" O   THR A  29 "
    ideal  model  delta    sigma   weight residual
    1.237  1.183  0.054 1.39e-02 5.18e+03 1.50e+01
  bond pdb=" C   THR A  29 "
       pdb=" N   ASN A  30 "
    ideal  model  delta    sigma   weight residual
    1.335  1.268  0.067 1.86e-02 2.89e+03 1.31e+01
  ... (remaining 4365 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.14: 5755
        3.14 -     6.27: 160
        6.27 -     9.41: 17
        9.41 -    12.55: 8
       12.55 -    15.69: 1
  Bond angle restraints: 5941
  Sorted by residual:
  angle pdb=" C   THR A  29 "
        pdb=" N   ASN A  30 "
        pdb=" CA  ASN A  30 "
      ideal   model   delta    sigma   weight residual
     123.03  107.34   15.69 1.34e+00 5.57e-01 1.37e+02
  angle pdb=" CA  PHE A  32 "
        pdb=" CB  PHE A  32 "
        pdb=" CG  PHE A  32 "
      ideal   model   delta    sigma   weight residual
     113.80  122.82   -9.02 1.00e+00 1.00e+00 8.13e+01
  angle pdb=" CA  PRO C 589 "
        pdb=" N   PRO C 589 "
        pdb=" CD  PRO C 589 "
      ideal   model   delta    sigma   weight residual
     112.00  100.80   11.20 1.40e+00 5.10e-01 6.40e+01
  angle pdb=" CA  THR A  33 "
        pdb=" CB  THR A  33 "
        pdb=" OG1 THR A  33 "
      ideal   model   delta    sigma   weight residual
     109.60   99.45   10.15 1.50e+00 4.44e-01 4.58e+01
  angle pdb=" N   PHE A  32 "
        pdb=" CA  PHE A  32 "
        pdb=" CB  PHE A  32 "
      ideal   model   delta    sigma   weight residual
     110.65  101.83    8.82 1.56e+00 4.11e-01 3.20e+01
  ... (remaining 5936 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.46: 2592
       25.46 -    50.91: 87
       50.91 -    76.36: 22
       76.36 -   101.82: 2
      101.82 -   127.27: 3
  Dihedral angle restraints: 2706
    sinusoidal: 1215
      harmonic: 1491
  Sorted by residual:
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -170.09   84.09     1      1.00e+01 1.00e-02 8.61e+01
  dihedral pdb=" CD  ARG A  76 "
           pdb=" NE  ARG A  76 "
           pdb=" CZ  ARG A  76 "
           pdb=" NH1 ARG A  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   54.52  -54.52     1      1.00e+01 1.00e-02 4.03e+01
  dihedral pdb=" N   THR A  29 "
           pdb=" C   THR A  29 "
           pdb=" CA  THR A  29 "
           pdb=" CB  THR A  29 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  109.20   14.20     0      2.50e+00 1.60e-01 3.23e+01
  ... (remaining 2703 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.316: 673
       0.316 -    0.632: 2
       0.632 -    0.949: 0
       0.949 -    1.265: 0
       1.265 -    1.581: 1
  Chirality restraints: 676
  Sorted by residual:
  chirality pdb=" C1  NAG A 307 "
            pdb=" ND2 ASN A 278 "
            pdb=" C2  NAG A 307 "
            pdb=" O5  NAG A 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.82   -1.58 2.00e-01 2.50e+01 6.25e+01
  chirality pdb=" C1  NAG A 302 "
            pdb=" ND2 ASN A  61 "
            pdb=" C2  NAG A 302 "
            pdb=" O5  NAG A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.95   -0.45 2.00e-01 2.50e+01 5.07e+00
  chirality pdb=" CA  ASN A  30 "
            pdb=" N   ASN A  30 "
            pdb=" C   ASN A  30 "
            pdb=" CB  ASN A  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.67e+00
  ... (remaining 673 not shown)

  Planarity restraints: 760
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 301 "   -0.156 2.00e-02 2.50e+03   1.31e-01 2.16e+02
        pdb=" C7  NAG A 301 "    0.038 2.00e-02 2.50e+03
        pdb=" C8  NAG A 301 "   -0.112 2.00e-02 2.50e+03
        pdb=" N2  NAG A 301 "    0.219 2.00e-02 2.50e+03
        pdb=" O7  NAG A 301 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  76 "   -0.750 9.50e-02 1.11e+02   3.37e-01 7.76e+01
        pdb=" NE  ARG A  76 "    0.063 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  76 "   -0.042 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  76 "    0.018 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  76 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 588 "   -0.127 5.00e-02 4.00e+02   1.84e-01 5.39e+01
        pdb=" N   PRO C 589 "    0.317 5.00e-02 4.00e+02
        pdb=" CA  PRO C 589 "   -0.100 5.00e-02 4.00e+02
        pdb=" CD  PRO C 589 "   -0.090 5.00e-02 4.00e+02
  ... (remaining 757 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.58: 43
        2.58 -     3.16: 3367
        3.16 -     3.74: 6091
        3.74 -     4.32: 8918
        4.32 -     4.90: 14637
  Nonbonded interactions: 33056
  Sorted by model distance:
  nonbonded pdb=" O   GLN A  52 "
            pdb=" OD1 ASP A  53 "
     model   vdw
     2.006 3.040
  nonbonded pdb=" OH  TYR C 453 "
            pdb=" OE1 GLU C 493 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" OH  TYR A  89 "
            pdb=" OE2 GLU A 188 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" N   THR A  33 "
            pdb=" OG1 THR A  33 "
     model   vdw
     2.286 2.496
  nonbonded pdb=" NZ  LYS A  75 "
            pdb=" OD1 ASN A  79 "
     model   vdw
     2.321 3.120
  ... (remaining 33051 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             13.490
  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:                     6.360
  Find NCS groups from input model:        0.020
  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:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
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      :  0.008   0.098   4387  Z= 0.369
  Angle     :  1.334  15.686   5986  Z= 0.745
  Chirality :  0.091   1.581    676
  Planarity :  0.017   0.337    750
  Dihedral  : 13.819 127.274   1730
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 2.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.57 %
    Favored  : 89.43 %
  Cbeta Deviations :  0.63 %
  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 aren not related in a simple way.
  whole:  0.30 (0.35), residues: 498
  helix: -2.83 (0.87), residues: 19
  sheet:  1.28 (0.41), residues: 147
  loop : -0.08 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.051   0.002   ARG A  76 
 TYR   0.036   0.004   TYR C 380 
 PHE   0.073   0.004   PHE C 565 
 TRP   0.016   0.003   TRP C 452 
 HIS   0.004   0.001   HIS C 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00755 ( 4370)
  covalent geometry    : angle       1.27799 ( 5941)
  SS BOND              : bond        0.00524 (    6)
  SS BOND              : angle       2.66947 (   12)
  hydrogen bonds       : bond        0.11458 (  122)
  hydrogen bonds       : angle       8.74567 (  306)
  link_BETA1-4         : bond        0.00030 (    1)
  link_BETA1-4         : angle       0.46197 (    3)
  link_NAG-ASN         : bond        0.00741 (   10)
  link_NAG-ASN         : angle       5.37829 (   30)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   30 ASN cc_start: 0.8184 (p0) cc_final: 0.7810 (p0)
REVERT: A   33 THR cc_start: 0.8215 (p) cc_final: 0.7967 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0716
  time to fit residues: 6.4709
Evaluate side-chains
  53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0770
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 113 GLN
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 GLN
A 235 GLN
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 580 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.193311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.160165 restraints weight = 4983.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.161201 restraints weight = 4402.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.163647 restraints weight = 3600.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.165228 restraints weight = 2886.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.165752 restraints weight = 2640.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
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      :  0.004   0.043   4387  Z= 0.183
  Angle     :  0.722  12.215   5986  Z= 0.366
  Chirality :  0.050   0.274    676
  Planarity :  0.007   0.092    750
  Dihedral  :  9.691  79.892    786
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 10.79 %
    Favored  : 88.11 %
  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 aren not related in a simple way.
  whole:  0.14 (0.36), residues: 498
  helix: -2.37 (0.82), residues: 28
  sheet:  1.02 (0.40), residues: 148
  loop : -0.07 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 355 
 TYR   0.018   0.002   TYR A 261 
 PHE   0.022   0.002   PHE A 131 
 TRP   0.014   0.001   TRP C 353 
 HIS   0.003   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 4370)
  covalent geometry    : angle       0.67911 ( 5941)
  SS BOND              : bond        0.00217 (    6)
  SS BOND              : angle       1.11092 (   12)
  hydrogen bonds       : bond        0.03984 (  122)
  hydrogen bonds       : angle       7.13163 (  306)
  link_BETA1-4         : bond        0.00145 (    1)
  link_BETA1-4         : angle       1.07264 (    3)
  link_NAG-ASN         : bond        0.00864 (   10)
  link_NAG-ASN         : angle       3.49394 (   30)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 THR cc_start: 0.7827 (p) cc_final: 0.7596 (p)
  outliers start: 5
  outliers final: 4
  residues processed: 65
  average time/residue: 0.0661
  time to fit residues: 5.6366
Evaluate side-chains
  58 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  553 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 23 optimal weight:    0.4980
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 445 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.188959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.154684 restraints weight = 5018.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.156018 restraints weight = 4449.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.158123 restraints weight = 3582.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.159564 restraints weight = 2985.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.159762 restraints weight = 2661.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4387  Z= 0.191
  Angle     :  0.687  11.700   5986  Z= 0.348
  Chirality :  0.050   0.300    676
  Planarity :  0.006   0.071    750
  Dihedral  :  9.401  74.144    786
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 11.23 %
    Favored  : 86.56 %
  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 aren not related in a simple way.
  whole: -0.07 (0.36), residues: 498
  helix: -2.36 (0.89), residues: 21
  sheet:  0.83 (0.40), residues: 150
  loop : -0.28 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 466 
 TYR   0.021   0.002   TYR A 261 
 PHE   0.019   0.002   PHE A 271 
 TRP   0.011   0.001   TRP C 452 
 HIS   0.003   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 4370)
  covalent geometry    : angle       0.64417 ( 5941)
  SS BOND              : bond        0.00257 (    6)
  SS BOND              : angle       1.20336 (   12)
  hydrogen bonds       : bond        0.03652 (  122)
  hydrogen bonds       : angle       6.83034 (  306)
  link_BETA1-4         : bond        0.00012 (    1)
  link_BETA1-4         : angle       0.73736 (    3)
  link_NAG-ASN         : bond        0.00772 (   10)
  link_NAG-ASN         : angle       3.36426 (   30)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 ASN cc_start: 0.7448 (p0) cc_final: 0.6933 (p0)
REVERT: A   32 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8882 (m-80)
  outliers start: 10
  outliers final: 8
  residues processed: 71
  average time/residue: 0.0719
  time to fit residues: 6.5621
Evaluate side-chains
  66 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  362 VAL
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  445 HIS
Chi-restraints excluded: chain C residue  553 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0040
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
A 113 GLN
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 414 GLN
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.188159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.154208 restraints weight = 4996.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.155740 restraints weight = 4370.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.157930 restraints weight = 3601.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.158565 restraints weight = 2957.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.159114 restraints weight = 2690.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4387  Z= 0.172
  Angle     :  0.681  11.178   5986  Z= 0.336
  Chirality :  0.050   0.305    676
  Planarity :  0.005   0.061    750
  Dihedral  :  8.813  69.181    786
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 13.88 %
    Favored  : 83.70 %
  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 aren not related in a simple way.
  whole: -0.29 (0.36), residues: 498
  helix: -2.92 (0.65), residues: 28
  sheet:  0.70 (0.40), residues: 149
  loop : -0.35 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 355 
 TYR   0.019   0.002   TYR A 261 
 PHE   0.011   0.002   PHE A 131 
 TRP   0.008   0.001   TRP C 353 
 HIS   0.016   0.002   HIS C 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 4370)
  covalent geometry    : angle       0.62042 ( 5941)
  SS BOND              : bond        0.00219 (    6)
  SS BOND              : angle       1.32237 (   12)
  hydrogen bonds       : bond        0.03375 (  122)
  hydrogen bonds       : angle       6.62715 (  306)
  link_BETA1-4         : bond        0.00000 (    1)
  link_BETA1-4         : angle       0.72249 (    3)
  link_NAG-ASN         : bond        0.00641 (   10)
  link_NAG-ASN         : angle       3.93059 (   30)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A   30 ASN cc_start: 0.7420 (p0) cc_final: 0.6966 (p0)
REVERT: A   32 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8870 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 67
  average time/residue: 0.0639
  time to fit residues: 5.8496
Evaluate side-chains
  66 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  362 VAL
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  553 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0970
   chunk 42 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 21 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 235 GLN
C 394 ASN
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.192955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.159389 restraints weight = 4878.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.160680 restraints weight = 4535.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.162071 restraints weight = 3601.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.162850 restraints weight = 3299.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.163612 restraints weight = 2889.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4387  Z= 0.174
  Angle     :  0.655  10.643   5986  Z= 0.330
  Chirality :  0.049   0.305    676
  Planarity :  0.005   0.056    750
  Dihedral  :  8.108  66.918    786
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.20 %
    Favored  : 82.38 %
  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 aren not related in a simple way.
  whole: -0.49 (0.36), residues: 498
  helix: -2.51 (0.87), residues: 21
  sheet:  0.43 (0.40), residues: 152
  loop : -0.52 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 355 
 TYR   0.019   0.002   TYR A 261 
 PHE   0.012   0.002   PHE A  90 
 TRP   0.008   0.001   TRP C 353 
 HIS   0.002   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 4370)
  covalent geometry    : angle       0.61319 ( 5941)
  SS BOND              : bond        0.00352 (    6)
  SS BOND              : angle       1.31575 (   12)
  hydrogen bonds       : bond        0.03338 (  122)
  hydrogen bonds       : angle       6.56838 (  306)
  link_BETA1-4         : bond        0.00156 (    1)
  link_BETA1-4         : angle       0.69633 (    3)
  link_NAG-ASN         : bond        0.00653 (   10)
  link_NAG-ASN         : angle       3.22696 (   30)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A   30 ASN cc_start: 0.7458 (p0) cc_final: 0.7015 (p0)
REVERT: A   32 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8851 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0919
  time to fit residues: 7.1474
Evaluate side-chains
  63 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  362 VAL
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  553 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 23 optimal weight:    0.3980
   chunk 42 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0030
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 474 GLN
** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.193378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.159998 restraints weight = 4983.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.162255 restraints weight = 4207.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.163444 restraints weight = 3309.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.165136 restraints weight = 2934.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.165298 restraints weight = 2589.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.3336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4387  Z= 0.152
  Angle     :  0.626  10.049   5986  Z= 0.316
  Chirality :  0.048   0.307    676
  Planarity :  0.005   0.054    750
  Dihedral  :  7.500  63.645    786
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.76 %
    Favored  : 82.82 %
  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 aren not related in a simple way.
  whole: -0.61 (0.36), residues: 498
  helix: -2.52 (0.87), residues: 21
  sheet:  0.30 (0.40), residues: 153
  loop : -0.59 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 100 
 TYR   0.018   0.001   TYR A 261 
 PHE   0.011   0.002   PHE A  90 
 TRP   0.007   0.001   TRP C 353 
 HIS   0.002   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4370)
  covalent geometry    : angle       0.58769 ( 5941)
  SS BOND              : bond        0.00187 (    6)
  SS BOND              : angle       1.13323 (   12)
  hydrogen bonds       : bond        0.03189 (  122)
  hydrogen bonds       : angle       6.35584 (  306)
  link_BETA1-4         : bond        0.00291 (    1)
  link_BETA1-4         : angle       0.73767 (    3)
  link_NAG-ASN         : bond        0.00591 (   10)
  link_NAG-ASN         : angle       3.04809 (   30)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8811 (m-80)
REVERT: A   41 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8770 (mmmt)
  outliers start: 11
  outliers final: 10
  residues processed: 63
  average time/residue: 0.0618
  time to fit residues: 5.1480
Evaluate side-chains
  64 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   77 PHE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  362 VAL
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  553 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0030
   chunk 40 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 414 GLN
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.192452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.158002 restraints weight = 4955.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.161125 restraints weight = 3746.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.163363 restraints weight = 3108.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.164666 restraints weight = 2717.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.165940 restraints weight = 2491.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4387  Z= 0.142
  Angle     :  0.608   9.609   5986  Z= 0.308
  Chirality :  0.048   0.305    676
  Planarity :  0.005   0.051    750
  Dihedral  :  6.901  61.086    786
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 14.54 %
    Favored  : 82.16 %
  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 aren not related in a simple way.
  whole: -0.56 (0.36), residues: 498
  helix: -2.43 (0.89), residues: 21
  sheet:  0.33 (0.40), residues: 151
  loop : -0.55 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 100 
 TYR   0.016   0.001   TYR A 261 
 PHE   0.023   0.002   PHE A 131 
 TRP   0.006   0.001   TRP C 353 
 HIS   0.002   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 4370)
  covalent geometry    : angle       0.57261 ( 5941)
  SS BOND              : bond        0.00164 (    6)
  SS BOND              : angle       1.22100 (   12)
  hydrogen bonds       : bond        0.03062 (  122)
  hydrogen bonds       : angle       6.24368 (  306)
  link_BETA1-4         : bond        0.00229 (    1)
  link_BETA1-4         : angle       0.64101 (    3)
  link_NAG-ASN         : bond        0.00576 (   10)
  link_NAG-ASN         : angle       2.87810 (   30)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8805 (m-80)
  outliers start: 15
  outliers final: 12
  residues processed: 67
  average time/residue: 0.0707
  time to fit residues: 6.1192
Evaluate side-chains
  66 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  362 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  553 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0270
   chunk 22 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.6640

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 487 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 = 0.4160 r_free = 0.4160 target = 0.194110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.159549 restraints weight = 4966.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.162740 restraints weight = 3744.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.164931 restraints weight = 3097.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.166295 restraints weight = 2719.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.167553 restraints weight = 2482.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4387  Z= 0.171
  Angle     :  0.628   9.081   5986  Z= 0.322
  Chirality :  0.048   0.296    676
  Planarity :  0.005   0.052    750
  Dihedral  :  6.757  63.727    786
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.64 %
    Favored  : 81.06 %
  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 aren not related in a simple way.
  whole: -0.75 (0.36), residues: 498
  helix: -2.52 (0.90), residues: 21
  sheet:  0.17 (0.40), residues: 152
  loop : -0.68 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 100 
 TYR   0.019   0.001   TYR A 261 
 PHE   0.021   0.002   PHE A  77 
 TRP   0.008   0.001   TRP C 353 
 HIS   0.002   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 4370)
  covalent geometry    : angle       0.59596 ( 5941)
  SS BOND              : bond        0.00242 (    6)
  SS BOND              : angle       1.24810 (   12)
  hydrogen bonds       : bond        0.03152 (  122)
  hydrogen bonds       : angle       6.33675 (  306)
  link_BETA1-4         : bond        0.00209 (    1)
  link_BETA1-4         : angle       0.65927 (    3)
  link_NAG-ASN         : bond        0.00531 (   10)
  link_NAG-ASN         : angle       2.77667 (   30)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8854 (m-80)
  outliers start: 15
  outliers final: 11
  residues processed: 67
  average time/residue: 0.0692
  time to fit residues: 6.0746
Evaluate side-chains
  69 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  362 VAL
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  553 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0980
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 414 GLN
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.194366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.160362 restraints weight = 4980.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.163509 restraints weight = 3765.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.165713 restraints weight = 3091.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.167164 restraints weight = 2699.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.168385 restraints weight = 2457.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.3810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4387  Z= 0.158
  Angle     :  0.615   8.840   5986  Z= 0.316
  Chirality :  0.048   0.296    676
  Planarity :  0.005   0.052    750
  Dihedral  :  6.551  62.948    786
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.42 %
    Favored  : 81.28 %
  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 aren not related in a simple way.
  whole: -0.79 (0.36), residues: 498
  helix: -2.47 (0.92), residues: 21
  sheet:  0.08 (0.40), residues: 152
  loop : -0.68 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 100 
 TYR   0.018   0.002   TYR A 261 
 PHE   0.019   0.002   PHE A  77 
 TRP   0.007   0.001   TRP C 353 
 HIS   0.002   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 4370)
  covalent geometry    : angle       0.58405 ( 5941)
  SS BOND              : bond        0.00194 (    6)
  SS BOND              : angle       1.18884 (   12)
  hydrogen bonds       : bond        0.03078 (  122)
  hydrogen bonds       : angle       6.27479 (  306)
  link_BETA1-4         : bond        0.00358 (    1)
  link_BETA1-4         : angle       0.69869 (    3)
  link_NAG-ASN         : bond        0.00523 (   10)
  link_NAG-ASN         : angle       2.68513 (   30)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8844 (m-80)
  outliers start: 15
  outliers final: 13
  residues processed: 66
  average time/residue: 0.0657
  time to fit residues: 5.6171
Evaluate side-chains
  71 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  339 HIS
Chi-restraints excluded: chain C residue  362 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  553 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0670
   chunk 31 optimal weight:    0.9990
   chunk 36 optimal weight:    0.1980
   chunk 5 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 487 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 = 0.4144 r_free = 0.4144 target = 0.192174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.158004 restraints weight = 4936.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.161161 restraints weight = 3730.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.163409 restraints weight = 3073.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.164828 restraints weight = 2690.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.165642 restraints weight = 2453.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4387  Z= 0.139
  Angle     :  0.597   8.543   5986  Z= 0.309
  Chirality :  0.047   0.296    676
  Planarity :  0.005   0.052    750
  Dihedral  :  6.159  60.048    786
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.52 %
    Favored  : 80.62 %
  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 aren not related in a simple way.
  whole: -0.78 (0.36), residues: 498
  helix: -2.37 (0.95), residues: 21
  sheet:  0.08 (0.40), residues: 152
  loop : -0.68 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 100 
 TYR   0.017   0.001   TYR A 261 
 PHE   0.019   0.002   PHE A  77 
 TRP   0.006   0.001   TRP C 353 
 HIS   0.002   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4370)
  covalent geometry    : angle       0.56844 ( 5941)
  SS BOND              : bond        0.00254 (    6)
  SS BOND              : angle       1.13116 (   12)
  hydrogen bonds       : bond        0.02981 (  122)
  hydrogen bonds       : angle       6.13501 (  306)
  link_BETA1-4         : bond        0.00365 (    1)
  link_BETA1-4         : angle       0.67736 (    3)
  link_NAG-ASN         : bond        0.00510 (   10)
  link_NAG-ASN         : angle       2.57194 (   30)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 12
  residues processed: 57
  average time/residue: 0.0856
  time to fit residues: 6.1717
Evaluate side-chains
  60 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  362 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  553 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 22 optimal weight:    0.2980
   chunk 23 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0670
   chunk 26 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 487 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 = 0.4165 r_free = 0.4165 target = 0.194556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.161134 restraints weight = 4946.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.164203 restraints weight = 3722.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.166214 restraints weight = 3059.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.167862 restraints weight = 2680.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.168778 restraints weight = 2429.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4387  Z= 0.146
  Angle     :  0.595   8.336   5986  Z= 0.309
  Chirality :  0.047   0.289    676
  Planarity :  0.005   0.052    750
  Dihedral  :  6.077  60.766    786
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.30 %
    Favored  : 80.84 %
  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 aren not related in a simple way.
  whole: -0.82 (0.36), residues: 498
  helix: -2.36 (0.94), residues: 21
  sheet:  0.09 (0.40), residues: 152
  loop : -0.72 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 100 
 TYR   0.018   0.001   TYR A 261 
 PHE   0.013   0.001   PHE C 565 
 TRP   0.007   0.001   TRP C 353 
 HIS   0.002   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4370)
  covalent geometry    : angle       0.56719 ( 5941)
  SS BOND              : bond        0.00182 (    6)
  SS BOND              : angle       1.17991 (   12)
  hydrogen bonds       : bond        0.03019 (  122)
  hydrogen bonds       : angle       6.17304 (  306)
  link_BETA1-4         : bond        0.00362 (    1)
  link_BETA1-4         : angle       0.66651 (    3)
  link_NAG-ASN         : bond        0.00491 (   10)
  link_NAG-ASN         : angle       2.49587 (   30)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1151.61 seconds
wall clock time: 20 minutes 35.68 seconds (1235.68 seconds total)