Starting phenix.real_space_refine
on Tue Feb  3 13:46:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9loz_63264/02_2026/9loz_63264.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9loz_63264/02_2026/9loz_63264.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9loz_63264/02_2026/9loz_63264.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9loz_63264/02_2026/9loz_63264.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9loz_63264/02_2026/9loz_63264.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9loz_63264/02_2026/9loz_63264.cif"
  }
  resolution = 3.55
  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=  -0.001 sd=   0.030
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    2082      2.51       5
     N     548      2.21       5
     O     617      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3262
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1557
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 13, 'TRANS': 180}
    Chain: "B"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 914
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
    Chain: "C"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 763
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 8, 'TRANS': 91}
    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
  Time building chain proxies: 0.97, per 1000 atoms: 0.30
  Number of scatterers: 3262
  At special positions: 0
  Unit cell: (69.84, 67.9, 94.09, 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     617      8.00
     N     548      7.00
     C    2082      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  21 " - pdb=" SG  CYS C  87 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 343 "
      " NAG A 602 " - " ASN A 354 "
  Time building additional restraints: 0.22
  Conformation dependent library (CDL) restraints added in 91.3 milliseconds
  

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  748

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 10 sheets defined
      10.0% alpha, 38.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 351 through 353
      No H-bonds generated for 'chain 'A' and resid 351 through 353'
    Processing helix  chain 'A' and resid 364 through 371
      removed outlier: 3.841A  pdb=" N   VAL A 367 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   TYR A 369 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
      removed outlier: 3.596A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.200A  pdb=" N   SER A 408 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 61 through 64
      removed outlier: 3.740A  pdb=" N   LYS B  64 " --> pdb=" O   ASP B  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 61 through 64'
    Processing helix  chain 'C' and resid 28 through 31
    Processing sheet with id=AA1, first strand: chain 'A' and resid 348 through 349
      removed outlier: 7.461A  pdb=" N   ALA A 348 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 9.878A  pdb=" N   LYS A 403 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 348 through 349
      removed outlier: 7.461A  pdb=" N   ALA A 348 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 9.878A  pdb=" N   LYS A 403 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   CYS A 432 " --> pdb=" O   LEU A 513 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 7
      removed outlier: 3.562A  pdb=" N   GLN B   3 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   VAL B   5 " --> pdb=" O   GLU B  23 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   THR B  77 " --> pdb=" O   ASP B  72 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ASP B  72 " --> pdb=" O   THR B  77 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.595A  pdb=" N   THR B 111 " --> pdb=" O   TYR B  93 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   TYR B  93 " --> pdb=" O   THR B 111 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   ARG B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   TRP B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.595A  pdb=" N   THR B 111 " --> pdb=" O   TYR B  93 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   TYR B  93 " --> pdb=" O   THR B 111 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   CYS B  95 " --> pdb=" O   TRP B 107 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   TRP B 107 " --> pdb=" O   CYS B  95 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   ARG B  97 " --> pdb=" O   ASP B 105 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   TYR B 103 " --> pdb=" O   TYR B  99 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 8 through 11
      removed outlier: 6.391A  pdb=" N   TRP C  34 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 8 through 11
      removed outlier: 3.549A  pdb=" N   HIS C  89 " --> pdb=" O   THR C  96 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   THR C  96 " --> pdb=" O   HIS C  89 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 17 through 22
      removed outlier: 3.608A  pdb=" N   ASP C  69 " --> pdb=" O   SER C  66 " (cutoff:3.500A)

    103 hydrogen bonds defined for protein.
    240 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: 0.48

  Time building geometry restraints manager: 0.29 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 568
        1.32 -     1.45: 1007
        1.45 -     1.58: 1762
        1.58 -     1.70: 0
        1.70 -     1.83: 18
  Bond restraints: 3355
  Sorted by residual:
  bond pdb=" N   ARG A 346 "
       pdb=" CA  ARG A 346 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.19e-02 7.06e+03 8.17e+00
  bond pdb=" C   THR B  77 "
       pdb=" O   THR B  77 "
    ideal  model  delta    sigma   weight residual
    1.234  1.197  0.037 1.31e-02 5.83e+03 8.11e+00
  bond pdb=" N   ASN B  73 "
       pdb=" CA  ASN B  73 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.23e-02 6.61e+03 7.62e+00
  bond pdb=" N   ASP B  72 "
       pdb=" CA  ASP B  72 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.23e-02 6.61e+03 7.51e+00
  bond pdb=" N   LYS B  75 "
       pdb=" CA  LYS B  75 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.22e-02 6.72e+03 7.51e+00
  ... (remaining 3350 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 4338
        1.91 -     3.82: 185
        3.82 -     5.73: 29
        5.73 -     7.64: 5
        7.64 -     9.56: 3
  Bond angle restraints: 4560
  Sorted by residual:
  angle pdb=" C   ASN B  73 "
        pdb=" CA  ASN B  73 "
        pdb=" CB  ASN B  73 "
      ideal   model   delta    sigma   weight residual
     110.85  101.29    9.56 1.70e+00 3.46e-01 3.16e+01
  angle pdb=" C   GLN C  37 "
        pdb=" N   LYS C  38 "
        pdb=" CA  LYS C  38 "
      ideal   model   delta    sigma   weight residual
     120.49  113.37    7.12 1.42e+00 4.96e-01 2.51e+01
  angle pdb=" C   ASN B  76 "
        pdb=" CA  ASN B  76 "
        pdb=" CB  ASN B  76 "
      ideal   model   delta    sigma   weight residual
     111.73  105.08    6.65 1.42e+00 4.96e-01 2.19e+01
  angle pdb=" N   SER B  74 "
        pdb=" CA  SER B  74 "
        pdb=" C   SER B  74 "
      ideal   model   delta    sigma   weight residual
     111.14  115.84   -4.70 1.08e+00 8.57e-01 1.90e+01
  angle pdb=" C   ASN A 343 "
        pdb=" CA  ASN A 343 "
        pdb=" CB  ASN A 343 "
      ideal   model   delta    sigma   weight residual
     112.12  105.81    6.31 1.50e+00 4.44e-01 1.77e+01
  ... (remaining 4555 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 1820
       17.84 -    35.67: 133
       35.67 -    53.51: 30
       53.51 -    71.35: 8
       71.35 -    89.18: 2
  Dihedral angle restraints: 1993
    sinusoidal: 808
      harmonic: 1185
  Sorted by residual:
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   28.04   64.96     1      1.00e+01 1.00e-02 5.54e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  128.73  -35.73     1      1.00e+01 1.00e-02 1.81e+01
  dihedral pdb=" CA  CYS A 336 "
           pdb=" C   CYS A 336 "
           pdb=" N   PRO A 337 "
           pdb=" CA  PRO A 337 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.10  -20.90     0      5.00e+00 4.00e-02 1.75e+01
  ... (remaining 1990 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.248: 478
       0.248 -    0.496: 2
       0.496 -    0.744: 0
       0.744 -    0.992: 0
       0.992 -    1.240: 1
  Chirality restraints: 481
  Sorted by residual:
  chirality pdb=" C1  NAG A 601 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG A 601 "
            pdb=" O5  NAG A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.16   -1.24 2.00e-01 2.50e+01 3.84e+01
  chirality pdb=" CA  ASN B  73 "
            pdb=" N   ASN B  73 "
            pdb=" C   ASN B  73 "
            pdb=" CB  ASN B  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CA  SER B  74 "
            pdb=" N   SER B  74 "
            pdb=" C   SER B  74 "
            pdb=" CB  SER B  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  ... (remaining 478 not shown)

  Planarity restraints: 592
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 601 "   -0.313 2.00e-02 2.50e+03   2.74e-01 9.41e+02
        pdb=" C7  NAG A 601 "    0.068 2.00e-02 2.50e+03
        pdb=" C8  NAG A 601 "   -0.098 2.00e-02 2.50e+03
        pdb=" N2  NAG A 601 "    0.492 2.00e-02 2.50e+03
        pdb=" O7  NAG A 601 "   -0.149 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 602 "   -0.224 2.00e-02 2.50e+03   1.90e-01 4.49e+02
        pdb=" C7  NAG A 602 "    0.057 2.00e-02 2.50e+03
        pdb=" C8  NAG A 602 "   -0.154 2.00e-02 2.50e+03
        pdb=" N2  NAG A 602 "    0.320 2.00e-02 2.50e+03
        pdb=" O7  NAG A 602 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  38 "   -0.056 5.00e-02 4.00e+02   8.46e-02 1.15e+01
        pdb=" N   PRO C  39 "    0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO C  39 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO C  39 "   -0.046 5.00e-02 4.00e+02
  ... (remaining 589 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 190
        2.73 -     3.27: 3096
        3.27 -     3.81: 4958
        3.81 -     4.36: 6194
        4.36 -     4.90: 10961
  Nonbonded interactions: 25399
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  17 "
            pdb=" O   MET B  82 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" NH2 ARG C  53 "
            pdb=" O   PHE C  61 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" NH2 ARG A 454 "
            pdb=" O   SER A 469 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" O   SER A 455 "
            pdb=" OH  TYR B  33 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" NH1 ARG A 457 "
            pdb=" OD2 ASP A 467 "
     model   vdw
     2.339 3.120
  ... (remaining 25394 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:             3.540
  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:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.060
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   3363  Z= 0.335
  Angle     :  0.925   9.700   4578  Z= 0.555
  Chirality :  0.079   1.240    481
  Planarity :  0.015   0.274    590
  Dihedral  : 13.224  89.183   1227
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.38), residues: 405
  helix: -3.09 (0.91), residues: 21
  sheet: -0.80 (0.47), residues: 113
  loop : -0.70 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  97 
 TYR   0.021   0.002   TYR B  33 
 PHE   0.014   0.002   PHE B  67 
 TRP   0.012   0.002   TRP A 436 
 HIS   0.003   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00658 ( 3355)
  covalent geometry    : angle       0.90292 ( 4560)
  SS BOND              : bond        0.00209 (    6)
  SS BOND              : angle       1.19651 (   12)
  hydrogen bonds       : bond        0.25844 (   95)
  hydrogen bonds       : angle      11.84417 (  240)
  link_NAG-ASN         : bond        0.00481 (    2)
  link_NAG-ASN         : angle       5.54370 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A  390 LEU cc_start: 0.8454 (tt) cc_final: 0.8237 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1003
  time to fit residues: 7.0142
Evaluate side-chains
  51 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.2980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.142207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.112211 restraints weight = 4663.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.115630 restraints weight = 2975.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.117653 restraints weight = 2249.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.119195 restraints weight = 1893.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.120253 restraints weight = 1681.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   3363  Z= 0.144
  Angle     :  0.643  11.652   4578  Z= 0.314
  Chirality :  0.050   0.257    481
  Planarity :  0.005   0.059    590
  Dihedral  :  7.263  58.859    501
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  6.32 %
    Favored  : 93.10 %
  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: -0.68 (0.40), residues: 405
  helix: -2.92 (1.01), residues: 21
  sheet: -0.20 (0.46), residues: 121
  loop : -0.30 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  60 
 TYR   0.012   0.001   TYR B  33 
 PHE   0.014   0.002   PHE C  70 
 TRP   0.012   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3355)
  covalent geometry    : angle       0.62675 ( 4560)
  SS BOND              : bond        0.00164 (    6)
  SS BOND              : angle       0.80636 (   12)
  hydrogen bonds       : bond        0.04201 (   95)
  hydrogen bonds       : angle       7.18514 (  240)
  link_NAG-ASN         : bond        0.01016 (    2)
  link_NAG-ASN         : angle       3.90388 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.128 
Fit side-chains
REVERT: C   16 ARG cc_start: 0.7707 (ptm160) cc_final: 0.7328 (ttm-80)
  outliers start: 2
  outliers final: 1
  residues processed: 55
  average time/residue: 0.0990
  time to fit residues: 6.3645
Evaluate side-chains
  48 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 37 optimal weight:    0.4980
   chunk 27 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0770
   chunk 32 optimal weight:    0.3980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
B   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.143303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.113155 restraints weight = 4685.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.116586 restraints weight = 3012.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.118898 restraints weight = 2283.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.120360 restraints weight = 1900.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.120949 restraints weight = 1685.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   3363  Z= 0.135
  Angle     :  0.589   9.837   4578  Z= 0.289
  Chirality :  0.049   0.293    481
  Planarity :  0.004   0.050    590
  Dihedral  :  6.909  56.232    501
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  7.47 %
    Favored  : 91.09 %
  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: -0.40 (0.40), residues: 405
  helix: -3.06 (0.98), residues: 21
  sheet:  0.10 (0.45), residues: 126
  loop : -0.13 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  31 
 TYR   0.012   0.001   TYR B  33 
 PHE   0.020   0.002   PHE A 375 
 TRP   0.011   0.001   TRP A 436 
 HIS   0.002   0.000   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 3355)
  covalent geometry    : angle       0.57989 ( 4560)
  SS BOND              : bond        0.00201 (    6)
  SS BOND              : angle       0.66579 (   12)
  hydrogen bonds       : bond        0.03715 (   95)
  hydrogen bonds       : angle       6.27489 (  240)
  link_NAG-ASN         : bond        0.00317 (    2)
  link_NAG-ASN         : angle       2.92693 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.122 
Fit side-chains
REVERT: C   16 ARG cc_start: 0.7669 (ptm160) cc_final: 0.7294 (ttm-80)
  outliers start: 5
  outliers final: 3
  residues processed: 53
  average time/residue: 0.0758
  time to fit residues: 4.8381
Evaluate side-chains
  49 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  114 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.0670
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 37 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
B   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.142243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.112501 restraints weight = 4621.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.115889 restraints weight = 2949.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.118156 restraints weight = 2233.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.119234 restraints weight = 1858.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.120523 restraints weight = 1677.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   3363  Z= 0.148
  Angle     :  0.584   9.835   4578  Z= 0.289
  Chirality :  0.048   0.273    481
  Planarity :  0.004   0.046    590
  Dihedral  :  6.794  55.594    501
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  9.48 %
    Favored  : 88.79 %
  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: -0.23 (0.41), residues: 405
  helix: -3.14 (0.90), residues: 21
  sheet:  0.27 (0.46), residues: 125
  loop : -0.03 (0.38), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  60 
 TYR   0.013   0.001   TYR B  33 
 PHE   0.013   0.001   PHE C  70 
 TRP   0.011   0.001   TRP A 436 
 HIS   0.002   0.000   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 3355)
  covalent geometry    : angle       0.57596 ( 4560)
  SS BOND              : bond        0.00172 (    6)
  SS BOND              : angle       0.63872 (   12)
  hydrogen bonds       : bond        0.03555 (   95)
  hydrogen bonds       : angle       5.89527 (  240)
  link_NAG-ASN         : bond        0.00368 (    2)
  link_NAG-ASN         : angle       2.63737 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.152 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 57
  average time/residue: 0.0957
  time to fit residues: 6.4494
Evaluate side-chains
  50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain C residue   71 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.3980
   chunk 9 optimal weight:    0.2980
   chunk 24 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0770
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0970
   chunk 36 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   overall best weight:    0.2736

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

Flipped N/Q/H residues before XYZ refinement:
B   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.145853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.116149 restraints weight = 4626.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.119613 restraints weight = 2949.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.121956 restraints weight = 2224.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.123261 restraints weight = 1845.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.124383 restraints weight = 1647.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3363  Z= 0.098
  Angle     :  0.541   9.752   4578  Z= 0.268
  Chirality :  0.046   0.239    481
  Planarity :  0.004   0.044    590
  Dihedral  :  6.519  54.829    501
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.92 %
    Favored  : 87.93 %
  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: -0.11 (0.41), residues: 405
  helix: -2.97 (0.98), residues: 21
  sheet:  0.28 (0.46), residues: 128
  loop :  0.10 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  60 
 TYR   0.009   0.001   TYR B  33 
 PHE   0.020   0.001   PHE A 374 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.001   0.000   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 3355)
  covalent geometry    : angle       0.53478 ( 4560)
  SS BOND              : bond        0.00171 (    6)
  SS BOND              : angle       0.72281 (   12)
  hydrogen bonds       : bond        0.03180 (   95)
  hydrogen bonds       : angle       5.17029 (  240)
  link_NAG-ASN         : bond        0.00327 (    2)
  link_NAG-ASN         : angle       2.13875 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.123 
Fit side-chains
REVERT: C   16 ARG cc_start: 0.7562 (ptm160) cc_final: 0.7177 (ttm-80)
  outliers start: 4
  outliers final: 1
  residues processed: 58
  average time/residue: 0.0925
  time to fit residues: 6.3145
Evaluate side-chains
  51 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    0.1980
   chunk 9 optimal weight:    0.0870
   chunk 18 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 8 optimal weight:    0.3980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
B   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.145528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.115320 restraints weight = 4693.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.118679 restraints weight = 3040.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.120983 restraints weight = 2319.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.122423 restraints weight = 1933.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.123136 restraints weight = 1719.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3363  Z= 0.122
  Angle     :  0.564   9.723   4578  Z= 0.276
  Chirality :  0.047   0.249    481
  Planarity :  0.004   0.042    590
  Dihedral  :  6.528  54.861    501
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.64 %
    Favored  : 86.21 %
  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:  0.16 (0.41), residues: 405
  helix: -3.64 (1.06), residues: 13
  sheet:  0.47 (0.47), residues: 125
  loop :  0.22 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  31 
 TYR   0.013   0.001   TYR B  33 
 PHE   0.012   0.001   PHE C  70 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.001   0.000   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3355)
  covalent geometry    : angle       0.55889 ( 4560)
  SS BOND              : bond        0.00129 (    6)
  SS BOND              : angle       0.67448 (   12)
  hydrogen bonds       : bond        0.03136 (   95)
  hydrogen bonds       : angle       5.12169 (  240)
  link_NAG-ASN         : bond        0.00325 (    2)
  link_NAG-ASN         : angle       2.19183 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.119 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 56
  average time/residue: 0.0965
  time to fit residues: 6.3709
Evaluate side-chains
  54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain C residue   71 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 1 optimal weight:    0.1980
   chunk 28 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.143539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.112941 restraints weight = 4795.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.116272 restraints weight = 3133.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.118406 restraints weight = 2396.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.119539 restraints weight = 2019.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.120777 restraints weight = 1825.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   3363  Z= 0.159
  Angle     :  0.594   9.716   4578  Z= 0.291
  Chirality :  0.048   0.259    481
  Planarity :  0.004   0.041    590
  Dihedral  :  6.677  55.167    501
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 13.22 %
    Favored  : 85.92 %
  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:  0.03 (0.41), residues: 405
  helix: -3.72 (1.04), residues: 13
  sheet:  0.38 (0.46), residues: 127
  loop :  0.12 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  31 
 TYR   0.016   0.001   TYR B  33 
 PHE   0.023   0.002   PHE A 374 
 TRP   0.011   0.001   TRP A 436 
 HIS   0.001   0.000   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 3355)
  covalent geometry    : angle       0.58760 ( 4560)
  SS BOND              : bond        0.00145 (    6)
  SS BOND              : angle       0.68199 (   12)
  hydrogen bonds       : bond        0.03229 (   95)
  hydrogen bonds       : angle       5.26796 (  240)
  link_NAG-ASN         : bond        0.00352 (    2)
  link_NAG-ASN         : angle       2.32925 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
REVERT: C   16 ARG cc_start: 0.7637 (ptm160) cc_final: 0.7274 (ttm-80)
  outliers start: 3
  outliers final: 3
  residues processed: 51
  average time/residue: 0.0685
  time to fit residues: 4.1868
Evaluate side-chains
  50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain C residue   71 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0070
   chunk 5 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    0.3980
   chunk 7 optimal weight:    0.4980
   overall best weight:    0.4398

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.144398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.114272 restraints weight = 4767.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.117661 restraints weight = 3074.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.119934 restraints weight = 2340.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.121370 restraints weight = 1957.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.121968 restraints weight = 1740.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3363  Z= 0.123
  Angle     :  0.587   9.706   4578  Z= 0.282
  Chirality :  0.047   0.239    481
  Planarity :  0.004   0.040    590
  Dihedral  :  6.565  55.191    501
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 14.37 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.42), residues: 405
  helix: -3.69 (1.06), residues: 13
  sheet:  0.56 (0.47), residues: 126
  loop :  0.18 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  31 
 TYR   0.012   0.001   TYR B  33 
 PHE   0.020   0.001   PHE C  70 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.001   0.000   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3355)
  covalent geometry    : angle       0.58210 ( 4560)
  SS BOND              : bond        0.00109 (    6)
  SS BOND              : angle       0.64015 (   12)
  hydrogen bonds       : bond        0.03069 (   95)
  hydrogen bonds       : angle       5.04154 (  240)
  link_NAG-ASN         : bond        0.00326 (    2)
  link_NAG-ASN         : angle       2.09928 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.125 
Fit side-chains
REVERT: C   16 ARG cc_start: 0.7602 (ptm160) cc_final: 0.7241 (ttm-80)
  outliers start: 3
  outliers final: 2
  residues processed: 54
  average time/residue: 0.0914
  time to fit residues: 5.8540
Evaluate side-chains
  51 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain B residue  111 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0050
   chunk 33 optimal weight:    0.0980
   chunk 1 optimal weight:    0.4980
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.3794

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.145722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.115117 restraints weight = 4682.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.118377 restraints weight = 3061.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.120674 restraints weight = 2345.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.122164 restraints weight = 1968.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.123013 restraints weight = 1749.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3363  Z= 0.116
  Angle     :  0.557   9.697   4578  Z= 0.275
  Chirality :  0.047   0.234    481
  Planarity :  0.004   0.040    590
  Dihedral  :  6.498  55.153    501
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 15.23 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.42), residues: 405
  helix: -3.58 (1.10), residues: 13
  sheet:  0.55 (0.47), residues: 128
  loop :  0.20 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  31 
 TYR   0.009   0.001   TYR A 453 
 PHE   0.024   0.001   PHE A 374 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.001   0.000   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3355)
  covalent geometry    : angle       0.55250 ( 4560)
  SS BOND              : bond        0.00125 (    6)
  SS BOND              : angle       0.60155 (   12)
  hydrogen bonds       : bond        0.03111 (   95)
  hydrogen bonds       : angle       4.96550 (  240)
  link_NAG-ASN         : bond        0.00311 (    2)
  link_NAG-ASN         : angle       2.00000 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.073 
Fit side-chains
   revert: symmetry clash
REVERT: C   16 ARG cc_start: 0.7588 (ptm160) cc_final: 0.7226 (ttm-80)
  outliers start: 4
  outliers final: 3
  residues processed: 56
  average time/residue: 0.0572
  time to fit residues: 3.8013
Evaluate side-chains
  54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain C residue  105 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0980
   chunk 14 optimal weight:    0.8980
   chunk 32 optimal weight:    0.1980
   chunk 22 optimal weight:    0.6980
   chunk 21 optimal weight:    0.1980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.3780

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.145168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.115034 restraints weight = 4735.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.118377 restraints weight = 3061.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.120490 restraints weight = 2333.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.122014 restraints weight = 1957.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.122891 restraints weight = 1738.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3363  Z= 0.115
  Angle     :  0.566   9.689   4578  Z= 0.278
  Chirality :  0.047   0.230    481
  Planarity :  0.004   0.040    590
  Dihedral  :  6.476  55.120    501
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 15.52 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.42), residues: 405
  helix: -3.51 (1.15), residues: 13
  sheet:  0.50 (0.48), residues: 129
  loop :  0.27 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  31 
 TYR   0.011   0.001   TYR B  33 
 PHE   0.022   0.001   PHE C  70 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.001   0.000   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 3355)
  covalent geometry    : angle       0.56145 ( 4560)
  SS BOND              : bond        0.00117 (    6)
  SS BOND              : angle       0.60586 (   12)
  hydrogen bonds       : bond        0.03071 (   95)
  hydrogen bonds       : angle       4.85058 (  240)
  link_NAG-ASN         : bond        0.00297 (    2)
  link_NAG-ASN         : angle       1.93666 (    6)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
REVERT: C   16 ARG cc_start: 0.7587 (ptm160) cc_final: 0.7227 (ttm-80)
  outliers start: 3
  outliers final: 3
  residues processed: 55
  average time/residue: 0.0534
  time to fit residues: 3.5282
Evaluate side-chains
  54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain C residue  105 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    0.0870
   chunk 10 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.6158

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.143622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.112926 restraints weight = 4841.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.116335 restraints weight = 3135.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.118572 restraints weight = 2386.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.119883 restraints weight = 2001.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.120843 restraints weight = 1789.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   3363  Z= 0.156
  Angle     :  0.615  10.225   4578  Z= 0.296
  Chirality :  0.048   0.246    481
  Planarity :  0.004   0.040    590
  Dihedral  :  6.629  55.325    501
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 15.23 %
    Favored  : 83.91 %
  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:  0.08 (0.42), residues: 405
  helix: -3.51 (1.19), residues: 13
  sheet:  0.42 (0.47), residues: 129
  loop :  0.14 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  53 
 TYR   0.014   0.001   TYR B  33 
 PHE   0.024   0.002   PHE C  70 
 TRP   0.011   0.001   TRP A 436 
 HIS   0.001   0.000   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 3355)
  covalent geometry    : angle       0.61010 ( 4560)
  SS BOND              : bond        0.00141 (    6)
  SS BOND              : angle       0.63105 (   12)
  hydrogen bonds       : bond        0.03194 (   95)
  hydrogen bonds       : angle       5.06278 (  240)
  link_NAG-ASN         : bond        0.00315 (    2)
  link_NAG-ASN         : angle       2.14762 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 842.01 seconds
wall clock time: 15 minutes 8.39 seconds (908.39 seconds total)