Starting phenix.real_space_refine
on Tue Aug  4 17:19:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/36az_77344/08_2026/36az_77344.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/36az_77344/08_2026/36az_77344.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/36az_77344/08_2026/36az_77344.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/36az_77344/08_2026/36az_77344.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/36az_77344/08_2026/36az_77344.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/36az_77344/08_2026/36az_77344.cif"
  }
  resolution = 3.9
  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=  -0.043 sd=   0.155
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      27      5.16       5
     C    3317      2.51       5
     N     881      2.21       5
     O    1005      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5230
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "H"
      Number of atoms: 996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 996
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 5, 'TRANS': 124}
    Chain: "L"
      Number of atoms: 883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 883
          Classifications: {'peptide': 114}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108}
    Chain: "A"
      Number of atoms: 1558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1558
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
    Chain: "B"
      Number of atoms: 838
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 838
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 6, 'TRANS': 102}
    Chain: "C"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 941
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.30, per 1000 atoms: 0.25
  Number of scatterers: 5230
  At special positions: 0
  Unit cell: (61.132, 100.13, 105.4, 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      27     16.00
     O    1005      8.00
     N     881      7.00
     C    3317      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.08
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.07
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.09
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  97 " - pdb=" SG  CYS C 102 " distance=2.06

  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 "
  Time building additional restraints: 0.38
  Conformation dependent library (CDL) restraints added in 187.3 milliseconds
  

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1216

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 16 sheets defined
      11.7% alpha, 35.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.849A  pdb=" N   ASP H  31 " --> pdb=" O   THR H  28 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 52A through 54
    Processing helix  chain 'H' and resid 61 through 64
    Processing helix  chain 'H' and resid 96 through 100
    Processing helix  chain 'L' and resid 30B through 30F
      removed outlier: 4.306A  pdb=" N   LYS L  30F" --> pdb=" O   SER L  30C" (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 405 through 411
      removed outlier: 4.158A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'B' and resid 30 through 31
      No H-bonds generated for 'chain 'B' and resid 30 through 31'
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.517A  pdb=" N   PHE B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 64
    Processing helix  chain 'C' and resid 73 through 75
      No H-bonds generated for 'chain 'C' and resid 73 through 75'
    Processing helix  chain 'C' and resid 83 through 87
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 7
      removed outlier: 3.525A  pdb=" N   LEU H  78 " --> pdb=" O   CYS H  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59
      removed outlier: 6.607A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   ARG H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   MET H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13
      removed outlier: 7.014A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358
      removed outlier: 4.182A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.847A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AB2, first strand: chain 'B' and resid 4 through 6
    Processing sheet with id=AB3, first strand: chain 'B' and resid 11 through 13
      removed outlier: 6.909A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   TYR B  49 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 11 through 13
      removed outlier: 6.909A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12
      removed outlier: 3.503A  pdb=" N   GLY C  49 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ARG C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   TRP C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12

    195 hydrogen bonds defined for protein.
    420 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: 0.80

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 968
        1.32 -     1.45: 1465
        1.45 -     1.57: 2890
        1.57 -     1.70: 0
        1.70 -     1.82: 36
  Bond restraints: 5359
  Sorted by residual:
  bond pdb=" CA  PRO L  43 "
       pdb=" C   PRO L  43 "
    ideal  model  delta    sigma   weight residual
    1.514  1.531 -0.017 5.50e-03 3.31e+04 9.30e+00
  bond pdb=" N   PRO A 463 "
       pdb=" CA  PRO A 463 "
    ideal  model  delta    sigma   weight residual
    1.467  1.434  0.033 1.21e-02 6.83e+03 7.52e+00
  bond pdb=" NE  ARG C  66 "
       pdb=" CZ  ARG C  66 "
    ideal  model  delta    sigma   weight residual
    1.326  1.355 -0.029 1.10e-02 8.26e+03 7.16e+00
  bond pdb=" CG  ASP H 113 "
       pdb=" OD2 ASP H 113 "
    ideal  model  delta    sigma   weight residual
    1.249  1.199  0.050 1.90e-02 2.77e+03 6.95e+00
  bond pdb=" NE  ARG A 509 "
       pdb=" CZ  ARG A 509 "
    ideal  model  delta    sigma   weight residual
    1.326  1.354 -0.028 1.10e-02 8.26e+03 6.57e+00
  ... (remaining 5354 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 6234
        1.67 -     3.33: 846
        3.33 -     5.00: 148
        5.00 -     6.67: 32
        6.67 -     8.33: 12
  Bond angle restraints: 7272
  Sorted by residual:
  angle pdb=" C   GLN L  42 "
        pdb=" N   PRO L  43 "
        pdb=" CA  PRO L  43 "
      ideal   model   delta    sigma   weight residual
     119.66  127.00   -7.34 7.30e-01 1.88e+00 1.01e+02
  angle pdb=" C   GLY C   8 "
        pdb=" N   PRO C   9 "
        pdb=" CA  PRO C   9 "
      ideal   model   delta    sigma   weight residual
     119.78  127.73   -7.95 1.03e+00 9.43e-01 5.95e+01
  angle pdb=" C   GLY H 104 "
        pdb=" N   PRO H 105 "
        pdb=" CA  PRO H 105 "
      ideal   model   delta    sigma   weight residual
     119.56  127.17   -7.61 1.01e+00 9.80e-01 5.68e+01
  angle pdb=" C   LEU A 425 "
        pdb=" N   PRO A 426 "
        pdb=" CA  PRO A 426 "
      ideal   model   delta    sigma   weight residual
     119.78  127.37   -7.59 1.03e+00 9.43e-01 5.42e+01
  angle pdb=" C   ILE B  58 "
        pdb=" N   PRO B  59 "
        pdb=" CA  PRO B  59 "
      ideal   model   delta    sigma   weight residual
     119.64  126.99   -7.35 1.01e+00 9.80e-01 5.30e+01
  ... (remaining 7267 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.05: 3013
       16.05 -    32.10: 109
       32.10 -    48.15: 31
       48.15 -    64.20: 15
       64.20 -    80.24: 7
  Dihedral angle restraints: 3175
    sinusoidal: 1252
      harmonic: 1923
  Sorted by residual:
  dihedral pdb=" CB  CYS B  23 "
           pdb=" SG  CYS B  23 "
           pdb=" SG  CYS B  88 "
           pdb=" CB  CYS B  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.23   39.77     1      1.00e+01 1.00e-02 2.22e+01
  dihedral pdb=" CA  ALA C  94 "
           pdb=" C   ALA C  94 "
           pdb=" N   PRO C  95 "
           pdb=" CA  PRO C  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.70   19.30     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CB  CYS C  22 "
           pdb=" SG  CYS C  22 "
           pdb=" SG  CYS C  92 "
           pdb=" CB  CYS C  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.22   31.22     1      1.00e+01 1.00e-02 1.39e+01
  ... (remaining 3172 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 436
       0.043 -    0.086: 200
       0.086 -    0.130: 109
       0.130 -    0.173: 34
       0.173 -    0.216: 4
  Chirality restraints: 783
  Sorted by residual:
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  ILE L  75 "
            pdb=" N   ILE L  75 "
            pdb=" C   ILE L  75 "
            pdb=" CB  ILE L  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.38e-01
  chirality pdb=" CA  VAL H   2 "
            pdb=" N   VAL H   2 "
            pdb=" C   VAL H   2 "
            pdb=" CB  VAL H   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 7.94e-01
  ... (remaining 780 not shown)

  Planarity restraints: 932
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO C  95 "    0.010 2.00e-02 2.50e+03   1.98e-02 3.93e+00
        pdb=" C   PRO C  95 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   PRO C  95 "    0.013 2.00e-02 2.50e+03
        pdb=" N   TYR C  96 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 343 "    0.016 2.00e-02 2.50e+03   1.77e-02 3.91e+00
        pdb=" CG  ASN A 343 "   -0.005 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 343 "   -0.005 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 343 "   -0.028 2.00e-02 2.50e+03
        pdb=" C1  NAG A 601 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR L  49 "   -0.010 2.00e-02 2.50e+03   1.95e-02 3.79e+00
        pdb=" C   TYR L  49 "    0.034 2.00e-02 2.50e+03
        pdb=" O   TYR L  49 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   TRP L  50 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 929 not shown)

  Histogram of nonbonded interaction distances:
        2.47 -     2.96: 2525
        2.96 -     3.44: 4603
        3.44 -     3.93: 8509
        3.93 -     4.41: 9801
        4.41 -     4.90: 15976
  Nonbonded interactions: 41414
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 429 "
            pdb=" OG1 THR A 430 "
     model   vdw
     2.472 3.040
  nonbonded pdb=" OG  SER A 366 "
            pdb=" N   VAL A 367 "
     model   vdw
     2.501 3.120
  nonbonded pdb=" O   SER L  93 "
            pdb=" OG1 THR L  94 "
     model   vdw
     2.509 3.040
  nonbonded pdb=" N   ASP A 339 "
            pdb=" OD1 ASP A 339 "
     model   vdw
     2.525 3.120
  nonbonded pdb=" NZ  LYS B  39 "
            pdb=" OE1 GLU B  81 "
     model   vdw
     2.534 3.120
  ... (remaining 41409 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:             5.200
  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:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.560
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
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      :  0.011   0.079   5369  Z= 0.599
  Angle     :  1.275   8.334   7293  Z= 0.870
  Chirality :  0.063   0.216    783
  Planarity :  0.005   0.020    931
  Dihedral  : 11.090  80.244   1932
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 0.88
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  2.73 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  1.59 %
    Favored  : 98.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  2.10 (0.34), residues: 659
  helix: -4.47 (0.37), residues: 20
  sheet:  1.61 (0.35), residues: 200
  loop :  1.81 (0.32), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  66 
 TYR   0.026   0.005   TYR A 369 
 PHE   0.022   0.003   PHE A 429 
 TRP   0.016   0.004   TRP H  36 
 HIS   0.004   0.001   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01071 /  0.59 ( 5359)
  covalent geometry    : angle       1.27081 /  0.87 ( 7272)
  SS BOND              : bond        0.03228 /  1.56 (    9)
  SS BOND              : angle       2.39188 /  1.58 (   18)
  hydrogen bonds       : bond        0.19946 / 13.42 (  179)
  hydrogen bonds       : angle       9.54443 /  6.40 (  420)
  link_NAG-ASN         : bond        0.07890 /  4.15 (    1)
  link_NAG-ASN         : angle       2.03308 /  1.15 (    3)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 267
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.5920 (m-80) cc_final: 0.5442 (m-80)
REVERT: H   38 ARG cc_start: 0.8019 (ptt180) cc_final: 0.7742 (ptt90)
REVERT: H   45 LEU cc_start: 0.9000 (mt) cc_final: 0.8618 (mm)
REVERT: H   82 MET cc_start: 0.6842 (mtp) cc_final: 0.6359 (mtp)
REVERT: H   98 TYR cc_start: 0.7167 (t80) cc_final: 0.6943 (t80)
REVERT: H  112 PHE cc_start: 0.8225 (p90) cc_final: 0.7871 (p90)
REVERT: L   11 LEU cc_start: 0.9026 (tp) cc_final: 0.8716 (mt)
REVERT: A  380 TYR cc_start: 0.6067 (m-80) cc_final: 0.5788 (m-10)
REVERT: A  465 GLU cc_start: 0.7251 (tp30) cc_final: 0.6964 (tp30)
REVERT: B   11 LEU cc_start: 0.8420 (tp) cc_final: 0.8035 (tp)
REVERT: B   27 GLN cc_start: 0.8565 (pt0) cc_final: 0.8087 (pp30)
REVERT: B   32 TYR cc_start: 0.7573 (m-80) cc_final: 0.7267 (m-80)
REVERT: B   36 TYR cc_start: 0.8543 (m-80) cc_final: 0.8087 (m-80)
REVERT: B   87 TYR cc_start: 0.8860 (m-80) cc_final: 0.8118 (m-80)
REVERT: B   98 PHE cc_start: 0.8543 (m-80) cc_final: 0.8277 (m-80)
REVERT: C   63 PHE cc_start: 0.8155 (m-80) cc_final: 0.7954 (m-10)
REVERT: C   87 THR cc_start: 0.8572 (m) cc_final: 0.8268 (p)
REVERT: C  107 ASP cc_start: 0.8036 (p0) cc_final: 0.7825 (p0)
  outliers start: 2
  outliers final: 1
  residues processed: 269
  average time/residue: 0.1158
  time to fit residues: 36.9072
Evaluate side-chains
  183 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  429 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  39 GLN
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  27 GLN
L  38 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  38 GLN
C  39 GLN
C 111 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.078693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.067942 restraints weight = 19880.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.070164 restraints weight = 10692.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.071650 restraints weight = 6721.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.072659 restraints weight = 4704.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.073274 restraints weight = 3601.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.5076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   5369  Z= 0.232
  Angle     :  0.786   7.745   7293  Z= 0.424
  Chirality :  0.051   0.209    783
  Planarity :  0.005   0.037    931
  Dihedral  :  5.685  49.636    764
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 16.73
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  3.03 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 16.08 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.87 (0.33), residues: 659
  helix: -3.76 (0.86), residues: 20
  sheet:  1.00 (0.34), residues: 230
  loop :  0.70 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  41 
 TYR   0.024   0.002   TYR B  91 
 PHE   0.021   0.003   PHE L  71 
 TRP   0.026   0.003   TRP A 353 
 HIS   0.007   0.002   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00533 /  0.23 ( 5359)
  covalent geometry    : angle       0.78410 /  0.42 ( 7272)
  SS BOND              : bond        0.00381 /  0.19 (    9)
  SS BOND              : angle       0.86969 /  0.49 (   18)
  hydrogen bonds       : bond        0.04968 /  3.34 (  179)
  hydrogen bonds       : angle       7.43799 /  5.04 (  420)
  link_NAG-ASN         : bond        0.00009 /  0.00 (    1)
  link_NAG-ASN         : angle       2.34769 /  1.30 (    3)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 190
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 ARG cc_start: 0.8062 (tpp80) cc_final: 0.7311 (tpp-160)
REVERT: H   20 LEU cc_start: 0.8099 (mt) cc_final: 0.7495 (mp)
REVERT: H   29 PHE cc_start: 0.5882 (m-80) cc_final: 0.5441 (m-80)
REVERT: H   39 GLN cc_start: 0.8351 (pt0) cc_final: 0.8051 (pt0)
REVERT: H  112 PHE cc_start: 0.8055 (p90) cc_final: 0.7786 (p90)
REVERT: L   11 LEU cc_start: 0.8793 (tp) cc_final: 0.8484 (mt)
REVERT: L   78 LEU cc_start: 0.9016 (tp) cc_final: 0.8680 (mt)
REVERT: A  424 LYS cc_start: 0.8025 (tptm) cc_final: 0.7803 (tptp)
REVERT: A  448 ASN cc_start: 0.8294 (t0) cc_final: 0.8046 (t0)
REVERT: A  495 TYR cc_start: 0.8395 (m-80) cc_final: 0.7755 (m-80)
REVERT: B   11 LEU cc_start: 0.8513 (tp) cc_final: 0.8226 (tp)
REVERT: B   38 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8228 (tm-30)
REVERT: B   39 LYS cc_start: 0.8977 (mttt) cc_final: 0.8642 (mmtm)
REVERT: B   98 PHE cc_start: 0.8393 (m-80) cc_final: 0.8171 (m-80)
REVERT: C    4 LEU cc_start: 0.8318 (mt) cc_final: 0.8101 (mm)
REVERT: C   28 THR cc_start: 0.8527 (m) cc_final: 0.8291 (p)
REVERT: C   41 ARG cc_start: 0.8728 (ttp80) cc_final: 0.8490 (ttp80)
REVERT: C   46 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7651 (mt-10)
REVERT: C   47 TRP cc_start: 0.8031 (t60) cc_final: 0.7714 (t60)
REVERT: C   64 GLN cc_start: 0.8787 (tp-100) cc_final: 0.8587 (tp-100)
REVERT: C  116 THR cc_start: 0.8440 (m) cc_final: 0.7991 (p)
  outliers start: 23
  outliers final: 16
  residues processed: 198
  average time/residue: 0.1104
  time to fit residues: 26.5591
Evaluate side-chains
  191 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 174
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  114 TYR
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 GLN
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  481 ASN
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   38 GLN
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  111 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 28 optimal weight:    0.3980
   chunk 10 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 19 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  42 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.075767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.065493 restraints weight = 19969.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.067550 restraints weight = 10801.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.068904 restraints weight = 6831.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.069803 restraints weight = 4875.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.070431 restraints weight = 3807.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.6175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   5369  Z= 0.220
  Angle     :  0.741   6.222   7293  Z= 0.398
  Chirality :  0.047   0.150    783
  Planarity :  0.005   0.044    931
  Dihedral  :  5.572  43.319    764
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.95 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 16.43 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.33 (0.33), residues: 659
  helix: -3.63 (0.88), residues: 20
  sheet:  0.89 (0.36), residues: 220
  loop :  0.12 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  95 
 TYR   0.024   0.002   TYR B  91 
 PHE   0.017   0.002   PHE B  62 
 TRP   0.038   0.002   TRP A 353 
 HIS   0.008   0.002   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00490 /  0.22 ( 5359)
  covalent geometry    : angle       0.73656 /  0.40 ( 7272)
  SS BOND              : bond        0.00377 /  0.18 (    9)
  SS BOND              : angle       0.91394 /  0.63 (   18)
  hydrogen bonds       : bond        0.04589 /  3.11 (  179)
  hydrogen bonds       : angle       6.95120 /  4.74 (  420)
  link_NAG-ASN         : bond        0.00376 /  0.20 (    1)
  link_NAG-ASN         : angle       3.71943 /  2.04 (    3)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 179
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7318 (tpp-160)
REVERT: H   20 LEU cc_start: 0.8418 (mt) cc_final: 0.7382 (mp)
REVERT: H   98 TYR cc_start: 0.7302 (t80) cc_final: 0.7017 (t80)
REVERT: H  112 PHE cc_start: 0.7972 (p90) cc_final: 0.7652 (p90)
REVERT: L    6 GLN cc_start: 0.8334 (mp10) cc_final: 0.8024 (pm20)
REVERT: L   27 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8683 (pt0)
REVERT: L   78 LEU cc_start: 0.8872 (tp) cc_final: 0.8617 (tp)
REVERT: A  353 TRP cc_start: 0.5687 (m-10) cc_final: 0.5419 (m-10)
REVERT: A  406 GLU cc_start: 0.7083 (mp0) cc_final: 0.6878 (mp0)
REVERT: A  429 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6844 (t80)
REVERT: A  440 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8928 (mppt)
REVERT: A  448 ASN cc_start: 0.8257 (t0) cc_final: 0.8048 (t0)
REVERT: A  495 TYR cc_start: 0.8586 (m-80) cc_final: 0.7838 (m-80)
REVERT: B   11 LEU cc_start: 0.8571 (tp) cc_final: 0.8288 (tp)
REVERT: B   71 PHE cc_start: 0.5928 (p90) cc_final: 0.5426 (p90)
REVERT: B   95 ARG cc_start: 0.7124 (tpp-160) cc_final: 0.6921 (tpp-160)
REVERT: C   46 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7568 (mt-10)
REVERT: C   72 ASP cc_start: 0.7535 (t0) cc_final: 0.7239 (t0)
REVERT: C   77 THR cc_start: 0.8808 (m) cc_final: 0.8456 (p)
REVERT: C  116 THR cc_start: 0.8544 (m) cc_final: 0.8141 (p)
  outliers start: 29
  outliers final: 15
  residues processed: 190
  average time/residue: 0.1007
  time to fit residues: 23.3696
Evaluate side-chains
  182 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 164
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   27 GLN
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  365 TYR
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   70 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  38 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.074039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.063763 restraints weight = 19745.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.065828 restraints weight = 10462.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.067159 restraints weight = 6562.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.068076 restraints weight = 4655.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.068592 restraints weight = 3608.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.6798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5369  Z= 0.208
  Angle     :  0.759   7.411   7293  Z= 0.400
  Chirality :  0.048   0.170    783
  Planarity :  0.005   0.039    931
  Dihedral  :  5.600  36.349    764
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 17.61
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.46 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 18.55 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.00 (0.33), residues: 659
  helix: -3.90 (0.72), residues: 20
  sheet:  0.61 (0.35), residues: 222
  loop : -0.08 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  95 
 TYR   0.025   0.002   TYR B  91 
 PHE   0.010   0.002   PHE A 497 
 TRP   0.021   0.002   TRP A 353 
 HIS   0.008   0.002   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00464 /  0.21 ( 5359)
  covalent geometry    : angle       0.75469 /  0.40 ( 7272)
  SS BOND              : bond        0.00331 /  0.16 (    9)
  SS BOND              : angle       0.68849 /  0.37 (   18)
  hydrogen bonds       : bond        0.04258 /  2.86 (  179)
  hydrogen bonds       : angle       6.76294 /  4.63 (  420)
  link_NAG-ASN         : bond        0.00493 /  0.26 (    1)
  link_NAG-ASN         : angle       4.31640 /  2.53 (    3)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 175
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.5784 (m-80) cc_final: 0.5534 (m-80)
REVERT: H   82 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7433 (mmt)
REVERT: H  112 PHE cc_start: 0.8024 (p90) cc_final: 0.7743 (p90)
REVERT: L  105 GLU cc_start: 0.8178 (mp0) cc_final: 0.7943 (pm20)
REVERT: A  353 TRP cc_start: 0.5682 (m-10) cc_final: 0.5436 (m-10)
REVERT: A  429 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6991 (t80)
REVERT: A  440 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9019 (mmmm)
REVERT: A  448 ASN cc_start: 0.8313 (t0) cc_final: 0.8090 (t0)
REVERT: B   11 LEU cc_start: 0.8674 (tp) cc_final: 0.8317 (tp)
REVERT: B   35 TRP cc_start: 0.7907 (m100) cc_final: 0.7282 (m100)
REVERT: B   38 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8134 (tm-30)
REVERT: B   39 LYS cc_start: 0.9020 (mmtm) cc_final: 0.8108 (mptt)
REVERT: B   95 ARG cc_start: 0.7000 (tpp-160) cc_final: 0.6787 (tpp-160)
REVERT: C   13 LYS cc_start: 0.6576 (mmtt) cc_final: 0.6327 (mmtt)
REVERT: C   41 ARG cc_start: 0.8577 (ttp80) cc_final: 0.8244 (ttp80)
REVERT: C   72 ASP cc_start: 0.7634 (t0) cc_final: 0.7246 (t0)
REVERT: C  116 THR cc_start: 0.8552 (m) cc_final: 0.8270 (p)
  outliers start: 36
  outliers final: 20
  residues processed: 192
  average time/residue: 0.1089
  time to fit residues: 25.4320
Evaluate side-chains
  185 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   27 GLN
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  365 TYR
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  481 ASN
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   38 GLN
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   82 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 25 optimal weight:    0.3980
   chunk 47 optimal weight:    4.9990
   chunk 59 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 17 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  61 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.073186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.063019 restraints weight = 19792.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.065020 restraints weight = 10784.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.066332 restraints weight = 6897.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.067225 restraints weight = 4930.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.067787 restraints weight = 3854.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.7345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   5369  Z= 0.203
  Angle     :  0.787   9.526   7293  Z= 0.411
  Chirality :  0.048   0.221    783
  Planarity :  0.005   0.055    931
  Dihedral  :  5.839  46.523    764
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 18.77
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.46 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  6.89 %
    Allowed  : 19.96 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.34 (0.33), residues: 659
  helix: -4.22 (0.55), residues: 21
  sheet:  0.42 (0.35), residues: 218
  loop : -0.31 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  18 
 TYR   0.024   0.002   TYR B  91 
 PHE   0.028   0.002   PHE H  27 
 TRP   0.014   0.002   TRP H  33 
 HIS   0.008   0.002   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00454 /  0.20 ( 5359)
  covalent geometry    : angle       0.77633 /  0.41 ( 7272)
  SS BOND              : bond        0.00622 /  0.30 (    9)
  SS BOND              : angle       1.29949 /  0.75 (   18)
  hydrogen bonds       : bond        0.04150 /  2.78 (  179)
  hydrogen bonds       : angle       6.68488 /  4.55 (  420)
  link_NAG-ASN         : bond        0.00150 /  0.08 (    1)
  link_NAG-ASN         : angle       5.99434 /  3.46 (    3)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 173
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.5428 (m-80) cc_final: 0.5130 (m-80)
REVERT: H   38 ARG cc_start: 0.8205 (ptt180) cc_final: 0.6293 (ptt180)
REVERT: H   46 GLU cc_start: 0.8109 (tp30) cc_final: 0.7806 (pm20)
REVERT: H  112 PHE cc_start: 0.7868 (p90) cc_final: 0.7659 (p90)
REVERT: L  103 LYS cc_start: 0.8307 (tptm) cc_final: 0.8052 (tptp)
REVERT: A  440 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9052 (mmmm)
REVERT: A  448 ASN cc_start: 0.8255 (t0) cc_final: 0.8021 (t0)
REVERT: B    3 VAL cc_start: 0.8812 (t) cc_final: 0.8518 (p)
REVERT: B   11 LEU cc_start: 0.8692 (tp) cc_final: 0.8282 (tt)
REVERT: B   35 TRP cc_start: 0.7964 (m100) cc_final: 0.7206 (m100)
REVERT: B   39 LYS cc_start: 0.9143 (mmtm) cc_final: 0.8879 (mmtm)
REVERT: B   45 ARG cc_start: 0.8377 (ttp-110) cc_final: 0.8150 (ttp80)
REVERT: B   95 ARG cc_start: 0.7032 (tpp-160) cc_final: 0.6758 (tpp-160)
REVERT: C    4 LEU cc_start: 0.8827 (mp) cc_final: 0.8572 (mm)
REVERT: C   41 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8199 (ttp80)
REVERT: C   72 ASP cc_start: 0.7756 (t0) cc_final: 0.7411 (t0)
REVERT: C   77 THR cc_start: 0.8832 (m) cc_final: 0.8480 (p)
REVERT: C   96 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.5732 (t80)
REVERT: C  111 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7479 (mm-40)
REVERT: C  116 THR cc_start: 0.8576 (m) cc_final: 0.8334 (p)
  outliers start: 39
  outliers final: 22
  residues processed: 190
  average time/residue: 0.1018
  time to fit residues: 23.3476
Evaluate side-chains
  185 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 160
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   30 ASN
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  365 TYR
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   96 TYR
Chi-restraints excluded: chain C residue   97 CYS
Chi-restraints excluded: chain C residue  111 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.9580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.070311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.060109 restraints weight = 20141.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.062093 restraints weight = 10913.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.063384 restraints weight = 6945.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.064259 restraints weight = 4970.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.064874 restraints weight = 3893.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.7892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   5369  Z= 0.291
  Angle     :  0.891  11.384   7293  Z= 0.464
  Chirality :  0.050   0.170    783
  Planarity :  0.006   0.053    931
  Dihedral  :  5.939  34.059    762
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 23.44
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.44 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  6.89 %
    Allowed  : 22.97 %
    Favored  : 70.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.87 (0.32), residues: 659
  helix: -4.28 (0.56), residues: 21
  sheet: -0.14 (0.34), residues: 232
  loop : -0.58 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  71 
 TYR   0.024   0.003   TYR H  98 
 PHE   0.021   0.003   PHE B  62 
 TRP   0.024   0.003   TRP A 353 
 HIS   0.009   0.002   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00655 /  0.29 ( 5359)
  covalent geometry    : angle       0.87138 /  0.46 ( 7272)
  SS BOND              : bond        0.00530 /  0.26 (    9)
  SS BOND              : angle       1.50462 /  0.91 (   18)
  hydrogen bonds       : bond        0.04512 /  3.06 (  179)
  hydrogen bonds       : angle       6.98122 /  4.81 (  420)
  link_NAG-ASN         : bond        0.01121 /  0.59 (    1)
  link_NAG-ASN         : angle       8.76963 /  4.91 (    3)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 172
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.5724 (m-80) cc_final: 0.5379 (m-80)
REVERT: H  112 PHE cc_start: 0.7950 (p90) cc_final: 0.7572 (p90)
REVERT: L  103 LYS cc_start: 0.8215 (tptm) cc_final: 0.7942 (tptp)
REVERT: L  105 GLU cc_start: 0.8383 (pm20) cc_final: 0.7906 (pm20)
REVERT: A  345 THR cc_start: 0.8837 (p) cc_final: 0.8551 (t)
REVERT: A  440 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9117 (mmmm)
REVERT: A  448 ASN cc_start: 0.8342 (t0) cc_final: 0.8067 (t0)
REVERT: A  453 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.6820 (p90)
REVERT: A  506 GLN cc_start: 0.7974 (mt0) cc_final: 0.7594 (mt0)
REVERT: B    3 VAL cc_start: 0.8899 (t) cc_final: 0.8606 (p)
REVERT: B   11 LEU cc_start: 0.8794 (tp) cc_final: 0.8378 (tt)
REVERT: B   35 TRP cc_start: 0.7989 (m100) cc_final: 0.7208 (m100)
REVERT: B   47 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8819 (mm)
REVERT: B   95 ARG cc_start: 0.6999 (tpp-160) cc_final: 0.6670 (tpp-160)
REVERT: C   41 ARG cc_start: 0.8591 (ttp80) cc_final: 0.8209 (ttp80)
REVERT: C   64 GLN cc_start: 0.8660 (tp40) cc_final: 0.8199 (tt0)
REVERT: C   72 ASP cc_start: 0.7968 (t0) cc_final: 0.7584 (t0)
REVERT: C   96 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.5385 (t80)
REVERT: C  111 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7606 (mm-40)
REVERT: C  116 THR cc_start: 0.8639 (m) cc_final: 0.8427 (p)
  outliers start: 39
  outliers final: 28
  residues processed: 191
  average time/residue: 0.0990
  time to fit residues: 22.9769
Evaluate side-chains
  197 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 164
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   30 ASN
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  365 TYR
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  453 TYR
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   23 LYS
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   96 TYR
Chi-restraints excluded: chain C residue   97 CYS
Chi-restraints excluded: chain C residue  111 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 17 optimal weight:    0.2980
   chunk 61 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 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 = 0.3436 r_free = 0.3436 target = 0.071167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.061089 restraints weight = 20247.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.063116 restraints weight = 10894.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.064423 restraints weight = 6871.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.065318 restraints weight = 4878.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.065878 restraints weight = 3789.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.8164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   5369  Z= 0.212
  Angle     :  0.864  10.580   7293  Z= 0.446
  Chirality :  0.050   0.182    783
  Planarity :  0.006   0.063    931
  Dihedral  :  5.956  39.400    762
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 21.40
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.68 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 25.27 %
    Favored  : 68.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.87 (0.32), residues: 659
  helix: -4.33 (0.49), residues: 21
  sheet:  0.16 (0.35), residues: 214
  loop : -0.76 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  95 
 TYR   0.021   0.002   TYR A 423 
 PHE   0.033   0.003   PHE A 400 
 TRP   0.023   0.002   TRP A 353 
 HIS   0.009   0.002   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00488 /  0.21 ( 5359)
  covalent geometry    : angle       0.83914 /  0.44 ( 7272)
  SS BOND              : bond        0.00489 /  0.24 (    9)
  SS BOND              : angle       2.11119 /  1.67 (   18)
  hydrogen bonds       : bond        0.04020 /  2.74 (  179)
  hydrogen bonds       : angle       6.71741 /  4.61 (  420)
  link_NAG-ASN         : bond        0.00357 /  0.19 (    1)
  link_NAG-ASN         : angle       8.89014 /  4.91 (    3)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 171
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    3 GLN cc_start: 0.7361 (mp10) cc_final: 0.7028 (mm-40)
REVERT: H   20 LEU cc_start: 0.8130 (mp) cc_final: 0.7763 (mp)
REVERT: H   29 PHE cc_start: 0.5931 (m-80) cc_final: 0.5632 (m-80)
REVERT: H   82 MET cc_start: 0.7515 (mmm) cc_final: 0.7235 (mmm)
REVERT: L   18 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7356 (ttp80)
REVERT: L  103 LYS cc_start: 0.8215 (tptm) cc_final: 0.7859 (tptp)
REVERT: L  105 GLU cc_start: 0.8378 (pm20) cc_final: 0.7875 (pm20)
REVERT: A  345 THR cc_start: 0.8903 (p) cc_final: 0.8650 (t)
REVERT: A  353 TRP cc_start: 0.6017 (m-10) cc_final: 0.5461 (m-10)
REVERT: A  440 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9069 (mmmm)
REVERT: A  448 ASN cc_start: 0.8275 (t0) cc_final: 0.8074 (t0)
REVERT: A  453 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.6552 (p90)
REVERT: A  506 GLN cc_start: 0.7857 (mt0) cc_final: 0.7317 (mt0)
REVERT: B    3 VAL cc_start: 0.8858 (t) cc_final: 0.8587 (p)
REVERT: B   11 LEU cc_start: 0.8787 (tp) cc_final: 0.8357 (tt)
REVERT: B   95 ARG cc_start: 0.7049 (tpp-160) cc_final: 0.6767 (tpp-160)
REVERT: C   13 LYS cc_start: 0.6471 (mmtt) cc_final: 0.6110 (mmtt)
REVERT: C   41 ARG cc_start: 0.8616 (ttp80) cc_final: 0.8254 (ttp80)
REVERT: C   72 ASP cc_start: 0.7936 (t0) cc_final: 0.7573 (t0)
REVERT: C   96 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.5253 (t80)
REVERT: C  111 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7665 (mm-40)
REVERT: C  116 THR cc_start: 0.8592 (m) cc_final: 0.8347 (p)
  outliers start: 34
  outliers final: 23
  residues processed: 188
  average time/residue: 0.1077
  time to fit residues: 24.4828
Evaluate side-chains
  190 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   30 ASN
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue  108 ARG
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  365 TYR
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  453 TYR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   96 TYR
Chi-restraints excluded: chain C residue  111 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0270
   chunk 43 optimal weight:    0.5980
   chunk 63 optimal weight:    0.2980
   chunk 61 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 52 optimal weight:    0.4980
   chunk 37 optimal weight:    0.4980
   chunk 30 optimal weight:    0.3980
   overall best weight:    0.3438

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.072842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.062773 restraints weight = 20051.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.064785 restraints weight = 10712.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.066075 restraints weight = 6761.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.066992 restraints weight = 4839.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.067555 restraints weight = 3742.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.8261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5369  Z= 0.176
  Angle     :  0.852   8.991   7293  Z= 0.441
  Chirality :  0.049   0.269    783
  Planarity :  0.005   0.047    931
  Dihedral  :  5.762  33.562    762
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 18.39
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.92 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 25.09 %
    Favored  : 68.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.32), residues: 659
  helix: -4.90 (0.26), residues: 21
  sheet:  0.15 (0.35), residues: 221
  loop : -0.85 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  95 
 TYR   0.018   0.002   TYR A 423 
 PHE   0.023   0.002   PHE A 375 
 TRP   0.019   0.002   TRP H  47 
 HIS   0.008   0.002   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00415 /  0.18 ( 5359)
  covalent geometry    : angle       0.84373 /  0.44 ( 7272)
  SS BOND              : bond        0.00432 /  0.22 (    9)
  SS BOND              : angle       1.29344 /  0.90 (   18)
  hydrogen bonds       : bond        0.03833 /  2.60 (  179)
  hydrogen bonds       : angle       6.37607 /  4.43 (  420)
  link_NAG-ASN         : bond        0.00482 /  0.25 (    1)
  link_NAG-ASN         : angle       5.36764 /  2.81 (    3)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 173
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.5994 (m-80) cc_final: 0.5628 (m-80)
REVERT: H   46 GLU cc_start: 0.7969 (tp30) cc_final: 0.7562 (pm20)
REVERT: H  112 PHE cc_start: 0.7870 (p90) cc_final: 0.7548 (p90)
REVERT: L   90 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7140 (pp30)
REVERT: L  108 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6117 (ptt180)
REVERT: A  353 TRP cc_start: 0.5906 (m-10) cc_final: 0.5455 (m-10)
REVERT: A  408 ARG cc_start: 0.8147 (ptm-80) cc_final: 0.7856 (ptm-80)
REVERT: A  453 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.6445 (p90)
REVERT: A  506 GLN cc_start: 0.7877 (mt0) cc_final: 0.7353 (mt0)
REVERT: B   11 LEU cc_start: 0.8759 (tp) cc_final: 0.8352 (tt)
REVERT: B   95 ARG cc_start: 0.7041 (tpp-160) cc_final: 0.6652 (tpp-160)
REVERT: C   41 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8140 (ttp80)
REVERT: C   72 ASP cc_start: 0.7875 (t0) cc_final: 0.7507 (t0)
REVERT: C   96 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.5281 (t80)
REVERT: C  111 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7634 (mm-40)
REVERT: C  114 MET cc_start: 0.8257 (mmm) cc_final: 0.7989 (mmm)
REVERT: C  116 THR cc_start: 0.8540 (m) cc_final: 0.8338 (p)
  outliers start: 34
  outliers final: 22
  residues processed: 186
  average time/residue: 0.0926
  time to fit residues: 20.9842
Evaluate side-chains
  192 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 166
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   50 ARG
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue  114 TYR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue  108 ARG
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  365 TYR
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  453 TYR
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   23 LYS
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   96 TYR
Chi-restraints excluded: chain C residue  111 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 23 optimal weight:    0.2980
   chunk 53 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0980
   chunk 36 optimal weight:    0.8980
   chunk 37 optimal weight:    0.1980
   chunk 44 optimal weight:    0.6980
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.3580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.072979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.063158 restraints weight = 20086.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.065063 restraints weight = 11010.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.066293 restraints weight = 7061.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.067137 restraints weight = 5094.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.067709 restraints weight = 4004.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.8446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5369  Z= 0.174
  Angle     :  0.854   8.944   7293  Z= 0.440
  Chirality :  0.049   0.230    783
  Planarity :  0.006   0.117    931
  Dihedral  :  5.710  34.225    762
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 18.39
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.68 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 27.03 %
    Favored  : 67.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.32), residues: 659
  helix: -4.95 (0.28), residues: 21
  sheet:  0.22 (0.36), residues: 221
  loop : -0.91 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG L  18 
 TYR   0.017   0.002   TYR A 453 
 PHE   0.024   0.002   PHE A 400 
 TRP   0.019   0.002   TRP H  47 
 HIS   0.008   0.002   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.17 ( 5359)
  covalent geometry    : angle       0.84669 /  0.44 ( 7272)
  SS BOND              : bond        0.00377 /  0.19 (    9)
  SS BOND              : angle       0.99674 /  0.61 (   18)
  hydrogen bonds       : bond        0.03865 /  2.63 (  179)
  hydrogen bonds       : angle       6.33023 /  4.41 (  420)
  link_NAG-ASN         : bond        0.00051 /  0.03 (    1)
  link_NAG-ASN         : angle       5.33563 /  2.83 (    3)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 169
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.7956 (tp30) cc_final: 0.7558 (pm20)
REVERT: H   99 TYR cc_start: 0.7765 (m-80) cc_final: 0.7305 (m-80)
REVERT: H  112 PHE cc_start: 0.7793 (p90) cc_final: 0.7396 (p90)
REVERT: A  353 TRP cc_start: 0.5888 (m-10) cc_final: 0.5486 (m-10)
REVERT: A  429 PHE cc_start: 0.7193 (t80) cc_final: 0.6878 (t80)
REVERT: A  453 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.6516 (p90)
REVERT: A  506 GLN cc_start: 0.7896 (mt0) cc_final: 0.7462 (mt0)
REVERT: B   11 LEU cc_start: 0.8727 (tp) cc_final: 0.8334 (tt)
REVERT: B   95 ARG cc_start: 0.7090 (tpp-160) cc_final: 0.6630 (tpp-160)
REVERT: C   41 ARG cc_start: 0.8476 (ttp80) cc_final: 0.8134 (ttp80)
REVERT: C   72 ASP cc_start: 0.7847 (t0) cc_final: 0.7426 (t0)
REVERT: C   96 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.5509 (t80)
REVERT: C  111 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7544 (mm-40)
REVERT: C  114 MET cc_start: 0.8189 (mmm) cc_final: 0.7926 (mmm)
  outliers start: 30
  outliers final: 21
  residues processed: 182
  average time/residue: 0.1005
  time to fit residues: 22.2669
Evaluate side-chains
  188 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 164
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue  114 TYR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  365 TYR
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  453 TYR
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   23 LYS
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   96 TYR
Chi-restraints excluded: chain C residue  111 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 41 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0980
   chunk 25 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 0 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 GLN
** B  89 GLN ** 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 = 0.3448 r_free = 0.3448 target = 0.071958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.062240 restraints weight = 20272.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.064199 restraints weight = 10924.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.065464 restraints weight = 6899.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.066313 restraints weight = 4893.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.066943 restraints weight = 3810.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.8695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   5369  Z= 0.206
  Angle     :  0.917  11.419   7293  Z= 0.471
  Chirality :  0.050   0.264    783
  Planarity :  0.006   0.093    931
  Dihedral  :  5.879  32.340    762
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 21.21
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.44 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 29.33 %
    Favored  : 66.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.33), residues: 659
  helix: -4.98 (0.27), residues: 21
  sheet:  0.06 (0.35), residues: 228
  loop : -0.93 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  18 
 TYR   0.025   0.002   TYR L  92 
 PHE   0.025   0.003   PHE A 400 
 TRP   0.034   0.002   TRP H  47 
 HIS   0.009   0.002   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00474 /  0.21 ( 5359)
  covalent geometry    : angle       0.91184 /  0.47 ( 7272)
  SS BOND              : bond        0.00519 /  0.26 (    9)
  SS BOND              : angle       1.09569 /  0.68 (   18)
  hydrogen bonds       : bond        0.04196 /  2.87 (  179)
  hydrogen bonds       : angle       6.35109 /  4.41 (  420)
  link_NAG-ASN         : bond        0.00147 /  0.08 (    1)
  link_NAG-ASN         : angle       4.68233 /  2.49 (    3)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 170
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   27 PHE cc_start: 0.8074 (p90) cc_final: 0.7814 (p90)
REVERT: H   29 PHE cc_start: 0.6434 (m-80) cc_final: 0.6084 (m-80)
REVERT: H   46 GLU cc_start: 0.8006 (tp30) cc_final: 0.7760 (pm20)
REVERT: H  112 PHE cc_start: 0.7877 (p90) cc_final: 0.7532 (p90)
REVERT: L   90 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7309 (pp30)
REVERT: A  353 TRP cc_start: 0.5952 (m-10) cc_final: 0.5662 (m-10)
REVERT: A  429 PHE cc_start: 0.7277 (t80) cc_final: 0.6952 (t80)
REVERT: A  453 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.6261 (p90)
REVERT: A  506 GLN cc_start: 0.7941 (mt0) cc_final: 0.7560 (mt0)
REVERT: B   11 LEU cc_start: 0.8741 (tp) cc_final: 0.8432 (tt)
REVERT: B   27 GLN cc_start: 0.8817 (pm20) cc_final: 0.8282 (pm20)
REVERT: B   39 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8858 (mptt)
REVERT: B   95 ARG cc_start: 0.7159 (tpp-160) cc_final: 0.6720 (tpp-160)
REVERT: C   38 ARG cc_start: 0.8156 (ptt90) cc_final: 0.6992 (ptt90)
REVERT: C   41 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8149 (ttp80)
REVERT: C   72 ASP cc_start: 0.7901 (t0) cc_final: 0.7494 (t0)
REVERT: C   90 TYR cc_start: 0.8268 (m-80) cc_final: 0.7632 (m-80)
REVERT: C   96 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.5729 (t80)
REVERT: C  111 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7534 (mm-40)
REVERT: C  114 MET cc_start: 0.8197 (mmm) cc_final: 0.7929 (mmm)
  outliers start: 26
  outliers final: 22
  residues processed: 181
  average time/residue: 0.0992
  time to fit residues: 21.9089
Evaluate side-chains
  191 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 165
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   59 TYR
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   78 LEU
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  365 TYR
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  453 TYR
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   37 GLN
Chi-restraints excluded: chain B residue   39 LYS
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   23 LYS
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   96 TYR
Chi-restraints excluded: chain C residue  111 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0970
   chunk 13 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0670
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.4516

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 GLN
** B  89 GLN ** 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 = 0.3452 r_free = 0.3452 target = 0.072244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.062443 restraints weight = 20511.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.064436 restraints weight = 11139.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.065736 restraints weight = 7046.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.066546 restraints weight = 4986.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.067184 restraints weight = 3899.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.8855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5369  Z= 0.198
  Angle     :  0.916  10.057   7293  Z= 0.473
  Chirality :  0.050   0.266    783
  Planarity :  0.006   0.074    931
  Dihedral  :  5.850  33.496    762
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 21.21
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.13 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 29.51 %
    Favored  : 66.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.33), residues: 659
  helix: -4.94 (0.29), residues: 21
  sheet:  0.05 (0.35), residues: 228
  loop : -0.99 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  18 
 TYR   0.020   0.002   TYR B  91 
 PHE   0.026   0.003   PHE C 106 
 TRP   0.029   0.002   TRP H  47 
 HIS   0.009   0.002   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00459 /  0.20 ( 5359)
  covalent geometry    : angle       0.91240 /  0.47 ( 7272)
  SS BOND              : bond        0.00454 /  0.23 (    9)
  SS BOND              : angle       0.98271 /  0.60 (   18)
  hydrogen bonds       : bond        0.04219 /  2.91 (  179)
  hydrogen bonds       : angle       6.31644 /  4.38 (  420)
  link_NAG-ASN         : bond        0.00061 /  0.03 (    1)
  link_NAG-ASN         : angle       4.18872 /  2.22 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1267.13 seconds
wall clock time: 22 minutes 36.90 seconds (1356.90 seconds total)