Starting phenix.real_space_refine
on Thu Jul 24 08:11:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ekd_28199/07_2025/8ekd_28199.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ekd_28199/07_2025/8ekd_28199.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ekd_28199/07_2025/8ekd_28199.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ekd_28199/07_2025/8ekd_28199.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ekd_28199/07_2025/8ekd_28199.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ekd_28199/07_2025/8ekd_28199.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.003 sd=   0.278
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3152 atoms to isotropic.
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      13      5.16       5
     C    2075      2.51       5
     N     540      2.21       5
     O     611      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3239
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "E"
      Number of atoms: 968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 968
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "F"
      Number of atoms: 857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 857
          Classifications: {'peptide': 111}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105}
    Chain: "G"
      Number of atoms: 1400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1400
          Classifications: {'peptide': 174}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 10, 'TRANS': 163}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      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: 2.73, per 1000 atoms: 0.84
  Number of scatterers: 3239
  At special positions: 0
  Unit cell: (94.462, 60.818, 80.228, 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      13     16.00
     O     611      8.00
     N     540      7.00
     C    2075      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  94 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 379 " - pdb=" SG  CYS G 432 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG G 601 " - " ASN G 343 "
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 407.9 milliseconds
  

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  744

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 7 sheets defined
      6.6% alpha, 24.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'E' and resid 64 through 67
    Processing helix  chain 'G' and resid 337 through 343
    Processing helix  chain 'G' and resid 365 through 371
      removed outlier: 3.907A  pdb=" N   TYR G 369 " --> pdb=" O   TYR G 365 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 405 through 407
      No H-bonds generated for 'chain 'G' and resid 405 through 407'
    Processing helix  chain 'G' and resid 416 through 421
      removed outlier: 3.549A  pdb=" N   TYR G 421 " --> pdb=" O   ASN G 417 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.506A  pdb=" N   GLN E   3 " --> pdb=" O   SER E  25 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER E  25 " --> pdb=" O   GLN E   3 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   SER E   7 " --> pdb=" O   SER E  21 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   SER E  21 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR E  82 " --> pdb=" O   SER E  73 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 12
    Processing sheet with id=AA3, first strand: chain 'E' and resid 60 through 62
      removed outlier: 7.212A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 7
      removed outlier: 3.506A  pdb=" N   ASN F  22 " --> pdb=" O   SER F   7 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 10 through 12
      removed outlier: 3.644A  pdb=" N   GLU F 110 " --> pdb=" O   LEU F  11 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   LEU F  39 " --> pdb=" O   TYR F  55 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   TYR F  55 " --> pdb=" O   LEU F  39 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   TRP F  41 " --> pdb=" O   LEU F  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 354 through 356
      removed outlier: 3.503A  pdb=" N   TYR G 396 " --> pdb=" O   SER G 514 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ASP G 398 " --> pdb=" O   VAL G 512 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 452 through 454

    71 hydrogen bonds defined for protein.
    189 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: 0.74

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 893
        1.33 -     1.45: 677
        1.45 -     1.57: 1735
        1.57 -     1.69: 1
        1.69 -     1.81: 17
  Bond restraints: 3323
  Sorted by residual:
  bond pdb=" N   GLN G 474 "
       pdb=" CA  GLN G 474 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.034 1.22e-02 6.72e+03 7.66e+00
  bond pdb=" CB  PRO G 507 "
       pdb=" CG  PRO G 507 "
    ideal  model  delta    sigma   weight residual
    1.492  1.630 -0.138 5.00e-02 4.00e+02 7.65e+00
  bond pdb=" CA  SER G 459 "
       pdb=" CB  SER G 459 "
    ideal  model  delta    sigma   weight residual
    1.527  1.487  0.040 1.44e-02 4.82e+03 7.58e+00
  bond pdb=" N   LYS G 458 "
       pdb=" CA  LYS G 458 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.21e-02 6.83e+03 7.41e+00
  bond pdb=" N   TYR G 473 "
       pdb=" CA  TYR G 473 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.032 1.31e-02 5.83e+03 5.91e+00
  ... (remaining 3318 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 4357
        2.23 -     4.46: 121
        4.46 -     6.69: 19
        6.69 -     8.91: 7
        8.91 -    11.14: 2
  Bond angle restraints: 4506
  Sorted by residual:
  angle pdb=" N   GLN G 474 "
        pdb=" CA  GLN G 474 "
        pdb=" C   GLN G 474 "
      ideal   model   delta    sigma   weight residual
     110.28  121.42  -11.14 1.48e+00 4.57e-01 5.67e+01
  angle pdb=" CA  PRO G 507 "
        pdb=" N   PRO G 507 "
        pdb=" CD  PRO G 507 "
      ideal   model   delta    sigma   weight residual
     112.00  103.04    8.96 1.40e+00 5.10e-01 4.09e+01
  angle pdb=" C   THR G 470 "
        pdb=" CA  THR G 470 "
        pdb=" CB  THR G 470 "
      ideal   model   delta    sigma   weight residual
     111.22  103.83    7.39 1.23e+00 6.61e-01 3.61e+01
  angle pdb=" CA  ALA G 475 "
        pdb=" C   ALA G 475 "
        pdb=" N   GLY G 476 "
      ideal   model   delta    sigma   weight residual
     119.63  114.99    4.64 8.10e-01 1.52e+00 3.28e+01
  angle pdb=" C   SER G 459 "
        pdb=" N   ASN G 460 "
        pdb=" CA  ASN G 460 "
      ideal   model   delta    sigma   weight residual
     120.82  112.85    7.97 1.41e+00 5.03e-01 3.19e+01
  ... (remaining 4501 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.36: 1670
       21.36 -    42.72: 236
       42.72 -    64.07: 26
       64.07 -    85.43: 9
       85.43 -   106.79: 8
  Dihedral angle restraints: 1949
    sinusoidal: 769
      harmonic: 1180
  Sorted by residual:
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  98 "
           pdb=" CB  CYS E  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.64   48.36     1      1.00e+01 1.00e-02 3.22e+01
  dihedral pdb=" CA  PRO F  65 "
           pdb=" C   PRO F  65 "
           pdb=" N   ASP F  66 "
           pdb=" CA  ASP F  66 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.07  -20.93     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" C2  NAG G 601 "
           pdb=" C3  NAG G 601 "
           pdb=" C4  NAG G 601 "
           pdb=" O4  NAG G 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   68.32  106.79     1      3.00e+01 1.11e-03 1.37e+01
  ... (remaining 1946 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 356
       0.045 -    0.091: 83
       0.091 -    0.136: 25
       0.136 -    0.182: 3
       0.182 -    0.227: 6
  Chirality restraints: 473
  Sorted by residual:
  chirality pdb=" CB  ILE E  51 "
            pdb=" CA  ILE E  51 "
            pdb=" CG1 ILE E  51 "
            pdb=" CG2 ILE E  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  THR G 470 "
            pdb=" N   THR G 470 "
            pdb=" C   THR G 470 "
            pdb=" CB  THR G 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.75   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ARG G 457 "
            pdb=" N   ARG G 457 "
            pdb=" C   ARG G 457 "
            pdb=" CB  ARG G 457 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.19 2.00e-01 2.50e+01 9.50e-01
  ... (remaining 470 not shown)

  Planarity restraints: 581
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER G 383 "   -0.079 5.00e-02 4.00e+02   1.17e-01 2.18e+01
        pdb=" N   PRO G 384 "    0.202 5.00e-02 4.00e+02
        pdb=" CA  PRO G 384 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO G 384 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN F  48 "   -0.054 5.00e-02 4.00e+02   8.05e-02 1.04e+01
        pdb=" N   PRO F  49 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO F  49 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO F  49 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU G 471 "   -0.015 2.00e-02 2.50e+03   3.16e-02 9.99e+00
        pdb=" C   GLU G 471 "    0.055 2.00e-02 2.50e+03
        pdb=" O   GLU G 471 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ILE G 472 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 578 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 256
        2.73 -     3.27: 3328
        3.27 -     3.82: 5704
        3.82 -     4.36: 6739
        4.36 -     4.90: 11108
  Nonbonded interactions: 27135
  Sorted by model distance:
  nonbonded pdb=" O   PRO F   8 "
            pdb=" OG1 THR F 107 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" O   PRO G 479 "
            pdb=" SG  CYS G 480 "
     model   vdw
     2.195 3.400
  nonbonded pdb=" OH  TYR E 106 "
            pdb=" O   TYR F  97 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OE1 GLU G 406 "
            pdb=" NE2 GLN G 409 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" O   GLY E 116 "
            pdb=" OG  SER F  62 "
     model   vdw
     2.239 3.040
  ... (remaining 27130 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:             0.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.890
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6241
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      :  0.005   0.138   3327  Z= 0.226
  Angle     :  0.883  11.143   4515  Z= 0.531
  Chirality :  0.049   0.227    473
  Planarity :  0.009   0.117    580
  Dihedral  : 19.664 106.791   1196
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 21.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 38.94 %
    Favored  : 59.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.40), residues: 399
  helix: -0.53 (1.97), residues: 7
  sheet: -1.25 (0.46), residues: 120
  loop : -1.07 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP E 121 
 HIS   0.002   0.001   HIS G 505 
 PHE   0.008   0.001   PHE E 118 
 TYR   0.017   0.002   TYR E 105 
 ARG   0.009   0.001   ARG F  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00368 (    1)
  link_NAG-ASN         : angle       0.65303 (    3)
  hydrogen bonds       : bond        0.26591 (   71)
  hydrogen bonds       : angle      11.38010 (  189)
  SS BOND              : bond        0.00140 (    3)
  SS BOND              : angle       0.76364 (    6)
  covalent geometry    : bond        0.00482 ( 3323)
  covalent geometry    : angle       0.88336 ( 4506)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  112 GLU cc_start: 0.5854 (pm20) cc_final: 0.5353 (pm20)
  outliers start: 6
  outliers final: 5
  residues processed: 100
  average time/residue: 0.1733
  time to fit residues: 20.5601
Evaluate side-chains
  102 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   37 ASN
Chi-restraints excluded: chain G residue  357 ARG
Chi-restraints excluded: chain G residue  456 PHE
Chi-restraints excluded: chain G residue  457 ARG
Chi-restraints excluded: chain G residue  459 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0870
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0000
   chunk 31 optimal weight:    0.5980
   chunk 12 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.4764

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

Flipped N/Q/H residues before XYZ refinement:
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.189371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.160798 restraints weight = 4076.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.166017 restraints weight = 2121.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.169537 restraints weight = 1404.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6317
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3327  Z= 0.138
  Angle     :  0.670   7.060   4515  Z= 0.343
  Chirality :  0.045   0.225    473
  Planarity :  0.007   0.075    580
  Dihedral  :  8.686  57.222    489
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 30.38 %
    Favored  : 64.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.40), residues: 399
  helix: -0.53 (1.96), residues: 7
  sheet: -1.17 (0.51), residues: 102
  loop : -1.04 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 
 PHE   0.008   0.001   PHE G 497 
 TYR   0.014   0.002   TYR E 105 
 ARG   0.003   0.001   ARG F  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00268 (    1)
  link_NAG-ASN         : angle       2.14794 (    3)
  hydrogen bonds       : bond        0.04096 (   71)
  hydrogen bonds       : angle       7.39980 (  189)
  SS BOND              : bond        0.00123 (    3)
  SS BOND              : angle       0.81422 (    6)
  covalent geometry    : bond        0.00322 ( 3323)
  covalent geometry    : angle       0.66736 ( 4506)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 TYR cc_start: 0.4356 (OUTLIER) cc_final: 0.3308 (m-80)
REVERT: E  112 GLU cc_start: 0.5510 (pm20) cc_final: 0.5123 (pm20)
REVERT: F   67 ARG cc_start: 0.5730 (ptt-90) cc_final: 0.5166 (ptt-90)
REVERT: G  357 ARG cc_start: 0.7532 (tmt170) cc_final: 0.7289 (tmm-80)
REVERT: G  406 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.6810 (mm-30)
REVERT: G  429 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7196 (p90)
REVERT: G  459 SER cc_start: 0.8413 (t) cc_final: 0.7762 (p)
  outliers start: 19
  outliers final: 9
  residues processed: 109
  average time/residue: 0.1567
  time to fit residues: 20.5054
Evaluate side-chains
  106 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   82 TYR
Chi-restraints excluded: chain E residue  105 TYR
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain G residue  401 VAL
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  429 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 37 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.174646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.145718 restraints weight = 4213.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.150352 restraints weight = 2297.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.153423 restraints weight = 1574.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6508
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   3327  Z= 0.269
  Angle     :  0.725   6.490   4515  Z= 0.374
  Chirality :  0.047   0.270    473
  Planarity :  0.006   0.061    580
  Dihedral  :  6.416  52.318    476
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 20.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  7.96 %
    Allowed  : 30.68 %
    Favored  : 61.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.40), residues: 399
  helix: -0.22 (2.01), residues: 7
  sheet: -0.96 (0.49), residues: 110
  loop : -1.07 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP E 121 
 HIS   0.001   0.001   HIS G 505 
 PHE   0.027   0.002   PHE E 118 
 TYR   0.017   0.002   TYR F  42 
 ARG   0.004   0.001   ARG G 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00726 (    1)
  link_NAG-ASN         : angle       1.61041 (    3)
  hydrogen bonds       : bond        0.04171 (   71)
  hydrogen bonds       : angle       6.92774 (  189)
  SS BOND              : bond        0.00407 (    3)
  SS BOND              : angle       0.82471 (    6)
  covalent geometry    : bond        0.00614 ( 3323)
  covalent geometry    : angle       0.72428 ( 4506)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 TYR cc_start: 0.4731 (OUTLIER) cc_final: 0.3764 (m-80)
REVERT: E  112 GLU cc_start: 0.5745 (pm20) cc_final: 0.5307 (pm20)
REVERT: F   67 ARG cc_start: 0.6064 (ptt-90) cc_final: 0.5600 (ptt-90)
REVERT: G  357 ARG cc_start: 0.7568 (tmt170) cc_final: 0.7355 (tmm-80)
REVERT: G  398 ASP cc_start: 0.8140 (m-30) cc_final: 0.7210 (m-30)
REVERT: G  406 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7190 (mm-30)
REVERT: G  409 GLN cc_start: 0.7061 (mt0) cc_final: 0.6487 (tt0)
REVERT: G  429 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.6828 (p90)
REVERT: G  459 SER cc_start: 0.8339 (t) cc_final: 0.7940 (p)
  outliers start: 27
  outliers final: 13
  residues processed: 119
  average time/residue: 0.1702
  time to fit residues: 24.2063
Evaluate side-chains
  114 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   82 TYR
Chi-restraints excluded: chain E residue  105 TYR
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue  109 VAL
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  401 VAL
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  473 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 31 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0040
   chunk 28 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 13 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
E 123 GLN
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  96 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 = 0.4108 r_free = 0.4108 target = 0.185280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.156535 restraints weight = 4143.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.161599 restraints weight = 2166.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.164870 restraints weight = 1441.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6384
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3327  Z= 0.148
  Angle     :  0.654   7.030   4515  Z= 0.334
  Chirality :  0.044   0.197    473
  Planarity :  0.006   0.059    580
  Dihedral  :  5.702  40.252    476
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  8.85 %
    Allowed  : 28.61 %
    Favored  : 62.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.41), residues: 399
  helix: -0.35 (1.91), residues: 7
  sheet: -0.74 (0.50), residues: 115
  loop : -1.04 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E 121 
 HIS   0.001   0.000   HIS G 505 
 PHE   0.021   0.001   PHE E 118 
 TYR   0.013   0.002   TYR E 105 
 ARG   0.004   0.000   ARG F  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00689 (    1)
  link_NAG-ASN         : angle       0.60251 (    3)
  hydrogen bonds       : bond        0.03335 (   71)
  hydrogen bonds       : angle       6.53408 (  189)
  SS BOND              : bond        0.00443 (    3)
  SS BOND              : angle       1.16091 (    6)
  covalent geometry    : bond        0.00338 ( 3323)
  covalent geometry    : angle       0.65354 ( 4506)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 TYR cc_start: 0.4409 (OUTLIER) cc_final: 0.3521 (m-80)
REVERT: F   67 ARG cc_start: 0.6116 (ptt-90) cc_final: 0.5801 (ptt-90)
REVERT: G  357 ARG cc_start: 0.7505 (tmt170) cc_final: 0.7216 (tmm-80)
REVERT: G  398 ASP cc_start: 0.8132 (m-30) cc_final: 0.7400 (m-30)
REVERT: G  406 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7285 (mm-30)
REVERT: G  409 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6485 (tt0)
REVERT: G  429 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.6989 (p90)
REVERT: G  495 TYR cc_start: 0.4436 (OUTLIER) cc_final: 0.3885 (m-80)
  outliers start: 30
  outliers final: 15
  residues processed: 121
  average time/residue: 0.1679
  time to fit residues: 24.4627
Evaluate side-chains
  117 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   17 SER
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   82 TYR
Chi-restraints excluded: chain E residue  105 TYR
Chi-restraints excluded: chain F residue    4 MET
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  401 VAL
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  410 ILE
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  473 TYR
Chi-restraints excluded: chain G residue  495 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 1 optimal weight:   30.0000
   chunk 14 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 4 optimal weight:    0.0370
   chunk 2 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.8862

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

Flipped N/Q/H residues before XYZ refinement:
F  85 GLN
F  96 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.180371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.151665 restraints weight = 4147.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.156382 restraints weight = 2243.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.159268 restraints weight = 1519.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6417
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3327  Z= 0.162
  Angle     :  0.667   8.097   4515  Z= 0.339
  Chirality :  0.044   0.228    473
  Planarity :  0.006   0.061    580
  Dihedral  :  5.511  36.089    476
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  8.85 %
    Allowed  : 30.68 %
    Favored  : 60.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.41), residues: 399
  helix: -0.59 (1.81), residues: 7
  sheet: -0.67 (0.50), residues: 115
  loop : -1.04 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 
 PHE   0.017   0.001   PHE E 118 
 TYR   0.013   0.002   TYR E 106 
 ARG   0.002   0.000   ARG F  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00508 (    1)
  link_NAG-ASN         : angle       0.52859 (    3)
  hydrogen bonds       : bond        0.03267 (   71)
  hydrogen bonds       : angle       6.34923 (  189)
  SS BOND              : bond        0.00273 (    3)
  SS BOND              : angle       0.93275 (    6)
  covalent geometry    : bond        0.00375 ( 3323)
  covalent geometry    : angle       0.66676 ( 4506)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 99
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 TYR cc_start: 0.4457 (OUTLIER) cc_final: 0.3516 (m-80)
REVERT: F   59 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6619 (tm-30)
REVERT: F   60 ARG cc_start: 0.6067 (ttm-80) cc_final: 0.5518 (tpp80)
REVERT: G  357 ARG cc_start: 0.7499 (tmt170) cc_final: 0.7210 (tmm-80)
REVERT: G  398 ASP cc_start: 0.8130 (m-30) cc_final: 0.7535 (m-30)
REVERT: G  406 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7311 (mm-30)
REVERT: G  409 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6468 (tt0)
REVERT: G  429 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.6796 (p90)
REVERT: G  495 TYR cc_start: 0.4503 (OUTLIER) cc_final: 0.3945 (m-80)
REVERT: G  501 TYR cc_start: 0.6438 (OUTLIER) cc_final: 0.5857 (m-10)
  outliers start: 30
  outliers final: 15
  residues processed: 119
  average time/residue: 0.2067
  time to fit residues: 29.0440
Evaluate side-chains
  118 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 ARG
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   82 TYR
Chi-restraints excluded: chain F residue    4 MET
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  369 TYR
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  434 ILE
Chi-restraints excluded: chain G residue  473 TYR
Chi-restraints excluded: chain G residue  495 TYR
Chi-restraints excluded: chain G residue  501 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 1 optimal weight:   30.0000
   chunk 3 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  96 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 = 0.4020 r_free = 0.4020 target = 0.176128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.146260 restraints weight = 4265.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.151074 restraints weight = 2275.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.154353 restraints weight = 1538.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041   3327  Z= 0.301
  Angle     :  0.783   9.068   4515  Z= 0.398
  Chirality :  0.047   0.264    473
  Planarity :  0.007   0.064    580
  Dihedral  :  5.987  35.843    476
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 21.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  8.85 %
    Allowed  : 30.38 %
    Favored  : 60.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.40), residues: 399
  helix: -1.59 (1.28), residues: 15
  sheet: -0.78 (0.48), residues: 115
  loop : -1.29 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP E 121 
 HIS   0.001   0.000   HIS G 505 
 PHE   0.019   0.002   PHE E 118 
 TYR   0.017   0.003   TYR G 380 
 ARG   0.003   0.001   ARG E  74 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00515 (    1)
  link_NAG-ASN         : angle       0.49021 (    3)
  hydrogen bonds       : bond        0.03893 (   71)
  hydrogen bonds       : angle       6.51130 (  189)
  SS BOND              : bond        0.00503 (    3)
  SS BOND              : angle       0.96086 (    6)
  covalent geometry    : bond        0.00685 ( 3323)
  covalent geometry    : angle       0.78302 ( 4506)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 TYR cc_start: 0.4493 (OUTLIER) cc_final: 0.3628 (m-80)
REVERT: G  357 ARG cc_start: 0.7640 (tmt170) cc_final: 0.7350 (tmm-80)
REVERT: G  371 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.5623 (p90)
REVERT: G  398 ASP cc_start: 0.8258 (m-30) cc_final: 0.7476 (m-30)
REVERT: G  406 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7454 (mt-10)
REVERT: G  409 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6822 (tt0)
REVERT: G  429 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.6688 (p90)
REVERT: G  495 TYR cc_start: 0.4558 (OUTLIER) cc_final: 0.3950 (m-80)
REVERT: G  501 TYR cc_start: 0.6686 (OUTLIER) cc_final: 0.6281 (m-10)
  outliers start: 30
  outliers final: 16
  residues processed: 124
  average time/residue: 0.1870
  time to fit residues: 27.5895
Evaluate side-chains
  124 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 ARG
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   82 TYR
Chi-restraints excluded: chain E residue  105 TYR
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue  109 VAL
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  369 TYR
Chi-restraints excluded: chain G residue  371 PHE
Chi-restraints excluded: chain G residue  401 VAL
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  410 ILE
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  434 ILE
Chi-restraints excluded: chain G residue  495 TYR
Chi-restraints excluded: chain G residue  501 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 36 optimal weight:    0.4980
   chunk 27 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0970
   chunk 25 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
F  43 GLN
F  85 GLN
** F  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.183010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.153450 restraints weight = 4162.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.158478 restraints weight = 2227.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.161518 restraints weight = 1500.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6399
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3327  Z= 0.133
  Angle     :  0.680   8.915   4515  Z= 0.340
  Chirality :  0.044   0.198    473
  Planarity :  0.006   0.061    580
  Dihedral  :  5.420  31.747    476
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  7.08 %
    Allowed  : 33.04 %
    Favored  : 59.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.41), residues: 399
  helix: -0.24 (1.96), residues: 7
  sheet: -0.68 (0.48), residues: 115
  loop : -1.09 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 
 PHE   0.015   0.001   PHE E 118 
 TYR   0.014   0.002   TYR E 105 
 ARG   0.004   0.000   ARG F  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00519 (    1)
  link_NAG-ASN         : angle       0.51635 (    3)
  hydrogen bonds       : bond        0.02998 (   71)
  hydrogen bonds       : angle       6.16159 (  189)
  SS BOND              : bond        0.00455 (    3)
  SS BOND              : angle       0.99994 (    6)
  covalent geometry    : bond        0.00307 ( 3323)
  covalent geometry    : angle       0.67975 ( 4506)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  118 PHE cc_start: 0.8017 (p90) cc_final: 0.7694 (p90)
REVERT: F   54 MET cc_start: 0.6805 (mtm) cc_final: 0.6538 (mtm)
REVERT: F   60 ARG cc_start: 0.5851 (ttm-80) cc_final: 0.5422 (tpp80)
REVERT: G  355 ARG cc_start: 0.7822 (mtt180) cc_final: 0.7528 (mtp180)
REVERT: G  357 ARG cc_start: 0.7536 (tmt170) cc_final: 0.7204 (tmm-80)
REVERT: G  371 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.5581 (p90)
REVERT: G  398 ASP cc_start: 0.8110 (m-30) cc_final: 0.7480 (m-30)
REVERT: G  406 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7007 (mm-30)
REVERT: G  409 GLN cc_start: 0.6981 (OUTLIER) cc_final: 0.6542 (tt0)
REVERT: G  429 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6837 (p90)
REVERT: G  495 TYR cc_start: 0.4321 (OUTLIER) cc_final: 0.4053 (m-80)
  outliers start: 24
  outliers final: 15
  residues processed: 120
  average time/residue: 0.1630
  time to fit residues: 23.3105
Evaluate side-chains
  119 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   86 ASN
Chi-restraints excluded: chain E residue  105 TYR
Chi-restraints excluded: chain F residue    4 MET
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   43 GLN
Chi-restraints excluded: chain F residue   94 CYS
Chi-restraints excluded: chain F residue  109 VAL
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  369 TYR
Chi-restraints excluded: chain G residue  371 PHE
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  410 ILE
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  434 ILE
Chi-restraints excluded: chain G residue  495 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 1 optimal weight:   30.0000
   chunk 31 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 25 optimal weight:    0.3980
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  96 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 = 0.4055 r_free = 0.4055 target = 0.180469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.150887 restraints weight = 4142.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.155771 restraints weight = 2196.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.158958 restraints weight = 1486.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   3327  Z= 0.247
  Angle     :  0.774   9.562   4515  Z= 0.387
  Chirality :  0.046   0.280    473
  Planarity :  0.006   0.065    580
  Dihedral  :  5.765  31.805    476
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 19.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  8.55 %
    Allowed  : 31.86 %
    Favored  : 59.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.40), residues: 399
  helix: -1.50 (1.31), residues: 15
  sheet: -0.75 (0.48), residues: 115
  loop : -1.29 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E 121 
 HIS   0.001   0.001   HIS G 505 
 PHE   0.016   0.002   PHE E 118 
 TYR   0.019   0.002   TYR G 473 
 ARG   0.003   0.001   ARG G 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00432 (    1)
  link_NAG-ASN         : angle       0.52564 (    3)
  hydrogen bonds       : bond        0.03403 (   71)
  hydrogen bonds       : angle       6.23074 (  189)
  SS BOND              : bond        0.00394 (    3)
  SS BOND              : angle       0.99262 (    6)
  covalent geometry    : bond        0.00568 ( 3323)
  covalent geometry    : angle       0.77331 ( 4506)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 TYR cc_start: 0.4565 (OUTLIER) cc_final: 0.3690 (m-80)
REVERT: G  357 ARG cc_start: 0.7632 (tmt170) cc_final: 0.7298 (tmm-80)
REVERT: G  371 PHE cc_start: 0.6729 (OUTLIER) cc_final: 0.5580 (p90)
REVERT: G  398 ASP cc_start: 0.8199 (m-30) cc_final: 0.7630 (m-30)
REVERT: G  406 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7276 (mm-30)
REVERT: G  409 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6420 (tt0)
REVERT: G  429 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.6592 (p90)
REVERT: G  495 TYR cc_start: 0.4578 (OUTLIER) cc_final: 0.3946 (m-80)
REVERT: G  501 TYR cc_start: 0.6606 (OUTLIER) cc_final: 0.6110 (m-10)
  outliers start: 29
  outliers final: 17
  residues processed: 120
  average time/residue: 0.1709
  time to fit residues: 24.2830
Evaluate side-chains
  124 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 ARG
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   82 TYR
Chi-restraints excluded: chain E residue   86 ASN
Chi-restraints excluded: chain E residue  105 TYR
Chi-restraints excluded: chain F residue    4 MET
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue  109 VAL
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  369 TYR
Chi-restraints excluded: chain G residue  371 PHE
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  410 ILE
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  434 ILE
Chi-restraints excluded: chain G residue  473 TYR
Chi-restraints excluded: chain G residue  495 TYR
Chi-restraints excluded: chain G residue  501 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 1 optimal weight:   30.0000
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 0 optimal weight:    9.9990
   chunk 11 optimal weight:    0.6980
   chunk 7 optimal weight:   10.0000
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  96 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 = 0.4100 r_free = 0.4100 target = 0.184800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.154941 restraints weight = 4174.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.159900 restraints weight = 2225.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.163183 restraints weight = 1504.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6421
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3327  Z= 0.163
  Angle     :  0.735   9.684   4515  Z= 0.364
  Chirality :  0.044   0.254    473
  Planarity :  0.006   0.065    580
  Dihedral  :  5.532  29.517    476
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  7.08 %
    Allowed  : 33.04 %
    Favored  : 59.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.41), residues: 399
  helix:  0.08 (2.11), residues: 7
  sheet: -0.72 (0.48), residues: 115
  loop : -1.17 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 121 
 HIS   0.001   0.000   HIS G 505 
 PHE   0.010   0.001   PHE E 118 
 TYR   0.013   0.002   TYR G 473 
 ARG   0.004   0.000   ARG F  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00456 (    1)
  link_NAG-ASN         : angle       0.45039 (    3)
  hydrogen bonds       : bond        0.03013 (   71)
  hydrogen bonds       : angle       6.05009 (  189)
  SS BOND              : bond        0.00243 (    3)
  SS BOND              : angle       0.98162 (    6)
  covalent geometry    : bond        0.00381 ( 3323)
  covalent geometry    : angle       0.73519 ( 4506)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   20 THR cc_start: 0.7613 (OUTLIER) cc_final: 0.7206 (p)
REVERT: G  357 ARG cc_start: 0.7510 (tmt170) cc_final: 0.7174 (tmm-80)
REVERT: G  371 PHE cc_start: 0.6726 (OUTLIER) cc_final: 0.5588 (p90)
REVERT: G  398 ASP cc_start: 0.8136 (m-30) cc_final: 0.7530 (m-30)
REVERT: G  406 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7312 (mm-30)
REVERT: G  409 GLN cc_start: 0.6977 (OUTLIER) cc_final: 0.6470 (tt0)
REVERT: G  429 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6587 (p90)
REVERT: G  495 TYR cc_start: 0.4544 (OUTLIER) cc_final: 0.4040 (m-80)
  outliers start: 24
  outliers final: 17
  residues processed: 113
  average time/residue: 0.1902
  time to fit residues: 25.2772
Evaluate side-chains
  116 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 ARG
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   86 ASN
Chi-restraints excluded: chain E residue  105 TYR
Chi-restraints excluded: chain F residue    4 MET
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain F residue  109 VAL
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  369 TYR
Chi-restraints excluded: chain G residue  371 PHE
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  410 ILE
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  434 ILE
Chi-restraints excluded: chain G residue  473 TYR
Chi-restraints excluded: chain G residue  495 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 1 optimal weight:   30.0000
   chunk 30 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  96 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 = 0.4110 r_free = 0.4110 target = 0.185795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.156126 restraints weight = 4115.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.161089 restraints weight = 2228.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.164337 restraints weight = 1516.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6430
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3327  Z= 0.162
  Angle     :  0.753  10.755   4515  Z= 0.371
  Chirality :  0.044   0.259    473
  Planarity :  0.006   0.066    580
  Dihedral  :  5.394  27.049    476
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  7.67 %
    Allowed  : 33.04 %
    Favored  : 59.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.41), residues: 399
  helix:  0.09 (2.09), residues: 7
  sheet: -0.71 (0.47), residues: 115
  loop : -1.18 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 
 PHE   0.008   0.001   PHE E 118 
 TYR   0.025   0.002   TYR F  55 
 ARG   0.002   0.000   ARG G 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00463 (    1)
  link_NAG-ASN         : angle       0.43774 (    3)
  hydrogen bonds       : bond        0.03077 (   71)
  hydrogen bonds       : angle       5.99682 (  189)
  SS BOND              : bond        0.00220 (    3)
  SS BOND              : angle       0.91780 (    6)
  covalent geometry    : bond        0.00380 ( 3323)
  covalent geometry    : angle       0.75340 ( 4506)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 TYR cc_start: 0.4584 (OUTLIER) cc_final: 0.3668 (m-80)
REVERT: F   20 THR cc_start: 0.7585 (OUTLIER) cc_final: 0.7179 (p)
REVERT: F   55 TYR cc_start: 0.7689 (p90) cc_final: 0.7330 (p90)
REVERT: G  357 ARG cc_start: 0.7481 (tmt170) cc_final: 0.7122 (tmm-80)
REVERT: G  371 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.5551 (p90)
REVERT: G  398 ASP cc_start: 0.8146 (m-30) cc_final: 0.7559 (m-30)
REVERT: G  406 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7321 (mm-30)
REVERT: G  409 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6445 (tt0)
REVERT: G  429 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.6559 (p90)
REVERT: G  495 TYR cc_start: 0.4448 (OUTLIER) cc_final: 0.4001 (m-80)
  outliers start: 26
  outliers final: 17
  residues processed: 114
  average time/residue: 0.1746
  time to fit residues: 23.5312
Evaluate side-chains
  118 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 ARG
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   82 TYR
Chi-restraints excluded: chain E residue   86 ASN
Chi-restraints excluded: chain E residue  105 TYR
Chi-restraints excluded: chain F residue    4 MET
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain F residue   94 CYS
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  109 VAL
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  369 TYR
Chi-restraints excluded: chain G residue  371 PHE
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  410 ILE
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  434 ILE
Chi-restraints excluded: chain G residue  480 CYS
Chi-restraints excluded: chain G residue  495 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.0030
   chunk 38 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0970
   chunk 10 optimal weight:    0.4980
   chunk 28 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.3988

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

Flipped N/Q/H residues before XYZ refinement:
F  43 GLN
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  96 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.187444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.158603 restraints weight = 4120.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.163544 restraints weight = 2225.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.166844 restraints weight = 1500.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6342
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3327  Z= 0.132
  Angle     :  0.747  10.663   4515  Z= 0.364
  Chirality :  0.044   0.236    473
  Planarity :  0.006   0.065    580
  Dihedral  :  5.141  24.057    476
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 15.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  7.67 %
    Allowed  : 32.74 %
    Favored  : 59.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.41), residues: 399
  helix:  0.04 (2.04), residues: 7
  sheet: -0.63 (0.47), residues: 115
  loop : -1.15 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 
 PHE   0.006   0.001   PHE G 429 
 TYR   0.024   0.002   TYR F  55 
 ARG   0.002   0.000   ARG G 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00445 (    1)
  link_NAG-ASN         : angle       0.51210 (    3)
  hydrogen bonds       : bond        0.02911 (   71)
  hydrogen bonds       : angle       5.89125 (  189)
  SS BOND              : bond        0.00153 (    3)
  SS BOND              : angle       0.89030 (    6)
  covalent geometry    : bond        0.00311 ( 3323)
  covalent geometry    : angle       0.74737 ( 4506)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1667.64 seconds
wall clock time: 30 minutes 4.79 seconds (1804.79 seconds total)