Starting phenix.real_space_refine
on Tue Mar  3 13:58:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ekd_28199/03_2026/8ekd_28199.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ekd_28199/03_2026/8ekd_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ekd_28199/03_2026/8ekd_28199.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ekd_28199/03_2026/8ekd_28199.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ekd_28199/03_2026/8ekd_28199.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ekd_28199/03_2026/8ekd_28199.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.93, per 1000 atoms: 0.29
  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: 0.31
  Conformation dependent library (CDL) restraints added in 142.3 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: 0.11
  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: 0.37

  Time building geometry restraints manager: 0.42 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:             0.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.280
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.150
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (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
 ARG   0.009   0.001   ARG F  60 
 TYR   0.017   0.002   TYR E 105 
 PHE   0.008   0.001   PHE E 118 
 TRP   0.040   0.002   TRP E 121 
 HIS   0.002   0.001   HIS G 505 

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

*********************** 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  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  112 GLU cc_start: 0.5853 (pm20) cc_final: 0.5353 (pm20)
  outliers start: 6
  outliers final: 5
  residues processed: 100
  average time/residue: 0.0779
  time to fit residues: 9.2255
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  : 0.120 
-------------------------------------------------------------------------------
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 24 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    0.0870
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7360

-------------------------------------------------------------------------------
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 = 0.4114 r_free = 0.4114 target = 0.185894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.156906 restraints weight = 4154.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.161921 restraints weight = 2187.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.165300 restraints weight = 1464.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.167007 restraints weight = 1122.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.168690 restraints weight = 960.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6329
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3327  Z= 0.158
  Angle     :  0.687   7.069   4515  Z= 0.351
  Chirality :  0.046   0.240    473
  Planarity :  0.007   0.074    580
  Dihedral  :  8.767  56.652    489
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 30.09 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.40), residues: 399
  helix: -0.51 (1.99), residues: 7
  sheet: -1.22 (0.52), residues: 97
  loop : -1.04 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F  60 
 TYR   0.014   0.002   TYR E 105 
 PHE   0.008   0.001   PHE G 497 
 TRP   0.018   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 3323)
  covalent geometry    : angle       0.68520 ( 4506)
  SS BOND              : bond        0.00188 (    3)
  SS BOND              : angle       0.82576 (    6)
  hydrogen bonds       : bond        0.04026 (   71)
  hydrogen bonds       : angle       7.35981 (  189)
  link_NAG-ASN         : bond        0.00230 (    1)
  link_NAG-ASN         : angle       1.79452 (    3)

*********************** 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
  121 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 TYR cc_start: 0.4434 (OUTLIER) cc_final: 0.3393 (m-80)
REVERT: E  112 GLU cc_start: 0.5564 (pm20) cc_final: 0.5141 (pm20)
REVERT: F   67 ARG cc_start: 0.5676 (ptt-90) cc_final: 0.5025 (ptt-90)
REVERT: G  357 ARG cc_start: 0.7539 (tmt170) cc_final: 0.7305 (tmm-80)
REVERT: G  406 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6851 (mm-30)
REVERT: G  429 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.7070 (p90)
REVERT: G  459 SER cc_start: 0.8428 (t) cc_final: 0.7779 (p)
  outliers start: 20
  outliers final: 10
  residues processed: 113
  average time/residue: 0.0695
  time to fit residues: 9.3735
Evaluate side-chains
  106 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
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  403 ARG
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 22 optimal weight:    3.9990
   chunk 10 optimal weight:    0.4980
   chunk 2 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 13 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4053 r_free = 0.4053 target = 0.180635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.152189 restraints weight = 4150.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.157034 restraints weight = 2230.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.160204 restraints weight = 1508.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.162257 restraints weight = 1161.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.163324 restraints weight = 971.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6345
moved from start:          0.1749

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= 0.154
  Angle     :  0.654   6.293   4515  Z= 0.333
  Chirality :  0.046   0.364    473
  Planarity :  0.006   0.061    580
  Dihedral  :  5.925  47.138    476
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 31.27 %
    Favored  : 62.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.40), residues: 399
  helix: -0.58 (1.83), residues: 7
  sheet: -0.82 (0.49), residues: 115
  loop : -1.07 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 403 
 TYR   0.013   0.001   TYR E 105 
 PHE   0.025   0.002   PHE E 118 
 TRP   0.017   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3323)
  covalent geometry    : angle       0.64546 ( 4506)
  SS BOND              : bond        0.00201 (    3)
  SS BOND              : angle       0.70784 (    6)
  hydrogen bonds       : bond        0.03644 (   71)
  hydrogen bonds       : angle       6.88745 (  189)
  link_NAG-ASN         : bond        0.01322 (    1)
  link_NAG-ASN         : angle       4.04235 (    3)

*********************** 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
  119 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 TYR cc_start: 0.4530 (OUTLIER) cc_final: 0.3575 (m-80)
REVERT: E  112 GLU cc_start: 0.5577 (pm20) cc_final: 0.5160 (pm20)
REVERT: F   60 ARG cc_start: 0.5802 (ttm-80) cc_final: 0.5414 (tpp80)
REVERT: F   67 ARG cc_start: 0.6003 (ptt-90) cc_final: 0.5561 (ptt-90)
REVERT: G  396 TYR cc_start: 0.6725 (m-10) cc_final: 0.6451 (m-10)
REVERT: G  398 ASP cc_start: 0.8066 (m-30) cc_final: 0.6664 (m-30)
REVERT: G  406 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7123 (mm-30)
REVERT: G  409 GLN cc_start: 0.6927 (mt0) cc_final: 0.6399 (tt0)
REVERT: G  429 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6872 (p90)
REVERT: G  459 SER cc_start: 0.8394 (t) cc_final: 0.8005 (p)
  outliers start: 20
  outliers final: 10
  residues processed: 111
  average time/residue: 0.0672
  time to fit residues: 8.9682
Evaluate side-chains
  108 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
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  111 ILE
Chi-restraints excluded: chain G residue  402 ILE
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 31 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0870
   chunk 13 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0000
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.4562

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.189129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.160187 restraints weight = 4130.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.165488 restraints weight = 2157.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.168884 restraints weight = 1430.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.170984 restraints weight = 1092.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.172643 restraints weight = 911.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6267
moved from start:          0.2099

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= 0.124
  Angle     :  0.644   7.473   4515  Z= 0.324
  Chirality :  0.045   0.322    473
  Planarity :  0.006   0.060    580
  Dihedral  :  5.263  32.487    476
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  7.37 %
    Allowed  : 30.97 %
    Favored  : 61.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.41), residues: 399
  helix: -0.83 (1.75), residues: 7
  sheet: -0.53 (0.50), residues: 115
  loop : -1.05 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 355 
 TYR   0.013   0.001   TYR E 105 
 PHE   0.023   0.001   PHE E 118 
 TRP   0.018   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3323)
  covalent geometry    : angle       0.63048 ( 4506)
  SS BOND              : bond        0.00303 (    3)
  SS BOND              : angle       1.07361 (    6)
  hydrogen bonds       : bond        0.03195 (   71)
  hydrogen bonds       : angle       6.46194 (  189)
  link_NAG-ASN         : bond        0.02421 (    1)
  link_NAG-ASN         : angle       5.07327 (    3)

*********************** 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
  125 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 TYR cc_start: 0.4389 (OUTLIER) cc_final: 0.3443 (m-80)
REVERT: E  112 GLU cc_start: 0.5503 (pm20) cc_final: 0.5106 (pm20)
REVERT: F   67 ARG cc_start: 0.5878 (ptt-90) cc_final: 0.5393 (ptt-90)
REVERT: G  398 ASP cc_start: 0.8046 (m-30) cc_final: 0.7728 (m-30)
REVERT: G  406 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7168 (mm-30)
REVERT: G  409 GLN cc_start: 0.6887 (mt0) cc_final: 0.6401 (tt0)
REVERT: G  429 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.6945 (p90)
REVERT: G  495 TYR cc_start: 0.4534 (OUTLIER) cc_final: 0.4155 (m-80)
  outliers start: 25
  outliers final: 11
  residues processed: 117
  average time/residue: 0.0674
  time to fit residues: 9.4152
Evaluate side-chains
  105 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
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   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  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 14 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 38 optimal weight:    0.4980
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0030
   chunk 4 optimal weight:    0.5980
   chunk 13 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.5190

-------------------------------------------------------------------------------
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 = 0.4151 r_free = 0.4151 target = 0.190280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.160832 restraints weight = 4082.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.166039 restraints weight = 2141.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.169602 restraints weight = 1438.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.171586 restraints weight = 1099.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.173107 restraints weight = 928.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6275
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3327  Z= 0.126
  Angle     :  0.648   6.589   4515  Z= 0.322
  Chirality :  0.045   0.279    473
  Planarity :  0.006   0.057    580
  Dihedral  :  4.976  27.027    476
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 15.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  7.67 %
    Allowed  : 31.56 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.41), residues: 399
  helix: -1.11 (1.69), residues: 7
  sheet: -0.43 (0.51), residues: 115
  loop : -1.06 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  60 
 TYR   0.014   0.001   TYR G 380 
 PHE   0.018   0.001   PHE E 118 
 TRP   0.021   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 3323)
  covalent geometry    : angle       0.63851 ( 4506)
  SS BOND              : bond        0.00233 (    3)
  SS BOND              : angle       0.95869 (    6)
  hydrogen bonds       : bond        0.03121 (   71)
  hydrogen bonds       : angle       6.20242 (  189)
  link_NAG-ASN         : bond        0.01968 (    1)
  link_NAG-ASN         : angle       4.31291 (    3)

*********************** 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
  126 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  112 GLU cc_start: 0.5441 (pm20) cc_final: 0.5094 (pm20)
REVERT: F   67 ARG cc_start: 0.5911 (ptt-90) cc_final: 0.5439 (ptt-90)
REVERT: G  406 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7214 (mm-30)
REVERT: G  409 GLN cc_start: 0.6896 (OUTLIER) cc_final: 0.6364 (tt0)
REVERT: G  429 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6909 (p90)
REVERT: G  495 TYR cc_start: 0.4601 (OUTLIER) cc_final: 0.4226 (m-80)
  outliers start: 26
  outliers final: 15
  residues processed: 118
  average time/residue: 0.0736
  time to fit residues: 10.3638
Evaluate side-chains
  112 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
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  105 TYR
Chi-restraints excluded: chain F residue   10 SER
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  101 LEU
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  456 PHE
Chi-restraints excluded: chain G residue  473 TYR
Chi-restraints excluded: chain G residue  495 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.179118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.149293 restraints weight = 4215.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.154149 restraints weight = 2247.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.157300 restraints weight = 1534.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.159318 restraints weight = 1198.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.160965 restraints weight = 1018.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6401
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3327  Z= 0.192
  Angle     :  0.712   8.121   4515  Z= 0.354
  Chirality :  0.045   0.255    473
  Planarity :  0.006   0.059    580
  Dihedral  :  5.177  25.960    476
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  7.08 %
    Allowed  : 32.15 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.41), residues: 399
  helix: -1.07 (1.67), residues: 7
  sheet: -0.43 (0.50), residues: 115
  loop : -1.07 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 403 
 TYR   0.014   0.002   TYR E 105 
 PHE   0.031   0.002   PHE E 118 
 TRP   0.025   0.002   TRP E 121 
 HIS   0.001   0.000   HIS G 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 3323)
  covalent geometry    : angle       0.70567 ( 4506)
  SS BOND              : bond        0.00322 (    3)
  SS BOND              : angle       0.72953 (    6)
  hydrogen bonds       : bond        0.03330 (   71)
  hydrogen bonds       : angle       6.26535 (  189)
  link_NAG-ASN         : bond        0.01680 (    1)
  link_NAG-ASN         : angle       3.83176 (    3)

*********************** 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
  121 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  112 GLU cc_start: 0.5610 (pm20) cc_final: 0.5262 (pm20)
REVERT: F   67 ARG cc_start: 0.5942 (ptt-90) cc_final: 0.5468 (ptt-90)
REVERT: G  396 TYR cc_start: 0.6669 (m-10) cc_final: 0.6459 (m-10)
REVERT: G  398 ASP cc_start: 0.8194 (m-30) cc_final: 0.7457 (m-30)
REVERT: G  406 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7268 (mm-30)
REVERT: G  409 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6412 (tt0)
REVERT: G  429 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6780 (p90)
REVERT: G  462 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7323 (mmtt)
REVERT: G  495 TYR cc_start: 0.4365 (OUTLIER) cc_final: 0.3961 (m-80)
REVERT: G  501 TYR cc_start: 0.6458 (OUTLIER) cc_final: 0.5962 (m-10)
  outliers start: 24
  outliers final: 14
  residues processed: 116
  average time/residue: 0.0754
  time to fit residues: 10.4034
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  : 0.118 
-------------------------------------------------------------------------------
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   20 THR
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  339 ASP
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  462 LYS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 7 optimal weight:    8.9990
   chunk 36 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0040
   chunk 38 optimal weight:    0.0770
   chunk 20 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.4550

-------------------------------------------------------------------------------
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 = 0.4109 r_free = 0.4109 target = 0.186067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.156318 restraints weight = 4215.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.161453 restraints weight = 2262.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.164764 restraints weight = 1535.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.167010 restraints weight = 1193.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.168408 restraints weight = 1001.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6297
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3327  Z= 0.126
  Angle     :  0.678   8.423   4515  Z= 0.335
  Chirality :  0.044   0.255    473
  Planarity :  0.005   0.057    580
  Dihedral  :  4.971  24.647    476
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 15.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  : 30.97 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.41), residues: 399
  helix: -1.12 (1.70), residues: 7
  sheet: -0.30 (0.50), residues: 114
  loop : -1.10 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  60 
 TYR   0.015   0.002   TYR G 380 
 PHE   0.027   0.001   PHE E 118 
 TRP   0.019   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 3323)
  covalent geometry    : angle       0.67237 ( 4506)
  SS BOND              : bond        0.00156 (    3)
  SS BOND              : angle       0.71310 (    6)
  hydrogen bonds       : bond        0.02915 (   71)
  hydrogen bonds       : angle       6.15073 (  189)
  link_NAG-ASN         : bond        0.01410 (    1)
  link_NAG-ASN         : angle       3.51380 (    3)

*********************** 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
  117 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  112 GLU cc_start: 0.5436 (pm20) cc_final: 0.5118 (pm20)
REVERT: F    4 MET cc_start: 0.5917 (tpt) cc_final: 0.5663 (tpt)
REVERT: F   55 TYR cc_start: 0.7100 (p90) cc_final: 0.6494 (p90)
REVERT: F   67 ARG cc_start: 0.6037 (ptt-90) cc_final: 0.5833 (ptt-90)
REVERT: F   96 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6855 (pp30)
REVERT: G  406 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7253 (mm-30)
REVERT: G  409 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6420 (tt0)
REVERT: G  429 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6734 (p90)
REVERT: G  462 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7210 (mmtt)
REVERT: G  495 TYR cc_start: 0.4561 (OUTLIER) cc_final: 0.4247 (m-80)
  outliers start: 22
  outliers final: 13
  residues processed: 111
  average time/residue: 0.0739
  time to fit residues: 9.7445
Evaluate side-chains
  109 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
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   20 THR
Chi-restraints excluded: chain F residue   96 GLN
Chi-restraints excluded: chain F residue  101 LEU
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  410 ILE
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  434 ILE
Chi-restraints excluded: chain G residue  462 LYS
Chi-restraints excluded: chain G residue  473 TYR
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 29 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 1 optimal weight:   20.0000
   chunk 5 optimal weight:    0.0040
   chunk 4 optimal weight:    0.1980
   chunk 28 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 33 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.4792

-------------------------------------------------------------------------------
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 = 0.4115 r_free = 0.4115 target = 0.186689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.156676 restraints weight = 4279.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.161763 restraints weight = 2306.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.165121 restraints weight = 1568.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.167186 restraints weight = 1217.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.168923 restraints weight = 1029.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6290
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3327  Z= 0.129
  Angle     :  0.689   8.189   4515  Z= 0.338
  Chirality :  0.044   0.249    473
  Planarity :  0.005   0.054    580
  Dihedral  :  4.903  24.011    476
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  : 31.27 %
    Favored  : 62.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.41), residues: 399
  helix: -1.15 (1.66), residues: 7
  sheet: -0.16 (0.50), residues: 114
  loop : -1.11 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 403 
 TYR   0.021   0.002   TYR F  55 
 PHE   0.019   0.001   PHE E 118 
 TRP   0.024   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3323)
  covalent geometry    : angle       0.68261 ( 4506)
  SS BOND              : bond        0.00170 (    3)
  SS BOND              : angle       0.73566 (    6)
  hydrogen bonds       : bond        0.02842 (   71)
  hydrogen bonds       : angle       6.04495 (  189)
  link_NAG-ASN         : bond        0.01483 (    1)
  link_NAG-ASN         : angle       3.56224 (    3)

*********************** 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
  116 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  112 GLU cc_start: 0.5422 (pm20) cc_final: 0.5100 (pm20)
REVERT: F    4 MET cc_start: 0.5888 (tpt) cc_final: 0.5686 (tpt)
REVERT: F   55 TYR cc_start: 0.7210 (p90) cc_final: 0.6996 (p90)
REVERT: F   67 ARG cc_start: 0.5574 (ptt-90) cc_final: 0.5240 (ptt-90)
REVERT: F   96 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6931 (pp30)
REVERT: G  406 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7112 (mm-30)
REVERT: G  409 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6472 (tt0)
REVERT: G  429 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6702 (p90)
REVERT: G  462 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7227 (mmtt)
REVERT: G  495 TYR cc_start: 0.4566 (OUTLIER) cc_final: 0.4274 (m-80)
  outliers start: 22
  outliers final: 14
  residues processed: 111
  average time/residue: 0.0711
  time to fit residues: 9.3078
Evaluate side-chains
  111 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
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   10 SER
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   96 GLN
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  410 ILE
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  434 ILE
Chi-restraints excluded: chain G residue  456 PHE
Chi-restraints excluded: chain G residue  462 LYS
Chi-restraints excluded: chain G residue  473 TYR
Chi-restraints excluded: chain G residue  495 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 2 optimal weight:    9.9990
   chunk 22 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4091 r_free = 0.4091 target = 0.184115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.154633 restraints weight = 4231.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.159517 restraints weight = 2278.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.162583 restraints weight = 1557.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.164948 restraints weight = 1220.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.166588 restraints weight = 1019.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6323
moved from start:          0.2897

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= 0.153
  Angle     :  0.712   8.926   4515  Z= 0.350
  Chirality :  0.045   0.248    473
  Planarity :  0.006   0.052    580
  Dihedral  :  4.971  24.967    476
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 17.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  7.96 %
    Allowed  : 29.20 %
    Favored  : 62.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.41), residues: 399
  helix: -1.27 (1.69), residues: 7
  sheet: -0.20 (0.50), residues: 114
  loop : -1.14 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 403 
 TYR   0.025   0.002   TYR F  55 
 PHE   0.015   0.001   PHE E 118 
 TRP   0.032   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3323)
  covalent geometry    : angle       0.70690 ( 4506)
  SS BOND              : bond        0.00209 (    3)
  SS BOND              : angle       0.55076 (    6)
  hydrogen bonds       : bond        0.02957 (   71)
  hydrogen bonds       : angle       6.05079 (  189)
  link_NAG-ASN         : bond        0.01423 (    1)
  link_NAG-ASN         : angle       3.46300 (    3)

*********************** 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
  119 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  112 GLU cc_start: 0.5226 (pm20) cc_final: 0.4934 (pm20)
REVERT: F    4 MET cc_start: 0.6114 (tpt) cc_final: 0.5780 (tpt)
REVERT: F   20 THR cc_start: 0.7529 (OUTLIER) cc_final: 0.7139 (p)
REVERT: F   96 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6893 (pp30)
REVERT: G  356 LYS cc_start: 0.8325 (mptt) cc_final: 0.8073 (mptt)
REVERT: G  371 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.5498 (p90)
REVERT: G  406 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7238 (mm-30)
REVERT: G  409 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6405 (tt0)
REVERT: G  429 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6684 (p90)
REVERT: G  462 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7251 (mmtt)
REVERT: G  495 TYR cc_start: 0.4093 (OUTLIER) cc_final: 0.3868 (m-80)
  outliers start: 27
  outliers final: 14
  residues processed: 113
  average time/residue: 0.0797
  time to fit residues: 10.5584
Evaluate side-chains
  113 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
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   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   96 GLN
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  462 LYS
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 34 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   chunk 21 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4125 r_free = 0.4125 target = 0.187400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.157743 restraints weight = 4210.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.162842 restraints weight = 2212.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.166185 restraints weight = 1491.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.168165 restraints weight = 1149.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.169960 restraints weight = 973.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6327
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3327  Z= 0.161
  Angle     :  0.731   9.455   4515  Z= 0.357
  Chirality :  0.045   0.246    473
  Planarity :  0.006   0.061    580
  Dihedral  :  5.004  24.902    476
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 18.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  7.96 %
    Allowed  : 28.61 %
    Favored  : 63.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.41), residues: 399
  helix: -1.06 (1.78), residues: 7
  sheet: -0.24 (0.49), residues: 114
  loop : -1.14 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  67 
 TYR   0.039   0.002   TYR F  55 
 PHE   0.014   0.002   PHE E 118 
 TRP   0.039   0.003   TRP E 121 
 HIS   0.001   0.000   HIS G 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 3323)
  covalent geometry    : angle       0.72647 ( 4506)
  SS BOND              : bond        0.00229 (    3)
  SS BOND              : angle       0.55744 (    6)
  hydrogen bonds       : bond        0.03039 (   71)
  hydrogen bonds       : angle       6.05455 (  189)
  link_NAG-ASN         : bond        0.01388 (    1)
  link_NAG-ASN         : angle       3.29911 (    3)

********************** 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
  121 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  112 GLU cc_start: 0.5217 (pm20) cc_final: 0.4927 (pm20)
REVERT: F    4 MET cc_start: 0.6171 (tpt) cc_final: 0.5771 (tpt)
REVERT: F   20 THR cc_start: 0.7511 (OUTLIER) cc_final: 0.7126 (p)
REVERT: F   55 TYR cc_start: 0.7580 (p90) cc_final: 0.7202 (p90)
REVERT: F   96 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6973 (pp30)
REVERT: G  371 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.5528 (p90)
REVERT: G  398 ASP cc_start: 0.8081 (m-30) cc_final: 0.7411 (m-30)
REVERT: G  406 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7254 (mm-30)
REVERT: G  409 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6435 (tt0)
REVERT: G  429 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6647 (p90)
REVERT: G  462 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7289 (mmtt)
  outliers start: 27
  outliers final: 15
  residues processed: 113
  average time/residue: 0.0755
  time to fit residues: 10.1602
Evaluate side-chains
  115 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
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   85 MET
Chi-restraints excluded: chain E residue   86 ASN
Chi-restraints excluded: chain E residue  105 TYR
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   96 GLN
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  462 LYS
Chi-restraints excluded: chain G residue  473 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.4112 r_free = 0.4112 target = 0.185813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.156312 restraints weight = 4249.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.161452 restraints weight = 2216.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.164895 restraints weight = 1483.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.166847 restraints weight = 1135.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.167936 restraints weight = 962.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6387
moved from start:          0.3047

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= 0.184
  Angle     :  0.752   9.734   4515  Z= 0.368
  Chirality :  0.045   0.258    473
  Planarity :  0.006   0.063    580
  Dihedral  :  5.160  25.135    476
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 18.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  : 29.79 %
    Favored  : 63.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.41), residues: 399
  helix: -1.01 (1.79), residues: 7
  sheet: -0.34 (0.49), residues: 117
  loop : -1.09 (0.37), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 403 
 TYR   0.037   0.002   TYR F  55 
 PHE   0.017   0.002   PHE G 374 
 TRP   0.039   0.003   TRP E 121 
 HIS   0.001   0.000   HIS G 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 3323)
  covalent geometry    : angle       0.74791 ( 4506)
  SS BOND              : bond        0.00260 (    3)
  SS BOND              : angle       0.73003 (    6)
  hydrogen bonds       : bond        0.03092 (   71)
  hydrogen bonds       : angle       6.11054 (  189)
  link_NAG-ASN         : bond        0.01373 (    1)
  link_NAG-ASN         : angle       3.14229 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 830.53 seconds
wall clock time: 14 minutes 54.94 seconds (894.94 seconds total)