Starting phenix.real_space_refine
on Tue Mar  3 15:43:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sy0_25512/03_2026/7sy0_25512.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sy0_25512/03_2026/7sy0_25512.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sy0_25512/03_2026/7sy0_25512.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sy0_25512/03_2026/7sy0_25512.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sy0_25512/03_2026/7sy0_25512.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sy0_25512/03_2026/7sy0_25512.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4186      2.51       5
     N    1081      2.21       5
     O    1249      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 6553
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1593
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "E"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
    Chain: "B"
      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
    Chain: "E"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 1.56, per 1000 atoms: 0.24
  Number of scatterers: 6553
  At special positions: 0
  Unit cell: (79, 84, 121, 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      37     16.00
     O    1249      8.00
     N    1081      7.00
     C    4186      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 133 " - pdb=" SG  CYS E 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 530 " - pdb=" SG  CYS E 542 " 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 B1301 " - " ASN B 343 "
      " NAG E 701 " - " ASN E  53 "
      " NAG E 702 " - " ASN E  90 "
      " NAG E 703 " - " ASN E 103 "
      " NAG E 704 " - " ASN E 322 "
      " NAG E 705 " - " ASN E 432 "
      " NAG E 706 " - " ASN E 546 "
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 248.8 milliseconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 7 sheets defined
      57.3% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 387
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.708A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 4.162A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LEU E  39 " --> pdb=" O   GLU E  35 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
    Processing helix  chain 'E' and resid 82 through 83
      No H-bonds generated for 'chain 'E' and resid 82 through 83'
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.781A  pdb=" N   GLU E  87 " --> pdb=" O   PRO E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 101
    Processing helix  chain 'E' and resid 103 through 108
      removed outlier: 4.028A  pdb=" N   VAL E 107 " --> pdb=" O   GLY E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 129
    Processing helix  chain 'E' and resid 146 through 155
      removed outlier: 3.933A  pdb=" N   ILE E 151 " --> pdb=" O   GLY E 147 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 157 through 194
      Proline residue:  E 178  - end of helix
      removed outlier: 3.725A  pdb=" N   VAL E 185 " --> pdb=" O   GLU E 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 198 through 205
    Processing helix  chain 'E' and resid 206 through 208
      No H-bonds generated for 'chain 'E' and resid 206 through 208'
    Processing helix  chain 'E' and resid 218 through 252
      removed outlier: 3.669A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU E 232 " --> pdb=" O   HIS E 228 " (cutoff:3.500A)
      Proline residue:  E 235  - end of helix
    Processing helix  chain 'E' and resid 265 through 267
      No H-bonds generated for 'chain 'E' and resid 265 through 267'
    Processing helix  chain 'E' and resid 275 through 279
      removed outlier: 3.784A  pdb=" N   TYR E 279 " --> pdb=" O   THR E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 301
    Processing helix  chain 'E' and resid 303 through 318
    Processing helix  chain 'E' and resid 324 through 331
      removed outlier: 3.541A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.701A  pdb=" N   TYR E 385 " --> pdb=" O   TYR E 381 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 386 through 388
      No H-bonds generated for 'chain 'E' and resid 386 through 388'
    Processing helix  chain 'E' and resid 389 through 393
    Processing helix  chain 'E' and resid 397 through 413
      removed outlier: 4.235A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   MET E 408 " --> pdb=" O   VAL E 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 414 through 421
    Processing helix  chain 'E' and resid 431 through 447
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.310A  pdb=" N   PHE E 452 " --> pdb=" O   GLY E 448 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 469 through 471
      No H-bonds generated for 'chain 'E' and resid 469 through 471'
    Processing helix  chain 'E' and resid 472 through 484
    Processing helix  chain 'E' and resid 499 through 502
      removed outlier: 3.726A  pdb=" N   SER E 502 " --> pdb=" O   ASP E 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 499 through 502'
    Processing helix  chain 'E' and resid 503 through 508
    Processing helix  chain 'E' and resid 512 through 533
      removed outlier: 4.458A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE E 523 " --> pdb=" O   THR E 519 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 538 through 542
    Processing helix  chain 'E' and resid 547 through 559
      removed outlier: 3.931A  pdb=" N   MET E 557 " --> pdb=" O   LYS E 553 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 565 through 574
    Processing helix  chain 'E' and resid 581 through 588
    Processing helix  chain 'E' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.911A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132
      removed outlier: 3.620A  pdb=" N   LEU E 142 " --> pdb=" O   VAL E 132 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263
      removed outlier: 5.966A  pdb=" N   LEU E 262 " --> pdb=" O   VAL E 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352
      removed outlier: 6.313A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    323 hydrogen bonds defined for protein.
    918 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: 0.78

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2086
        1.35 -     1.47: 1795
        1.47 -     1.60: 2796
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6735
  Sorted by residual:
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.458 -0.052 2.00e-02 2.50e+03 6.64e+00
  bond pdb=" C1  NAG E 704 "
       pdb=" O5  NAG E 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.452 -0.046 2.00e-02 2.50e+03 5.20e+00
  bond pdb=" C1  NAG E 705 "
       pdb=" O5  NAG E 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.35e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 3.95e+00
  bond pdb=" C   SER E 611 "
       pdb=" N   PRO E 612 "
    ideal  model  delta    sigma   weight residual
    1.334  1.379 -0.045 2.34e-02 1.83e+03 3.73e+00
  ... (remaining 6730 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 8817
        2.05 -     4.10: 289
        4.10 -     6.15: 36
        6.15 -     8.20: 6
        8.20 -    10.24: 4
  Bond angle restraints: 9152
  Sorted by residual:
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.82  128.96   -6.14 1.42e+00 4.96e-01 1.87e+01
  angle pdb=" CA  CYS E 141 "
        pdb=" CB  CYS E 141 "
        pdb=" SG  CYS E 141 "
      ideal   model   delta    sigma   weight residual
     114.40  123.65   -9.25 2.30e+00 1.89e-01 1.62e+01
  angle pdb=" CB  MET E 323 "
        pdb=" CG  MET E 323 "
        pdb=" SD  MET E 323 "
      ideal   model   delta    sigma   weight residual
     112.70  122.94  -10.24 3.00e+00 1.11e-01 1.17e+01
  angle pdb=" CA  ASN E 437 "
        pdb=" CB  ASN E 437 "
        pdb=" CG  ASN E 437 "
      ideal   model   delta    sigma   weight residual
     112.60  115.96   -3.36 1.00e+00 1.00e+00 1.13e+01
  angle pdb=" N   LYS E 234 "
        pdb=" CA  LYS E 234 "
        pdb=" C   LYS E 234 "
      ideal   model   delta    sigma   weight residual
     113.16  117.68   -4.52 1.42e+00 4.96e-01 1.01e+01
  ... (remaining 9147 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 3688
       17.12 -    34.25: 314
       34.25 -    51.37: 43
       51.37 -    68.50: 11
       68.50 -    85.62: 12
  Dihedral angle restraints: 4068
    sinusoidal: 1730
      harmonic: 2338
  Sorted by residual:
  dihedral pdb=" CB  CYS E 133 "
           pdb=" SG  CYS E 133 "
           pdb=" SG  CYS E 141 "
           pdb=" CB  CYS E 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -42.93  -43.07     1      1.00e+01 1.00e-02 2.59e+01
  dihedral pdb=" SG  CYS B 391 "
           pdb=" CB  CYS B 525 "
           pdb=" SG  CYS B 525 "
           pdb=" CA  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   17.52   61.48     1      2.00e+01 2.50e-03 1.25e+01
  dihedral pdb=" C   ASN B 360 "
           pdb=" N   ASN B 360 "
           pdb=" CA  ASN B 360 "
           pdb=" CB  ASN B 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.76    8.16     0      2.50e+00 1.60e-01 1.06e+01
  ... (remaining 4065 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 724
       0.055 -    0.109: 197
       0.109 -    0.164: 46
       0.164 -    0.218: 7
       0.218 -    0.273: 3
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" CA  ASN B 360 "
            pdb=" N   ASN B 360 "
            pdb=" C   ASN B 360 "
            pdb=" CB  ASN B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CB  VAL E 581 "
            pdb=" CA  VAL E 581 "
            pdb=" CG1 VAL E 581 "
            pdb=" CG2 VAL E 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CB  VAL E 318 "
            pdb=" CA  VAL E 318 "
            pdb=" CG1 VAL E 318 "
            pdb=" CG2 VAL E 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 974 not shown)

  Planarity restraints: 1185
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E  36 "    0.025 2.00e-02 2.50e+03   4.97e-02 2.47e+01
        pdb=" C   ALA E  36 "   -0.086 2.00e-02 2.50e+03
        pdb=" O   ALA E  36 "    0.032 2.00e-02 2.50e+03
        pdb=" N   GLU E  37 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 169 "    0.017 2.00e-02 2.50e+03   3.46e-02 1.20e+01
        pdb=" C   ARG E 169 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   ARG E 169 "    0.022 2.00e-02 2.50e+03
        pdb=" N   SER E 170 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE E  32 "    0.015 2.00e-02 2.50e+03   3.05e-02 9.31e+00
        pdb=" C   PHE E  32 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   PHE E  32 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ASN E  33 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1182 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1834
        2.82 -     3.34: 5957
        3.34 -     3.86: 11435
        3.86 -     4.38: 12999
        4.38 -     4.90: 22431
  Nonbonded interactions: 54656
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 500 "
            pdb=" OH  TYR E  41 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" OE1 GLU B 406 "
            pdb=" OH  TYR B 495 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" OD1 ASN B 487 "
            pdb=" OH  TYR E  83 "
     model   vdw
     2.338 3.040
  ... (remaining 54651 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.230
  Find NCS groups from input model:        0.030
  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:6.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
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   0.057   6748  Z= 0.237
  Angle     :  0.875  12.746   9185  Z= 0.467
  Chirality :  0.055   0.273    977
  Planarity :  0.007   0.065   1178
  Dihedral  : 13.353  85.622   2550
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.26), residues: 793
  helix: -0.06 (0.23), residues: 387
  sheet:  0.55 (0.66), residues: 52
  loop : -0.63 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E 460 
 TYR   0.032   0.002   TYR E 385 
 PHE   0.030   0.003   PHE E 369 
 TRP   0.022   0.002   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 6735)
  covalent geometry    : angle       0.84349 ( 9152)
  SS BOND              : bond        0.00598 (    6)
  SS BOND              : angle       2.68049 (   12)
  hydrogen bonds       : bond        0.14199 (  323)
  hydrogen bonds       : angle       6.30716 (  918)
  link_NAG-ASN         : bond        0.00898 (    7)
  link_NAG-ASN         : angle       4.58467 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: E  142 LEU cc_start: 0.9130 (mt) cc_final: 0.8923 (mt)
REVERT: E  149 ASN cc_start: 0.9200 (m-40) cc_final: 0.8949 (m-40)
REVERT: E  249 MET cc_start: 0.9324 (ttm) cc_final: 0.9031 (ttp)
REVERT: E  290 ASN cc_start: 0.8984 (t0) cc_final: 0.8685 (t0)
REVERT: E  347 THR cc_start: 0.8821 (m) cc_final: 0.8354 (p)
REVERT: E  371 THR cc_start: 0.9207 (m) cc_final: 0.8930 (p)
REVERT: E  441 LYS cc_start: 0.8993 (tttp) cc_final: 0.8594 (ttmm)
REVERT: E  455 MET cc_start: 0.8781 (tmm) cc_final: 0.8460 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.6059
  time to fit residues: 80.4551
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
E 154 ASN
** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.077607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.059744 restraints weight = 18247.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 3.47
r_work: 0.2844 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6748  Z= 0.137
  Angle     :  0.586   9.466   9185  Z= 0.298
  Chirality :  0.041   0.144    977
  Planarity :  0.005   0.039   1178
  Dihedral  :  4.959  48.432   1013
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  9.86 %
    Favored  : 88.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.28), residues: 793
  helix:  1.01 (0.25), residues: 402
  sheet:  0.85 (0.75), residues: 43
  loop : -0.11 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 466 
 TYR   0.011   0.001   TYR E 385 
 PHE   0.014   0.001   PHE E 369 
 TRP   0.018   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6735)
  covalent geometry    : angle       0.56302 ( 9152)
  SS BOND              : bond        0.00446 (    6)
  SS BOND              : angle       2.07481 (   12)
  hydrogen bonds       : bond        0.04144 (  323)
  hydrogen bonds       : angle       4.62767 (  918)
  link_NAG-ASN         : bond        0.00565 (    7)
  link_NAG-ASN         : angle       3.09137 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.267 
Fit side-chains
REVERT: B  484 GLU cc_start: 0.8781 (tt0) cc_final: 0.8532 (tp30)
REVERT: E   55 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8670 (p)
REVERT: E  149 ASN cc_start: 0.9212 (m-40) cc_final: 0.8889 (m110)
REVERT: E  224 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8208 (pp20)
REVERT: E  249 MET cc_start: 0.9296 (ttm) cc_final: 0.9004 (ttp)
REVERT: E  347 THR cc_start: 0.8785 (m) cc_final: 0.8312 (p)
REVERT: E  360 MET cc_start: 0.9121 (ttp) cc_final: 0.8764 (ttm)
REVERT: E  366 MET cc_start: 0.8569 (ttp) cc_final: 0.8321 (ttm)
REVERT: E  371 THR cc_start: 0.9150 (m) cc_final: 0.8941 (p)
REVERT: E  441 LYS cc_start: 0.8966 (tttp) cc_final: 0.8549 (ttmm)
REVERT: E  455 MET cc_start: 0.9099 (tmm) cc_final: 0.8828 (tmm)
REVERT: E  474 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7325 (mmt)
REVERT: E  578 ASN cc_start: 0.8504 (t0) cc_final: 0.8218 (p0)
  outliers start: 11
  outliers final: 4
  residues processed: 64
  average time/residue: 0.5682
  time to fit residues: 38.3908
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 6 optimal weight:    0.0000
   chunk 29 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 78 optimal weight:    7.9990
   chunk 36 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.6586

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

Flipped N/Q/H residues before XYZ refinement:
E 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.076436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.058419 restraints weight = 17996.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 3.44
r_work: 0.2827 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6748  Z= 0.133
  Angle     :  0.536   7.587   9185  Z= 0.271
  Chirality :  0.040   0.142    977
  Planarity :  0.004   0.042   1178
  Dihedral  :  4.663  50.690   1013
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.71 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.21 (0.29), residues: 793
  helix:  1.43 (0.26), residues: 402
  sheet:  0.88 (0.78), residues: 42
  loop :  0.15 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 466 
 TYR   0.012   0.001   TYR E 385 
 PHE   0.014   0.001   PHE E 369 
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6735)
  covalent geometry    : angle       0.51817 ( 9152)
  SS BOND              : bond        0.00347 (    6)
  SS BOND              : angle       1.36495 (   12)
  hydrogen bonds       : bond        0.03997 (  323)
  hydrogen bonds       : angle       4.33977 (  918)
  link_NAG-ASN         : bond        0.00471 (    7)
  link_NAG-ASN         : angle       2.77359 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: B  523 THR cc_start: 0.8559 (p) cc_final: 0.8302 (t)
REVERT: E  149 ASN cc_start: 0.9247 (m-40) cc_final: 0.8846 (m110)
REVERT: E  224 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8235 (pp20)
REVERT: E  249 MET cc_start: 0.9267 (ttm) cc_final: 0.8917 (ttp)
REVERT: E  332 MET cc_start: 0.8656 (ttp) cc_final: 0.8374 (ppp)
REVERT: E  347 THR cc_start: 0.8854 (m) cc_final: 0.8398 (p)
REVERT: E  366 MET cc_start: 0.8697 (ttp) cc_final: 0.8442 (ttm)
REVERT: E  441 LYS cc_start: 0.9064 (tttp) cc_final: 0.8606 (ttmm)
REVERT: E  455 MET cc_start: 0.9136 (tmm) cc_final: 0.8926 (tmm)
REVERT: E  578 ASN cc_start: 0.8572 (t0) cc_final: 0.8225 (p0)
  outliers start: 14
  outliers final: 5
  residues processed: 70
  average time/residue: 0.5209
  time to fit residues: 38.5517
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 26 optimal weight:    0.1980
   chunk 78 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    0.4980
   chunk 55 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.077134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.059496 restraints weight = 18414.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 3.40
r_work: 0.2816 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6748  Z= 0.137
  Angle     :  0.528   7.974   9185  Z= 0.267
  Chirality :  0.041   0.168    977
  Planarity :  0.004   0.040   1178
  Dihedral  :  4.562  51.486   1013
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 11.43 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.56 (0.30), residues: 793
  helix:  1.74 (0.26), residues: 387
  sheet:  0.81 (0.78), residues: 42
  loop :  0.40 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 457 
 TYR   0.011   0.001   TYR E 385 
 PHE   0.016   0.001   PHE E 369 
 TRP   0.014   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6735)
  covalent geometry    : angle       0.51431 ( 9152)
  SS BOND              : bond        0.00278 (    6)
  SS BOND              : angle       0.72301 (   12)
  hydrogen bonds       : bond        0.03875 (  323)
  hydrogen bonds       : angle       4.24665 (  918)
  link_NAG-ASN         : bond        0.00411 (    7)
  link_NAG-ASN         : angle       2.53130 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8740 (p)
REVERT: E  149 ASN cc_start: 0.9271 (m-40) cc_final: 0.8869 (m110)
REVERT: E  215 TYR cc_start: 0.8944 (m-10) cc_final: 0.8738 (m-80)
REVERT: E  224 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8223 (pp20)
REVERT: E  249 MET cc_start: 0.9282 (ttm) cc_final: 0.8958 (ttp)
REVERT: E  347 THR cc_start: 0.8878 (m) cc_final: 0.8424 (p)
REVERT: E  366 MET cc_start: 0.8659 (ttp) cc_final: 0.8422 (ttm)
REVERT: E  411 SER cc_start: 0.9028 (m) cc_final: 0.8820 (p)
REVERT: E  441 LYS cc_start: 0.9068 (tttp) cc_final: 0.8612 (ttmm)
REVERT: E  455 MET cc_start: 0.9165 (tmm) cc_final: 0.8945 (tmm)
REVERT: E  470 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8921 (tppp)
REVERT: E  522 GLN cc_start: 0.8546 (tt0) cc_final: 0.8190 (tt0)
  outliers start: 12
  outliers final: 6
  residues processed: 69
  average time/residue: 0.5578
  time to fit residues: 40.5976
Evaluate side-chains
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  470 LYS
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0070
   chunk 15 optimal weight:    0.0770
   chunk 23 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 33 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.076874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.058875 restraints weight = 18381.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 3.51
r_work: 0.2824 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6748  Z= 0.109
  Angle     :  0.502   9.187   9185  Z= 0.253
  Chirality :  0.040   0.141    977
  Planarity :  0.004   0.040   1178
  Dihedral  :  4.438  53.221   1013
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.71 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.70 (0.30), residues: 793
  helix:  1.86 (0.26), residues: 387
  sheet:  0.72 (0.77), residues: 42
  loop :  0.49 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 273 
 TYR   0.010   0.001   TYR E 385 
 PHE   0.014   0.001   PHE E 369 
 TRP   0.016   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6735)
  covalent geometry    : angle       0.49027 ( 9152)
  SS BOND              : bond        0.00251 (    6)
  SS BOND              : angle       0.64867 (   12)
  hydrogen bonds       : bond        0.03683 (  323)
  hydrogen bonds       : angle       4.14688 (  918)
  link_NAG-ASN         : bond        0.00384 (    7)
  link_NAG-ASN         : angle       2.29600 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8838 (p)
REVERT: E   75 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8435 (mp0)
REVERT: E  149 ASN cc_start: 0.9272 (m-40) cc_final: 0.8941 (m110)
REVERT: E  224 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8267 (pp20)
REVERT: E  249 MET cc_start: 0.9322 (ttm) cc_final: 0.8993 (ttp)
REVERT: E  323 MET cc_start: 0.9380 (mmm) cc_final: 0.8861 (mmm)
REVERT: E  332 MET cc_start: 0.8651 (ttp) cc_final: 0.8390 (ppp)
REVERT: E  347 THR cc_start: 0.8884 (m) cc_final: 0.8438 (p)
REVERT: E  441 LYS cc_start: 0.9085 (tttp) cc_final: 0.8559 (ttmm)
REVERT: E  552 GLN cc_start: 0.8973 (tp40) cc_final: 0.8558 (tm-30)
REVERT: E  571 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.8837 (tp30)
REVERT: E  578 ASN cc_start: 0.8613 (t0) cc_final: 0.8233 (p0)
  outliers start: 12
  outliers final: 5
  residues processed: 67
  average time/residue: 0.5801
  time to fit residues: 40.9530
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  571 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 50 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.074993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.056944 restraints weight = 18524.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 3.46
r_work: 0.2789 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6748  Z= 0.150
  Angle     :  0.529   7.112   9185  Z= 0.267
  Chirality :  0.041   0.144    977
  Planarity :  0.004   0.039   1178
  Dihedral  :  4.471  52.873   1013
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.57 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.79 (0.30), residues: 793
  helix:  1.89 (0.27), residues: 388
  sheet:  0.86 (0.79), residues: 42
  loop :  0.59 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG E 192 
 TYR   0.011   0.001   TYR E 385 
 PHE   0.014   0.001   PHE E 369 
 TRP   0.018   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6735)
  covalent geometry    : angle       0.51938 ( 9152)
  SS BOND              : bond        0.00256 (    6)
  SS BOND              : angle       0.62412 (   12)
  hydrogen bonds       : bond        0.03866 (  323)
  hydrogen bonds       : angle       4.17400 (  918)
  link_NAG-ASN         : bond        0.00352 (    7)
  link_NAG-ASN         : angle       2.19446 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8746 (p)
REVERT: E  149 ASN cc_start: 0.9298 (m-40) cc_final: 0.8977 (m110)
REVERT: E  224 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8293 (pp20)
REVERT: E  249 MET cc_start: 0.9281 (ttm) cc_final: 0.8898 (ttp)
REVERT: E  347 THR cc_start: 0.8890 (m) cc_final: 0.8492 (p)
REVERT: E  366 MET cc_start: 0.8852 (ttp) cc_final: 0.8644 (ttt)
REVERT: E  441 LYS cc_start: 0.9074 (tttp) cc_final: 0.8619 (tppp)
REVERT: E  552 GLN cc_start: 0.8970 (tp40) cc_final: 0.8573 (tm-30)
  outliers start: 13
  outliers final: 6
  residues processed: 65
  average time/residue: 0.5917
  time to fit residues: 40.4936
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 62 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.076098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.058724 restraints weight = 18637.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 3.41
r_work: 0.2790 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6748  Z= 0.139
  Angle     :  0.529   6.950   9185  Z= 0.267
  Chirality :  0.041   0.139    977
  Planarity :  0.004   0.039   1178
  Dihedral  :  4.458  53.977   1013
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.00 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.84 (0.30), residues: 793
  helix:  1.91 (0.26), residues: 386
  sheet:  0.88 (0.80), residues: 42
  loop :  0.65 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 192 
 TYR   0.010   0.001   TYR E 515 
 PHE   0.013   0.001   PHE E 369 
 TRP   0.020   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6735)
  covalent geometry    : angle       0.51984 ( 9152)
  SS BOND              : bond        0.00334 (    6)
  SS BOND              : angle       0.67174 (   12)
  hydrogen bonds       : bond        0.03814 (  323)
  hydrogen bonds       : angle       4.18730 (  918)
  link_NAG-ASN         : bond        0.00332 (    7)
  link_NAG-ASN         : angle       2.09949 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.231 
Fit side-chains
REVERT: E   55 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8781 (p)
REVERT: E   75 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8408 (mp0)
REVERT: E  149 ASN cc_start: 0.9270 (m-40) cc_final: 0.8989 (m110)
REVERT: E  224 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8303 (pp20)
REVERT: E  249 MET cc_start: 0.9295 (ttm) cc_final: 0.8940 (ttp)
REVERT: E  323 MET cc_start: 0.9371 (mmm) cc_final: 0.9136 (mmm)
REVERT: E  347 THR cc_start: 0.8881 (m) cc_final: 0.8516 (p)
REVERT: E  441 LYS cc_start: 0.9064 (tttp) cc_final: 0.8620 (tppp)
REVERT: E  455 MET cc_start: 0.9092 (tmm) cc_final: 0.8608 (tpt)
REVERT: E  552 GLN cc_start: 0.8976 (tp40) cc_final: 0.8577 (tm-30)
  outliers start: 14
  outliers final: 6
  residues processed: 65
  average time/residue: 0.5668
  time to fit residues: 38.7978
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  411 SER
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 76 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0870
   chunk 35 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.075310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.057489 restraints weight = 18519.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 3.45
r_work: 0.2802 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.3087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6748  Z= 0.127
  Angle     :  0.536   8.727   9185  Z= 0.270
  Chirality :  0.040   0.133    977
  Planarity :  0.004   0.043   1178
  Dihedral  :  4.444  54.601   1013
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.71 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.78 (0.30), residues: 793
  helix:  1.89 (0.26), residues: 387
  sheet:  0.67 (0.79), residues: 44
  loop :  0.60 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 192 
 TYR   0.010   0.001   TYR E 516 
 PHE   0.013   0.001   PHE E 369 
 TRP   0.022   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6735)
  covalent geometry    : angle       0.52599 ( 9152)
  SS BOND              : bond        0.00217 (    6)
  SS BOND              : angle       1.32605 (   12)
  hydrogen bonds       : bond        0.03724 (  323)
  hydrogen bonds       : angle       4.16097 (  918)
  link_NAG-ASN         : bond        0.00310 (    7)
  link_NAG-ASN         : angle       2.03994 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.189 
Fit side-chains
REVERT: E   55 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8771 (p)
REVERT: E  224 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8331 (pp20)
REVERT: E  249 MET cc_start: 0.9296 (ttm) cc_final: 0.8944 (ttp)
REVERT: E  323 MET cc_start: 0.9318 (mmm) cc_final: 0.9113 (mmm)
REVERT: E  329 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8572 (mt-10)
REVERT: E  347 THR cc_start: 0.8911 (m) cc_final: 0.8567 (p)
REVERT: E  441 LYS cc_start: 0.9054 (tttp) cc_final: 0.8599 (tppp)
REVERT: E  455 MET cc_start: 0.9095 (tmm) cc_final: 0.8611 (tpt)
REVERT: E  552 GLN cc_start: 0.8966 (tp40) cc_final: 0.8565 (tm-30)
REVERT: E  578 ASN cc_start: 0.8559 (t0) cc_final: 0.8226 (p0)
  outliers start: 12
  outliers final: 6
  residues processed: 62
  average time/residue: 0.5779
  time to fit residues: 37.8422
Evaluate side-chains
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  411 SER
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.075763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.057976 restraints weight = 18772.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.2923 rms_B_bonded: 3.44
r_work: 0.2785 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6748  Z= 0.143
  Angle     :  0.551   8.794   9185  Z= 0.278
  Chirality :  0.041   0.168    977
  Planarity :  0.004   0.041   1178
  Dihedral  :  4.434  54.402   1013
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.14 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.81 (0.30), residues: 793
  helix:  1.88 (0.26), residues: 386
  sheet:  0.70 (0.79), residues: 44
  loop :  0.66 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 192 
 TYR   0.010   0.001   TYR E 515 
 PHE   0.014   0.001   PHE E 369 
 TRP   0.024   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6735)
  covalent geometry    : angle       0.54176 ( 9152)
  SS BOND              : bond        0.00205 (    6)
  SS BOND              : angle       1.10867 (   12)
  hydrogen bonds       : bond        0.03841 (  323)
  hydrogen bonds       : angle       4.17857 (  918)
  link_NAG-ASN         : bond        0.00304 (    7)
  link_NAG-ASN         : angle       2.01273 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8735 (p)
REVERT: E  224 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8349 (pp20)
REVERT: E  249 MET cc_start: 0.9297 (ttm) cc_final: 0.8946 (ttp)
REVERT: E  347 THR cc_start: 0.8922 (m) cc_final: 0.8627 (p)
REVERT: E  441 LYS cc_start: 0.9067 (tttp) cc_final: 0.8609 (tppp)
REVERT: E  455 MET cc_start: 0.9089 (tmm) cc_final: 0.8552 (tpt)
REVERT: E  552 GLN cc_start: 0.8966 (tp40) cc_final: 0.8565 (tm-30)
REVERT: E  578 ASN cc_start: 0.8582 (t0) cc_final: 0.8223 (p0)
  outliers start: 12
  outliers final: 6
  residues processed: 61
  average time/residue: 0.5950
  time to fit residues: 38.3056
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  411 SER
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.074088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.056298 restraints weight = 18429.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 3.42
r_work: 0.2767 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.3208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6748  Z= 0.168
  Angle     :  0.575   9.111   9185  Z= 0.289
  Chirality :  0.042   0.143    977
  Planarity :  0.004   0.040   1178
  Dihedral  :  4.556  54.157   1013
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.29 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.84 (0.30), residues: 793
  helix:  1.89 (0.26), residues: 386
  sheet:  0.66 (0.79), residues: 44
  loop :  0.72 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 192 
 TYR   0.011   0.001   TYR E 515 
 PHE   0.014   0.001   PHE E 369 
 TRP   0.024   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 6735)
  covalent geometry    : angle       0.56537 ( 9152)
  SS BOND              : bond        0.00236 (    6)
  SS BOND              : angle       1.04381 (   12)
  hydrogen bonds       : bond        0.03962 (  323)
  hydrogen bonds       : angle       4.26244 (  918)
  link_NAG-ASN         : bond        0.00309 (    7)
  link_NAG-ASN         : angle       2.12693 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: B  420 ASP cc_start: 0.8815 (m-30) cc_final: 0.8562 (p0)
REVERT: E   55 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8662 (p)
REVERT: E  224 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8325 (pp20)
REVERT: E  249 MET cc_start: 0.9308 (ttm) cc_final: 0.8951 (ttp)
REVERT: E  347 THR cc_start: 0.8925 (m) cc_final: 0.8639 (p)
REVERT: E  441 LYS cc_start: 0.9074 (tttp) cc_final: 0.8605 (tppp)
REVERT: E  455 MET cc_start: 0.9099 (tmm) cc_final: 0.8593 (tpt)
REVERT: E  552 GLN cc_start: 0.8980 (tp40) cc_final: 0.8579 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 55
  average time/residue: 0.5674
  time to fit residues: 32.9247
Evaluate side-chains
  53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  224 GLU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  411 SER
Chi-restraints excluded: chain E residue  425 SER
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0670
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:
** E  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.074596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.056838 restraints weight = 18538.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 3.45
r_work: 0.2774 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6748  Z= 0.145
  Angle     :  0.561   9.329   9185  Z= 0.281
  Chirality :  0.041   0.148    977
  Planarity :  0.004   0.041   1178
  Dihedral  :  4.547  54.774   1013
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.57 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.83 (0.30), residues: 793
  helix:  1.87 (0.26), residues: 386
  sheet:  0.60 (0.79), residues: 44
  loop :  0.72 (0.35), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 192 
 TYR   0.010   0.001   TYR E 515 
 PHE   0.013   0.001   PHE E 369 
 TRP   0.024   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6735)
  covalent geometry    : angle       0.55237 ( 9152)
  SS BOND              : bond        0.00233 (    6)
  SS BOND              : angle       0.88499 (   12)
  hydrogen bonds       : bond        0.03861 (  323)
  hydrogen bonds       : angle       4.25726 (  918)
  link_NAG-ASN         : bond        0.00301 (    7)
  link_NAG-ASN         : angle       2.07616 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1915.37 seconds
wall clock time: 33 minutes 27.34 seconds (2007.34 seconds total)