Starting phenix.real_space_refine
on Thu Jul 24 22:26:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sy0_25512/07_2025/7sy0_25512.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sy0_25512/07_2025/7sy0_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sy0_25512/07_2025/7sy0_25512.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sy0_25512/07_2025/7sy0_25512.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sy0_25512/07_2025/7sy0_25512.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sy0_25512/07_2025/7sy0_25512.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.35, per 1000 atoms: 0.82
  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: 1.54
  Conformation dependent library (CDL) restraints added in 968.4 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: 0.74
  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: 1.80

  Time building geometry restraints manager: 1.78 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:             3.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.470
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.370
-------------------------------------------------------------------------------
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 : 2.42
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.022   0.002   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.030   0.003   PHE E 369 
 TYR   0.032   0.002   TYR E 385 
 ARG   0.011   0.001   ARG E 460 

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

*********************** 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  : 0.763 
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: 0.8572 (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: 1.2409
  time to fit residues: 165.2832
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  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0470
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.6880

-------------------------------------------------------------------------------
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 = 0.3356 r_free = 0.3356 target = 0.077169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.059361 restraints weight = 18170.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 3.47
r_work: 0.2834 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6748  Z= 0.143
  Angle     :  0.588   9.284   9185  Z= 0.300
  Chirality :  0.041   0.143    977
  Planarity :  0.005   0.039   1178
  Dihedral  :  4.991  48.531   1013
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.57 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.28), residues: 793
  helix:  1.01 (0.25), residues: 403
  sheet:  0.86 (0.75), residues: 43
  loop : -0.10 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 385 
 ARG   0.004   0.000   ARG B 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00550 (    7)
  link_NAG-ASN         : angle       3.12951 (   21)
  hydrogen bonds       : bond        0.04212 (  323)
  hydrogen bonds       : angle       4.63841 (  918)
  SS BOND              : bond        0.00452 (    6)
  SS BOND              : angle       2.07274 (   12)
  covalent geometry    : bond        0.00315 ( 6735)
  covalent geometry    : angle       0.56502 ( 9152)

*********************** 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
  70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.715 
Fit side-chains
REVERT: B  484 GLU cc_start: 0.8779 (tt0) cc_final: 0.8529 (tp30)
REVERT: E   55 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8664 (p)
REVERT: E  149 ASN cc_start: 0.9210 (m-40) cc_final: 0.8883 (m110)
REVERT: E  224 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8218 (pp20)
REVERT: E  249 MET cc_start: 0.9307 (ttm) cc_final: 0.9013 (ttp)
REVERT: E  347 THR cc_start: 0.8793 (m) cc_final: 0.8320 (p)
REVERT: E  360 MET cc_start: 0.9133 (ttp) cc_final: 0.8863 (ttm)
REVERT: E  366 MET cc_start: 0.8584 (ttp) cc_final: 0.8379 (ttm)
REVERT: E  371 THR cc_start: 0.9152 (m) cc_final: 0.8940 (p)
REVERT: E  441 LYS cc_start: 0.8983 (tttp) cc_final: 0.8601 (ttmm)
REVERT: E  455 MET cc_start: 0.9109 (tmm) cc_final: 0.8849 (tmm)
REVERT: E  474 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7319 (mmt)
REVERT: E  578 ASN cc_start: 0.8509 (t0) cc_final: 0.8223 (p0)
  outliers start: 13
  outliers final: 4
  residues processed: 66
  average time/residue: 1.1809
  time to fit residues: 82.5387
Evaluate side-chains
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
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 28 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    0.3980
   chunk 77 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0970
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.3362 r_free = 0.3362 target = 0.077663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.059370 restraints weight = 17819.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 3.47
r_work: 0.2805 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2318

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= 0.127
  Angle     :  0.535   7.559   9185  Z= 0.270
  Chirality :  0.040   0.140    977
  Planarity :  0.004   0.041   1178
  Dihedral  :  4.657  50.881   1013
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.00 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.29), residues: 793
  helix:  1.56 (0.26), residues: 393
  sheet:  0.91 (0.78), residues: 42
  loop :  0.21 (0.33), residues: 358

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

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00473 (    7)
  link_NAG-ASN         : angle       2.76520 (   21)
  hydrogen bonds       : bond        0.03961 (  323)
  hydrogen bonds       : angle       4.32693 (  918)
  SS BOND              : bond        0.00309 (    6)
  SS BOND              : angle       1.37035 (   12)
  covalent geometry    : bond        0.00285 ( 6735)
  covalent geometry    : angle       0.51734 ( 9152)

*********************** 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
  69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
REVERT: B  523 THR cc_start: 0.8531 (p) cc_final: 0.8269 (t)
REVERT: E  149 ASN cc_start: 0.9221 (m-40) cc_final: 0.8834 (m110)
REVERT: E  224 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8220 (pp20)
REVERT: E  249 MET cc_start: 0.9230 (ttm) cc_final: 0.8885 (ttp)
REVERT: E  347 THR cc_start: 0.8840 (m) cc_final: 0.8373 (p)
REVERT: E  441 LYS cc_start: 0.9008 (tttp) cc_final: 0.8550 (ttmm)
REVERT: E  455 MET cc_start: 0.9098 (tmm) cc_final: 0.8880 (tmm)
REVERT: E  578 ASN cc_start: 0.8555 (t0) cc_final: 0.8207 (p0)
  outliers start: 11
  outliers final: 6
  residues processed: 67
  average time/residue: 1.1252
  time to fit residues: 80.1662
Evaluate side-chains
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
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   91 LEU
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 63 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 15 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3333 r_free = 0.3333 target = 0.075785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.057840 restraints weight = 18371.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 3.44
r_work: 0.2804 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6748  Z= 0.145
  Angle     :  0.527   7.877   9185  Z= 0.267
  Chirality :  0.041   0.161    977
  Planarity :  0.004   0.040   1178
  Dihedral  :  4.581  51.371   1013
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 11.29 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.30), residues: 793
  helix:  1.75 (0.26), residues: 387
  sheet:  0.61 (0.77), residues: 44
  loop :  0.38 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00401 (    7)
  link_NAG-ASN         : angle       2.52886 (   21)
  hydrogen bonds       : bond        0.03920 (  323)
  hydrogen bonds       : angle       4.25595 (  918)
  SS BOND              : bond        0.00279 (    6)
  SS BOND              : angle       0.72043 (   12)
  covalent geometry    : bond        0.00326 ( 6735)
  covalent geometry    : angle       0.51333 ( 9152)

*********************** 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
  68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.723 
Fit side-chains
REVERT: B  484 GLU cc_start: 0.8766 (tt0) cc_final: 0.8562 (tp30)
REVERT: B  523 THR cc_start: 0.8431 (p) cc_final: 0.8211 (t)
REVERT: E   55 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8693 (p)
REVERT: E  149 ASN cc_start: 0.9259 (m-40) cc_final: 0.8883 (m110)
REVERT: E  224 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8253 (pp20)
REVERT: E  249 MET cc_start: 0.9286 (ttm) cc_final: 0.8958 (ttp)
REVERT: E  347 THR cc_start: 0.8886 (m) cc_final: 0.8435 (p)
REVERT: E  441 LYS cc_start: 0.9080 (tttp) cc_final: 0.8627 (ttmm)
REVERT: E  455 MET cc_start: 0.9172 (tmm) cc_final: 0.8959 (tmm)
REVERT: E  522 GLN cc_start: 0.8579 (tt0) cc_final: 0.8268 (tt0)
  outliers start: 14
  outliers final: 6
  residues processed: 66
  average time/residue: 1.1939
  time to fit residues: 83.5309
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
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  506 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0570
   chunk 49 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.3335 r_free = 0.3335 target = 0.076027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.057998 restraints weight = 18175.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 3.46
r_work: 0.2809 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.2748

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= 0.128
  Angle     :  0.512   8.624   9185  Z= 0.259
  Chirality :  0.041   0.132    977
  Planarity :  0.004   0.040   1178
  Dihedral  :  4.485  52.827   1013
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.30), residues: 793
  helix:  1.84 (0.27), residues: 387
  sheet:  0.83 (0.78), residues: 42
  loop :  0.51 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.011   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00378 (    7)
  link_NAG-ASN         : angle       2.31623 (   21)
  hydrogen bonds       : bond        0.03802 (  323)
  hydrogen bonds       : angle       4.18908 (  918)
  SS BOND              : bond        0.00251 (    6)
  SS BOND              : angle       0.67222 (   12)
  covalent geometry    : bond        0.00288 ( 6735)
  covalent geometry    : angle       0.50004 ( 9152)

*********************** 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
  66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8787 (p)
REVERT: E  149 ASN cc_start: 0.9273 (m-40) cc_final: 0.8961 (m110)
REVERT: E  224 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8234 (pp20)
REVERT: E  249 MET cc_start: 0.9336 (ttm) cc_final: 0.8994 (ttp)
REVERT: E  347 THR cc_start: 0.8915 (m) cc_final: 0.8506 (p)
REVERT: E  366 MET cc_start: 0.8782 (ttp) cc_final: 0.8456 (ttm)
REVERT: E  441 LYS cc_start: 0.9068 (tttp) cc_final: 0.8608 (ttmm)
REVERT: E  455 MET cc_start: 0.9172 (tmm) cc_final: 0.8972 (tmm)
  outliers start: 12
  outliers final: 7
  residues processed: 64
  average time/residue: 1.2322
  time to fit residues: 83.4191
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
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   91 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0030
   chunk 56 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 28 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5590

-------------------------------------------------------------------------------
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 = 0.3335 r_free = 0.3335 target = 0.075898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.058099 restraints weight = 18093.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 3.36
r_work: 0.2813 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6748  Z= 0.121
  Angle     :  0.518  10.399   9185  Z= 0.260
  Chirality :  0.040   0.144    977
  Planarity :  0.004   0.039   1178
  Dihedral  :  4.438  53.618   1013
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.71 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.30), residues: 793
  helix:  1.88 (0.26), residues: 387
  sheet:  0.57 (0.77), residues: 44
  loop :  0.56 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.010   0.001   TYR E 385 
 ARG   0.008   0.000   ARG E 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00345 (    7)
  link_NAG-ASN         : angle       2.17028 (   21)
  hydrogen bonds       : bond        0.03721 (  323)
  hydrogen bonds       : angle       4.17431 (  918)
  SS BOND              : bond        0.00237 (    6)
  SS BOND              : angle       0.62592 (   12)
  covalent geometry    : bond        0.00273 ( 6735)
  covalent geometry    : angle       0.50755 ( 9152)

*********************** 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
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
REVERT: B  468 ILE cc_start: 0.9237 (pt) cc_final: 0.9000 (pp)
REVERT: E   55 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8756 (p)
REVERT: E   75 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8418 (mp0)
REVERT: E  149 ASN cc_start: 0.9268 (m-40) cc_final: 0.8974 (m110)
REVERT: E  152 MET cc_start: 0.8083 (mmm) cc_final: 0.7862 (mmp)
REVERT: E  224 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8276 (pp20)
REVERT: E  249 MET cc_start: 0.9297 (ttm) cc_final: 0.8928 (ttp)
REVERT: E  323 MET cc_start: 0.9371 (mmm) cc_final: 0.8997 (mmm)
REVERT: E  332 MET cc_start: 0.8541 (ttp) cc_final: 0.8268 (ppp)
REVERT: E  347 THR cc_start: 0.8908 (m) cc_final: 0.8511 (p)
REVERT: E  441 LYS cc_start: 0.9064 (tttp) cc_final: 0.8607 (tppp)
REVERT: E  552 GLN cc_start: 0.8975 (tp40) cc_final: 0.8579 (tm-30)
  outliers start: 13
  outliers final: 5
  residues processed: 63
  average time/residue: 1.0911
  time to fit residues: 73.4342
Evaluate side-chains
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
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 38 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   chunk 42 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 60 optimal weight:    0.5980
   chunk 62 optimal weight:    0.4980
   chunk 67 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3329 r_free = 0.3329 target = 0.075676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.057881 restraints weight = 18289.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 3.39
r_work: 0.2802 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6748  Z= 0.130
  Angle     :  0.516   8.244   9185  Z= 0.260
  Chirality :  0.040   0.137    977
  Planarity :  0.003   0.038   1178
  Dihedral  :  4.408  54.001   1013
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.86 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.30), residues: 793
  helix:  1.91 (0.26), residues: 387
  sheet:  0.60 (0.78), residues: 44
  loop :  0.61 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.010   0.001   TYR E 515 
 ARG   0.006   0.000   ARG E 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00331 (    7)
  link_NAG-ASN         : angle       2.07824 (   21)
  hydrogen bonds       : bond        0.03750 (  323)
  hydrogen bonds       : angle       4.17005 (  918)
  SS BOND              : bond        0.00234 (    6)
  SS BOND              : angle       0.67561 (   12)
  covalent geometry    : bond        0.00295 ( 6735)
  covalent geometry    : angle       0.50672 ( 9152)

*********************** 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
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8759 (p)
REVERT: E   75 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8432 (mp0)
REVERT: E  149 ASN cc_start: 0.9299 (m-40) cc_final: 0.9027 (m110)
REVERT: E  224 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8300 (pp20)
REVERT: E  249 MET cc_start: 0.9357 (ttm) cc_final: 0.9016 (ttp)
REVERT: E  323 MET cc_start: 0.9363 (mmm) cc_final: 0.9096 (mmm)
REVERT: E  347 THR cc_start: 0.8926 (m) cc_final: 0.8567 (p)
REVERT: E  366 MET cc_start: 0.8851 (ttp) cc_final: 0.8595 (ttt)
REVERT: E  441 LYS cc_start: 0.9057 (tttp) cc_final: 0.8601 (tppp)
REVERT: E  552 GLN cc_start: 0.8966 (tp40) cc_final: 0.8561 (tm-30)
  outliers start: 14
  outliers final: 5
  residues processed: 63
  average time/residue: 1.1067
  time to fit residues: 74.2005
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  : 0.751 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 70 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 62 optimal weight:    0.3980
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3320 r_free = 0.3320 target = 0.075183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.057342 restraints weight = 18324.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 3.42
r_work: 0.2797 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.3075

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= 0.135
  Angle     :  0.532  11.144   9185  Z= 0.267
  Chirality :  0.041   0.136    977
  Planarity :  0.004   0.038   1178
  Dihedral  :  4.408  54.399   1013
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.29 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.30), residues: 793
  helix:  1.90 (0.26), residues: 387
  sheet:  0.65 (0.78), residues: 44
  loop :  0.69 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.010   0.001   TYR E 515 
 ARG   0.006   0.000   ARG E 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00309 (    7)
  link_NAG-ASN         : angle       2.02004 (   21)
  hydrogen bonds       : bond        0.03772 (  323)
  hydrogen bonds       : angle       4.18056 (  918)
  SS BOND              : bond        0.00272 (    6)
  SS BOND              : angle       0.72485 (   12)
  covalent geometry    : bond        0.00307 ( 6735)
  covalent geometry    : angle       0.52318 ( 9152)

*********************** 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
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8743 (p)
REVERT: E  149 ASN cc_start: 0.9256 (m-40) cc_final: 0.8980 (m110)
REVERT: E  152 MET cc_start: 0.8088 (mmm) cc_final: 0.7803 (mmp)
REVERT: E  224 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8329 (pp20)
REVERT: E  249 MET cc_start: 0.9370 (ttm) cc_final: 0.8994 (ttp)
REVERT: E  323 MET cc_start: 0.9316 (mmm) cc_final: 0.9089 (mmm)
REVERT: E  347 THR cc_start: 0.8902 (m) cc_final: 0.8601 (p)
REVERT: E  441 LYS cc_start: 0.9061 (tttp) cc_final: 0.8604 (tppp)
REVERT: E  455 MET cc_start: 0.9059 (tmm) cc_final: 0.8560 (tpt)
REVERT: E  552 GLN cc_start: 0.8969 (tp40) cc_final: 0.8562 (tm-30)
REVERT: E  578 ASN cc_start: 0.8667 (t0) cc_final: 0.8220 (p0)
  outliers start: 14
  outliers final: 6
  residues processed: 63
  average time/residue: 1.1146
  time to fit residues: 74.6952
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  : 0.765 
-------------------------------------------------------------------------------
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 20 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 41 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3319 r_free = 0.3319 target = 0.075074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.057249 restraints weight = 18525.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 3.44
r_work: 0.2791 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.3122

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= 0.140
  Angle     :  0.543  10.138   9185  Z= 0.273
  Chirality :  0.041   0.138    977
  Planarity :  0.004   0.040   1178
  Dihedral  :  4.463  54.578   1013
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.00 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.30), residues: 793
  helix:  1.90 (0.26), residues: 387
  sheet:  0.87 (0.80), residues: 42
  loop :  0.66 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.010   0.001   TYR E 515 
 ARG   0.005   0.000   ARG E 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00304 (    7)
  link_NAG-ASN         : angle       2.00609 (   21)
  hydrogen bonds       : bond        0.03795 (  323)
  hydrogen bonds       : angle       4.17992 (  918)
  SS BOND              : bond        0.00204 (    6)
  SS BOND              : angle       1.52851 (   12)
  covalent geometry    : bond        0.00319 ( 6735)
  covalent geometry    : angle       0.53283 ( 9152)

*********************** 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
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8737 (p)
REVERT: E  149 ASN cc_start: 0.9224 (m-40) cc_final: 0.8940 (m110)
REVERT: E  224 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8335 (pp20)
REVERT: E  249 MET cc_start: 0.9382 (ttm) cc_final: 0.9016 (ttp)
REVERT: E  323 MET cc_start: 0.9319 (mmm) cc_final: 0.9090 (mmm)
REVERT: E  347 THR cc_start: 0.8906 (m) cc_final: 0.8607 (p)
REVERT: E  441 LYS cc_start: 0.9066 (tttp) cc_final: 0.8607 (tppp)
REVERT: E  455 MET cc_start: 0.9090 (tmm) cc_final: 0.8604 (tpt)
REVERT: E  552 GLN cc_start: 0.8974 (tp40) cc_final: 0.8568 (tm-30)
REVERT: E  578 ASN cc_start: 0.8663 (t0) cc_final: 0.8216 (p0)
  outliers start: 12
  outliers final: 7
  residues processed: 62
  average time/residue: 1.2909
  time to fit residues: 84.7477
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0980
   chunk 50 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0170
   chunk 19 optimal weight:    0.2980
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.3818

-------------------------------------------------------------------------------
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 = 0.3344 r_free = 0.3344 target = 0.076615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.058651 restraints weight = 18635.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 3.54
r_work: 0.2821 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6748  Z= 0.109
  Angle     :  0.524   8.573   9185  Z= 0.264
  Chirality :  0.040   0.175    977
  Planarity :  0.004   0.042   1178
  Dihedral  :  4.363  55.609   1013
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 15.29 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.30), residues: 793
  helix:  1.92 (0.26), residues: 387
  sheet:  0.65 (0.79), residues: 44
  loop :  0.65 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP E 606 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.009   0.001   TYR E 516 
 ARG   0.005   0.000   ARG E 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00303 (    7)
  link_NAG-ASN         : angle       1.98153 (   21)
  hydrogen bonds       : bond        0.03591 (  323)
  hydrogen bonds       : angle       4.12121 (  918)
  SS BOND              : bond        0.00203 (    6)
  SS BOND              : angle       1.14152 (   12)
  covalent geometry    : bond        0.00245 ( 6735)
  covalent geometry    : angle       0.51445 ( 9152)

********************** 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
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
REVERT: B  420 ASP cc_start: 0.8801 (m-30) cc_final: 0.8542 (p0)
REVERT: B  468 ILE cc_start: 0.9237 (pt) cc_final: 0.9003 (pp)
REVERT: E   55 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8802 (p)
REVERT: E  149 ASN cc_start: 0.9215 (m-40) cc_final: 0.8934 (m110)
REVERT: E  224 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8352 (pp20)
REVERT: E  249 MET cc_start: 0.9362 (ttm) cc_final: 0.9003 (ttp)
REVERT: E  347 THR cc_start: 0.8900 (m) cc_final: 0.8605 (p)
REVERT: E  441 LYS cc_start: 0.9050 (tttp) cc_final: 0.8587 (ttmm)
REVERT: E  455 MET cc_start: 0.9073 (tmm) cc_final: 0.8607 (tpt)
REVERT: E  552 GLN cc_start: 0.8963 (tp40) cc_final: 0.8551 (tm-30)
REVERT: E  578 ASN cc_start: 0.8537 (t0) cc_final: 0.8210 (p0)
  outliers start: 8
  outliers final: 6
  residues processed: 60
  average time/residue: 1.0705
  time to fit residues: 68.8823
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
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 78 optimal weight:    7.9990
   chunk 63 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3321 r_free = 0.3321 target = 0.074970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.057221 restraints weight = 18695.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 3.45
r_work: 0.2792 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6748  Z= 0.143
  Angle     :  0.549   8.853   9185  Z= 0.276
  Chirality :  0.041   0.160    977
  Planarity :  0.004   0.041   1178
  Dihedral  :  4.433  54.567   1013
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.86 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.30), residues: 793
  helix:  1.90 (0.26), residues: 387
  sheet:  0.67 (0.79), residues: 44
  loop :  0.74 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP E 606 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.011   0.001   TYR E 516 
 ARG   0.007   0.000   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00299 (    7)
  link_NAG-ASN         : angle       1.94211 (   21)
  hydrogen bonds       : bond        0.03791 (  323)
  hydrogen bonds       : angle       4.16873 (  918)
  SS BOND              : bond        0.00228 (    6)
  SS BOND              : angle       1.07270 (   12)
  covalent geometry    : bond        0.00325 ( 6735)
  covalent geometry    : angle       0.54036 ( 9152)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4087.57 seconds
wall clock time: 70 minutes 52.24 seconds (4252.24 seconds total)