Starting phenix.real_space_refine
on Tue Feb  3 19:56:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sy6_25518/02_2026/7sy6_25518.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sy6_25518/02_2026/7sy6_25518.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sy6_25518/02_2026/7sy6_25518.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sy6_25518/02_2026/7sy6_25518.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sy6_25518/02_2026/7sy6_25518.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sy6_25518/02_2026/7sy6_25518.cif"
  }
  resolution = 2.81
  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=   0.000 sd=   0.032
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    4190      2.51       5
     N    1078      2.21       5
     O    1248      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-2.0-5952/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: 1.21, per 1000 atoms: 0.18
  Number of scatterers: 6553
  At special positions: 0
  Unit cell: (81, 83, 122, 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    1248      8.00
     N    1078      7.00
     C    4190      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=2.04
    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=2.02

  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: 0.50
  Conformation dependent library (CDL) restraints added in 138.4 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:
      38 helices and 7 sheets defined
      57.1% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  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: 3.746A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 3.706A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
      removed outlier: 3.577A  pdb=" N   GLN E  81 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.748A  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: 4.011A  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: 3.921A  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: 3.737A  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: 3.704A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.750A  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: 3.799A  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: 3.589A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.715A  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: 4.262A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.936A  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
      removed outlier: 3.524A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.336A  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: 3.725A  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: 4.403A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.663A  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: 3.919A  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: 3.969A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.803A  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: 3.705A  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: 6.054A  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: 6.354A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    322 hydrogen bonds defined for protein.
    915 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: 0.77

  Time building geometry restraints manager: 0.66 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: 2083
        1.35 -     1.47: 1790
        1.47 -     1.60: 2805
        1.60 -     1.72: 0
        1.72 -     1.84: 58
  Bond restraints: 6736
  Sorted by residual:
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.454 -0.048 2.00e-02 2.50e+03 5.73e+00
  bond pdb=" C1  NAG E 704 "
       pdb=" O5  NAG E 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.451 -0.045 2.00e-02 2.50e+03 5.08e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.62e+00
  bond pdb=" C1  NAG E 706 "
       pdb=" O5  NAG E 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.40e+00
  bond pdb=" C   SER E 611 "
       pdb=" N   PRO E 612 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 2.34e-02 1.83e+03 3.99e+00
  ... (remaining 6731 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 8819
        2.07 -     4.15: 288
        4.15 -     6.22: 39
        6.22 -     8.30: 5
        8.30 -    10.37: 4
  Bond angle restraints: 9155
  Sorted by residual:
  angle pdb=" CA  TYR B 495 "
        pdb=" CB  TYR B 495 "
        pdb=" CG  TYR B 495 "
      ideal   model   delta    sigma   weight residual
     113.90  124.27  -10.37 1.80e+00 3.09e-01 3.32e+01
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.82  128.92   -6.10 1.42e+00 4.96e-01 1.84e+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  123.31   -8.91 2.30e+00 1.89e-01 1.50e+01
  angle pdb=" C   PHE E  32 "
        pdb=" N   ASN E  33 "
        pdb=" CA  ASN E  33 "
      ideal   model   delta    sigma   weight residual
     121.19  126.70   -5.51 1.59e+00 3.96e-01 1.20e+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  115.93   -3.33 1.00e+00 1.00e+00 1.11e+01
  ... (remaining 9150 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.17: 3685
       17.17 -    34.34: 311
       34.34 -    51.51: 45
       51.51 -    68.68: 13
       68.68 -    85.85: 11
  Dihedral angle restraints: 4065
    sinusoidal: 1726
      harmonic: 2339
  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  -44.82  -41.18     1      1.00e+01 1.00e-02 2.38e+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   15.54   63.46     1      2.00e+01 2.50e-03 1.33e+01
  dihedral pdb=" CA  ALA E 396 "
           pdb=" C   ALA E 396 "
           pdb=" N   ASN E 397 "
           pdb=" CA  ASN E 397 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.31   16.69     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 4062 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 686
       0.051 -    0.103: 213
       0.103 -    0.154: 63
       0.154 -    0.205: 11
       0.205 -    0.256: 5
  Chirality restraints: 978
  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    2.25    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CB  VAL B 350 "
            pdb=" CA  VAL B 350 "
            pdb=" CG1 VAL B 350 "
            pdb=" CG2 VAL B 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.37e+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   -0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 975 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 169 "    0.015 2.00e-02 2.50e+03   3.12e-02 9.71e+00
        pdb=" C   ARG E 169 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   ARG E 169 "    0.020 2.00e-02 2.50e+03
        pdb=" N   SER E 170 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE E  32 "    0.014 2.00e-02 2.50e+03   2.92e-02 8.55e+00
        pdb=" C   PHE E  32 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   PHE E  32 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASN E  33 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E  36 "   -0.014 2.00e-02 2.50e+03   2.88e-02 8.29e+00
        pdb=" C   ALA E  36 "    0.050 2.00e-02 2.50e+03
        pdb=" O   ALA E  36 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLU E  37 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1853
        2.82 -     3.34: 5981
        3.34 -     3.86: 11402
        3.86 -     4.38: 13066
        4.38 -     4.90: 22509
  Nonbonded interactions: 54811
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.365 3.120
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.382 3.120
  nonbonded pdb=" OH  TYR E 237 "
            pdb=" O   VAL E 485 "
     model   vdw
     2.394 3.040
  ... (remaining 54806 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:             5.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.630
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:8.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
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   0.060   6749  Z= 0.249
  Angle     :  0.890  12.647   9188  Z= 0.477
  Chirality :  0.057   0.256    978
  Planarity :  0.007   0.060   1177
  Dihedral  : 13.403  85.851   2547
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.29 %
    Favored  : 97.57 %
  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: -0.71 (0.26), residues: 793
  helix: -0.21 (0.22), residues: 389
  sheet:  1.02 (0.73), residues: 43
  loop : -0.84 (0.29), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 460 
 TYR   0.046   0.002   TYR B 495 
 PHE   0.031   0.003   PHE E 369 
 TRP   0.020   0.002   TRP E 566 
 HIS   0.007   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 ( 6736)
  covalent geometry    : angle       0.86133 ( 9155)
  SS BOND              : bond        0.00549 (    6)
  SS BOND              : angle       2.72299 (   12)
  hydrogen bonds       : bond        0.13563 (  322)
  hydrogen bonds       : angle       6.20226 (  915)
  link_NAG-ASN         : bond        0.00829 (    7)
  link_NAG-ASN         : angle       4.36957 (   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
  121 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.267 
Fit side-chains
REVERT: B  405 ASP cc_start: 0.8361 (m-30) cc_final: 0.8003 (m-30)
REVERT: B  468 ILE cc_start: 0.9409 (pt) cc_final: 0.9167 (pp)
REVERT: E  256 ILE cc_start: 0.8954 (mp) cc_final: 0.8426 (mt)
REVERT: E  259 ILE cc_start: 0.8587 (tp) cc_final: 0.8232 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 121
  average time/residue: 0.5873
  time to fit residues: 74.0925
Evaluate side-chains
  69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
E 374 HIS
E 522 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.073758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.053432 restraints weight = 16379.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.2797 rms_B_bonded: 3.03
r_work: 0.2653 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6749  Z= 0.234
  Angle     :  0.657   9.896   9188  Z= 0.327
  Chirality :  0.044   0.202    978
  Planarity :  0.005   0.036   1177
  Dihedral  :  5.409  47.595   1013
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 10.71 %
    Favored  : 86.14 %
  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:  0.58 (0.28), residues: 793
  helix:  1.05 (0.25), residues: 387
  sheet:  0.83 (0.71), residues: 43
  loop : -0.32 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 559 
 TYR   0.022   0.001   TYR B 495 
 PHE   0.022   0.002   PHE E 369 
 TRP   0.019   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 6736)
  covalent geometry    : angle       0.63532 ( 9155)
  SS BOND              : bond        0.00446 (    6)
  SS BOND              : angle       2.06234 (   12)
  hydrogen bonds       : bond        0.04938 (  322)
  hydrogen bonds       : angle       4.79928 (  915)
  link_NAG-ASN         : bond        0.00414 (    7)
  link_NAG-ASN         : angle       3.22724 (   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
  93 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.268 
Fit side-chains
REVERT: B  405 ASP cc_start: 0.8862 (m-30) cc_final: 0.8463 (m-30)
REVERT: B  466 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8794 (mtp85)
REVERT: B  468 ILE cc_start: 0.9373 (pt) cc_final: 0.9159 (pp)
REVERT: B  528 LYS cc_start: 0.3360 (OUTLIER) cc_final: 0.2868 (pttt)
REVERT: E  142 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8958 (tp)
REVERT: E  259 ILE cc_start: 0.8510 (tp) cc_final: 0.8207 (pp)
REVERT: E  475 LYS cc_start: 0.8897 (ttpp) cc_final: 0.8592 (ttpp)
REVERT: E  480 MET cc_start: 0.8942 (mtp) cc_final: 0.8673 (mtm)
REVERT: E  589 GLU cc_start: 0.9018 (tp30) cc_final: 0.8219 (tp30)
  outliers start: 22
  outliers final: 7
  residues processed: 86
  average time/residue: 0.5392
  time to fit residues: 48.6792
Evaluate side-chains
  71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  378 LYS
Chi-restraints excluded: chain B residue  466 ARG
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  503 LEU
Chi-restraints excluded: chain E residue  548 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0170
   chunk 58 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
E 149 ASN
E 154 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.075037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.054824 restraints weight = 16160.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 3.02
r_work: 0.2704 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6749  Z= 0.144
  Angle     :  0.580   9.427   9188  Z= 0.283
  Chirality :  0.041   0.146    978
  Planarity :  0.004   0.033   1177
  Dihedral  :  4.945  51.032   1013
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 11.86 %
    Favored  : 85.14 %
  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:  0.92 (0.28), residues: 793
  helix:  1.32 (0.25), residues: 393
  sheet:  0.70 (0.70), residues: 43
  loop : -0.12 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 559 
 TYR   0.018   0.001   TYR B 495 
 PHE   0.018   0.001   PHE E 369 
 TRP   0.016   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6736)
  covalent geometry    : angle       0.56055 ( 9155)
  SS BOND              : bond        0.00477 (    6)
  SS BOND              : angle       1.91426 (   12)
  hydrogen bonds       : bond        0.04311 (  322)
  hydrogen bonds       : angle       4.55828 (  915)
  link_NAG-ASN         : bond        0.00410 (    7)
  link_NAG-ASN         : angle       2.81912 (   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
  89 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.256 
Fit side-chains
REVERT: B  357 ARG cc_start: 0.9052 (ttp-110) cc_final: 0.8828 (ttp-170)
REVERT: B  405 ASP cc_start: 0.8892 (m-30) cc_final: 0.8478 (m-30)
REVERT: B  471 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8655 (tt0)
REVERT: E  114 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8902 (mptt)
REVERT: E  475 LYS cc_start: 0.8909 (ttpp) cc_final: 0.8647 (ttpp)
REVERT: E  589 GLU cc_start: 0.9031 (tp30) cc_final: 0.8276 (tp30)
  outliers start: 21
  outliers final: 8
  residues processed: 83
  average time/residue: 0.5607
  time to fit residues: 48.9181
Evaluate side-chains
  73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain E residue  114 LYS
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  455 MET
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  503 LEU
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 77 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
E 586 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.071852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.051489 restraints weight = 16441.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 3.01
r_work: 0.2619 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   6749  Z= 0.282
  Angle     :  0.659  12.402   9188  Z= 0.325
  Chirality :  0.045   0.158    978
  Planarity :  0.004   0.034   1177
  Dihedral  :  5.201  50.358   1013
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 13.57 %
    Favored  : 82.57 %
  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:  1.07 (0.29), residues: 793
  helix:  1.39 (0.25), residues: 393
  sheet:  0.43 (0.70), residues: 43
  loop :  0.09 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 457 
 TYR   0.020   0.002   TYR B 495 
 PHE   0.022   0.002   PHE E 400 
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00644 ( 6736)
  covalent geometry    : angle       0.64534 ( 9155)
  SS BOND              : bond        0.00436 (    6)
  SS BOND              : angle       1.32555 (   12)
  hydrogen bonds       : bond        0.04947 (  322)
  hydrogen bonds       : angle       4.64393 (  915)
  link_NAG-ASN         : bond        0.00373 (    7)
  link_NAG-ASN         : angle       2.70160 (   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
  88 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 61
  time to evaluate  : 0.194 
Fit side-chains
REVERT: B  405 ASP cc_start: 0.8914 (m-30) cc_final: 0.8501 (m-30)
REVERT: B  466 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8762 (mtp85)
REVERT: B  471 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8621 (tt0)
REVERT: E  142 LEU cc_start: 0.8930 (tp) cc_final: 0.8700 (tp)
REVERT: E  270 MET cc_start: 0.8805 (mmm) cc_final: 0.8456 (tpt)
REVERT: E  589 GLU cc_start: 0.9177 (tp30) cc_final: 0.8424 (tp30)
  outliers start: 27
  outliers final: 9
  residues processed: 80
  average time/residue: 0.6327
  time to fit residues: 52.7753
Evaluate side-chains
  68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  378 LYS
Chi-restraints excluded: chain B residue  466 ARG
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  548 THR
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 0 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.073219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.052769 restraints weight = 16457.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 3.04
r_work: 0.2645 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6749  Z= 0.169
  Angle     :  0.593  12.967   9188  Z= 0.286
  Chirality :  0.042   0.139    978
  Planarity :  0.003   0.031   1177
  Dihedral  :  4.950  52.684   1013
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 15.00 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.18 (0.29), residues: 793
  helix:  1.51 (0.26), residues: 394
  sheet:  0.27 (0.72), residues: 43
  loop :  0.13 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 346 
 TYR   0.017   0.001   TYR B 495 
 PHE   0.017   0.001   PHE E 369 
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6736)
  covalent geometry    : angle       0.58103 ( 9155)
  SS BOND              : bond        0.00324 (    6)
  SS BOND              : angle       0.96740 (   12)
  hydrogen bonds       : bond        0.04309 (  322)
  hydrogen bonds       : angle       4.48177 (  915)
  link_NAG-ASN         : bond        0.00330 (    7)
  link_NAG-ASN         : angle       2.49871 (   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
  83 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 60
  time to evaluate  : 0.257 
Fit side-chains
REVERT: B  405 ASP cc_start: 0.8924 (m-30) cc_final: 0.8481 (m-30)
REVERT: B  466 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8829 (mtp85)
REVERT: B  471 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8659 (tt0)
REVERT: E  114 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8876 (mptt)
REVERT: E  589 GLU cc_start: 0.9132 (tp30) cc_final: 0.8401 (tp30)
  outliers start: 23
  outliers final: 10
  residues processed: 77
  average time/residue: 0.5982
  time to fit residues: 48.2625
Evaluate side-chains
  71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  466 ARG
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain E residue  114 LYS
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  548 THR
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   overall best weight:    1.0584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.072837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.052506 restraints weight = 16435.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.2778 rms_B_bonded: 3.00
r_work: 0.2637 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6749  Z= 0.195
  Angle     :  0.611  13.516   9188  Z= 0.295
  Chirality :  0.042   0.139    978
  Planarity :  0.004   0.031   1177
  Dihedral  :  4.961  52.809   1013
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.00 %
    Favored  : 82.00 %
  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:  1.26 (0.29), residues: 793
  helix:  1.56 (0.26), residues: 392
  sheet:  0.18 (0.72), residues: 43
  loop :  0.22 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 346 
 TYR   0.017   0.001   TYR B 495 
 PHE   0.018   0.001   PHE E 369 
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 6736)
  covalent geometry    : angle       0.60128 ( 9155)
  SS BOND              : bond        0.00364 (    6)
  SS BOND              : angle       0.94565 (   12)
  hydrogen bonds       : bond        0.04427 (  322)
  hydrogen bonds       : angle       4.47512 (  915)
  link_NAG-ASN         : bond        0.00300 (    7)
  link_NAG-ASN         : angle       2.31885 (   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
  77 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 56
  time to evaluate  : 0.186 
Fit side-chains
REVERT: B  405 ASP cc_start: 0.8917 (m-30) cc_final: 0.8469 (m-30)
REVERT: B  471 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8673 (tt0)
REVERT: E  114 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8871 (mptt)
REVERT: E  571 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8536 (tm-30)
REVERT: E  589 GLU cc_start: 0.9138 (tp30) cc_final: 0.8414 (tp30)
  outliers start: 21
  outliers final: 12
  residues processed: 71
  average time/residue: 0.6277
  time to fit residues: 46.6882
Evaluate side-chains
  69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  378 LYS
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain E residue  114 LYS
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  548 THR
Chi-restraints excluded: chain E residue  571 GLU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  601 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 35 optimal weight:    6.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.073704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.053459 restraints weight = 16375.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 3.03
r_work: 0.2666 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6749  Z= 0.153
  Angle     :  0.583  12.480   9188  Z= 0.278
  Chirality :  0.041   0.131    978
  Planarity :  0.003   0.031   1177
  Dihedral  :  4.819  54.142   1013
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 16.71 %
    Favored  : 81.00 %
  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:  1.30 (0.29), residues: 793
  helix:  1.58 (0.26), residues: 398
  sheet:  0.17 (0.74), residues: 43
  loop :  0.23 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 346 
 TYR   0.016   0.001   TYR B 495 
 PHE   0.017   0.001   PHE E 369 
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6736)
  covalent geometry    : angle       0.57343 ( 9155)
  SS BOND              : bond        0.00339 (    6)
  SS BOND              : angle       0.84936 (   12)
  hydrogen bonds       : bond        0.04154 (  322)
  hydrogen bonds       : angle       4.42463 (  915)
  link_NAG-ASN         : bond        0.00306 (    7)
  link_NAG-ASN         : angle       2.19717 (   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
  73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.203 
Fit side-chains
REVERT: B  405 ASP cc_start: 0.8913 (m-30) cc_final: 0.8480 (m-30)
REVERT: B  471 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8660 (tt0)
REVERT: E  589 GLU cc_start: 0.9128 (tp30) cc_final: 0.8440 (tp30)
  outliers start: 16
  outliers final: 9
  residues processed: 72
  average time/residue: 0.6118
  time to fit residues: 46.1134
Evaluate side-chains
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.073716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.053456 restraints weight = 16277.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.2806 rms_B_bonded: 3.02
r_work: 0.2667 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6749  Z= 0.156
  Angle     :  0.601  11.421   9188  Z= 0.284
  Chirality :  0.041   0.130    978
  Planarity :  0.004   0.031   1177
  Dihedral  :  4.809  54.170   1013
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.00 %
    Favored  : 80.57 %
  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:  1.39 (0.29), residues: 793
  helix:  1.64 (0.26), residues: 398
  sheet:  0.16 (0.73), residues: 43
  loop :  0.31 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 582 
 TYR   0.015   0.001   TYR B 495 
 PHE   0.017   0.001   PHE E 369 
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6736)
  covalent geometry    : angle       0.59255 ( 9155)
  SS BOND              : bond        0.00275 (    6)
  SS BOND              : angle       0.81004 (   12)
  hydrogen bonds       : bond        0.04165 (  322)
  hydrogen bonds       : angle       4.40300 (  915)
  link_NAG-ASN         : bond        0.00287 (    7)
  link_NAG-ASN         : angle       2.11228 (   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
  73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.251 
Fit side-chains
REVERT: B  357 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8797 (ttt180)
REVERT: B  405 ASP cc_start: 0.8919 (m-30) cc_final: 0.8470 (m-30)
REVERT: B  471 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8665 (tt0)
REVERT: E  383 MET cc_start: 0.9288 (mtm) cc_final: 0.9015 (mtm)
REVERT: E  589 GLU cc_start: 0.9130 (tp30) cc_final: 0.8446 (tp30)
  outliers start: 17
  outliers final: 11
  residues processed: 71
  average time/residue: 0.5543
  time to fit residues: 41.4139
Evaluate side-chains
  67 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  357 ARG
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  574 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:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 46 optimal weight:    0.4980
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.073850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.053451 restraints weight = 16380.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.2810 rms_B_bonded: 3.06
r_work: 0.2672 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6749  Z= 0.148
  Angle     :  0.595  11.560   9188  Z= 0.282
  Chirality :  0.041   0.130    978
  Planarity :  0.003   0.032   1177
  Dihedral  :  4.765  54.576   1013
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.57 %
    Favored  : 80.14 %
  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:  1.44 (0.29), residues: 793
  helix:  1.67 (0.26), residues: 399
  sheet:  0.16 (0.74), residues: 43
  loop :  0.35 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 346 
 TYR   0.014   0.001   TYR B 495 
 PHE   0.017   0.001   PHE E 369 
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6736)
  covalent geometry    : angle       0.58709 ( 9155)
  SS BOND              : bond        0.00256 (    6)
  SS BOND              : angle       0.77794 (   12)
  hydrogen bonds       : bond        0.04092 (  322)
  hydrogen bonds       : angle       4.37390 (  915)
  link_NAG-ASN         : bond        0.00282 (    7)
  link_NAG-ASN         : angle       2.07312 (   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
  72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.225 
Fit side-chains
REVERT: B  357 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8777 (ttt180)
REVERT: B  405 ASP cc_start: 0.8907 (m-30) cc_final: 0.8469 (m-30)
REVERT: B  471 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8661 (tt0)
REVERT: E  270 MET cc_start: 0.8689 (mmm) cc_final: 0.8485 (tpt)
REVERT: E  383 MET cc_start: 0.9258 (mtm) cc_final: 0.8975 (mtm)
REVERT: E  589 GLU cc_start: 0.9124 (tp30) cc_final: 0.8440 (tp30)
  outliers start: 16
  outliers final: 12
  residues processed: 70
  average time/residue: 0.5442
  time to fit residues: 40.0226
Evaluate side-chains
  70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  357 ARG
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  548 THR
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 34 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 28 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.073514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.053251 restraints weight = 16189.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.2803 rms_B_bonded: 3.02
r_work: 0.2665 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.3083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6749  Z= 0.169
  Angle     :  0.628  13.003   9188  Z= 0.293
  Chirality :  0.041   0.132    978
  Planarity :  0.004   0.034   1177
  Dihedral  :  4.812  54.407   1013
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.57 %
    Favored  : 80.29 %
  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:  1.44 (0.29), residues: 793
  helix:  1.65 (0.26), residues: 400
  sheet:  0.14 (0.74), residues: 43
  loop :  0.37 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 346 
 TYR   0.014   0.001   TYR B 495 
 PHE   0.018   0.001   PHE E 369 
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6736)
  covalent geometry    : angle       0.62109 ( 9155)
  SS BOND              : bond        0.00257 (    6)
  SS BOND              : angle       0.80362 (   12)
  hydrogen bonds       : bond        0.04208 (  322)
  hydrogen bonds       : angle       4.39541 (  915)
  link_NAG-ASN         : bond        0.00270 (    7)
  link_NAG-ASN         : angle       2.04512 (   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
  71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.250 
Fit side-chains
REVERT: B  357 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8770 (ttt180)
REVERT: B  405 ASP cc_start: 0.8909 (m-30) cc_final: 0.8455 (m-30)
REVERT: B  471 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8667 (tt0)
REVERT: E  270 MET cc_start: 0.8786 (mmm) cc_final: 0.8377 (tpt)
REVERT: E  589 GLU cc_start: 0.9144 (tp30) cc_final: 0.8461 (tp30)
  outliers start: 15
  outliers final: 10
  residues processed: 69
  average time/residue: 0.5359
  time to fit residues: 38.9272
Evaluate side-chains
  68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  357 ARG
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  548 THR
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 64 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0270
   chunk 19 optimal weight:    0.0010
   overall best weight:    0.5444

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.074580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.054270 restraints weight = 16261.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 3.03
r_work: 0.2691 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6749  Z= 0.128
  Angle     :  0.591  12.157   9188  Z= 0.277
  Chirality :  0.040   0.125    978
  Planarity :  0.003   0.036   1177
  Dihedral  :  4.659  55.153   1013
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.57 %
    Favored  : 80.29 %
  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:  1.48 (0.29), residues: 793
  helix:  1.70 (0.26), residues: 400
  sheet:  0.18 (0.74), residues: 43
  loop :  0.36 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 346 
 TYR   0.014   0.001   TYR B 495 
 PHE   0.016   0.001   PHE E 369 
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6736)
  covalent geometry    : angle       0.58323 ( 9155)
  SS BOND              : bond        0.00233 (    6)
  SS BOND              : angle       0.75315 (   12)
  hydrogen bonds       : bond        0.03940 (  322)
  hydrogen bonds       : angle       4.32792 (  915)
  link_NAG-ASN         : bond        0.00279 (    7)
  link_NAG-ASN         : angle       2.05926 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2077.08 seconds
wall clock time: 36 minutes 15.30 seconds (2175.30 seconds total)