Starting phenix.real_space_refine
on Tue Mar  3 15:38:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mjn_23879/03_2026/7mjn_23879.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mjn_23879/03_2026/7mjn_23879.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mjn_23879/03_2026/7mjn_23879.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mjn_23879/03_2026/7mjn_23879.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mjn_23879/03_2026/7mjn_23879.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mjn_23879/03_2026/7mjn_23879.cif"
  }
  resolution = 3.29
  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=   0.019
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    4175      2.51       5
     N    1075      2.21       5
     O    1239      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6526
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1594
          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: {'PTRANS': 27, '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: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 1.30, per 1000 atoms: 0.20
  Number of scatterers: 6526
  At special positions: 0
  Unit cell: (100, 72, 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    1239      8.00
     N    1075      7.00
     C    4175      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=2.03
    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 322 "
      " NAG E 704 " - " ASN E 546 "
  Time building additional restraints: 0.58
  Conformation dependent library (CDL) restraints added in 291.4 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 5 sheets defined
      56.3% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.587A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.924A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 371
      removed outlier: 3.622A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 390
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.519A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 52
      removed outlier: 3.807A  pdb=" N   GLN E  24 " --> pdb=" O   THR E  20 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
      removed outlier: 3.721A  pdb=" N   GLN E  81 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
    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: 3.871A  pdb=" N   GLU E  87 " --> pdb=" O   PRO E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 102
      removed outlier: 4.017A  pdb=" N   ALA E  99 " --> pdb=" O   LEU E  95 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   LEU E 100 " --> pdb=" O   GLN E  96 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 103 through 108
      removed outlier: 3.639A  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 147 through 155
    Processing helix  chain 'E' and resid 158 through 194
      Proline residue:  E 178  - end of helix
    Processing helix  chain 'E' and resid 198 through 204
    Processing helix  chain 'E' and resid 205 through 207
      No H-bonds generated for 'chain 'E' and resid 205 through 207'
    Processing helix  chain 'E' and resid 221 through 249
      removed outlier: 3.953A  pdb=" N   GLU E 227 " --> pdb=" O   ILE E 223 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   GLU E 232 " --> pdb=" O   HIS E 228 " (cutoff:3.500A)
      Proline residue:  E 235  - end of helix
      removed outlier: 3.721A  pdb=" N   MET E 249 " --> pdb=" O   ARG E 245 " (cutoff:3.500A)
    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
    Processing helix  chain 'E' and resid 294 through 300
    Processing helix  chain 'E' and resid 303 through 319
      removed outlier: 3.636A  pdb=" N   VAL E 318 " --> pdb=" O   PHE E 314 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 324 through 331
      removed outlier: 3.538A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.707A  pdb=" N   TYR E 385 " --> pdb=" O   TYR E 381 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 399 through 413
      removed outlier: 4.328A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU E 406 " --> pdb=" O   GLU E 402 " (cutoff:3.500A)
      removed outlier: 3.718A  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: 4.122A  pdb=" N   PHE E 438 " --> pdb=" O   THR E 434 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 466
      removed outlier: 4.564A  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
    Processing helix  chain 'E' and resid 503 through 508
    Processing helix  chain 'E' and resid 513 through 533
      removed outlier: 4.282A  pdb=" N   PHE E 523 " --> pdb=" O   THR E 519 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 547 through 559
      removed outlier: 3.631A  pdb=" N   LYS E 553 " --> pdb=" O   GLU E 549 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   MET E 557 " --> pdb=" O   LYS E 553 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 560 through 564
      removed outlier: 4.247A  pdb=" N   GLU E 564 " --> pdb=" O   GLY E 561 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 565 through 575
      removed outlier: 3.726A  pdb=" N   VAL E 573 " --> pdb=" O   ALA E 569 " (cutoff:3.500A)
    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: 3.757A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'E' and resid 262 through 263
      removed outlier: 5.932A  pdb=" N   LEU E 262 " --> pdb=" O   VAL E 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 347 through 352
      removed outlier: 6.070A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    309 hydrogen bonds defined for protein.
    891 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: 0.73

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2080
        1.35 -     1.47: 1755
        1.47 -     1.59: 2816
        1.59 -     1.71: 0
        1.71 -     1.83: 58
  Bond restraints: 6709
  Sorted by residual:
  bond pdb=" C   GLU E 145 "
       pdb=" N   PRO E 146 "
    ideal  model  delta    sigma   weight residual
    1.337  1.369 -0.033 1.06e-02 8.90e+03 9.53e+00
  bond pdb=" C1  NAG E 701 "
       pdb=" O5  NAG E 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.459 -0.053 2.00e-02 2.50e+03 7.09e+00
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.73e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.69e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.442 -0.036 2.00e-02 2.50e+03 3.29e+00
  ... (remaining 6704 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 8752
        1.89 -     3.77: 297
        3.77 -     5.66: 47
        5.66 -     7.55: 16
        7.55 -     9.43: 6
  Bond angle restraints: 9118
  Sorted by residual:
  angle pdb=" N   GLY E 147 "
        pdb=" CA  GLY E 147 "
        pdb=" C   GLY E 147 "
      ideal   model   delta    sigma   weight residual
     110.21  114.42   -4.21 9.10e-01 1.21e+00 2.14e+01
  angle pdb=" C   ASP E 292 "
        pdb=" N   VAL E 293 "
        pdb=" CA  VAL E 293 "
      ideal   model   delta    sigma   weight residual
     121.97  130.09   -8.12 1.80e+00 3.09e-01 2.04e+01
  angle pdb=" O   GLY E 147 "
        pdb=" C   GLY E 147 "
        pdb=" N   LEU E 148 "
      ideal   model   delta    sigma   weight residual
     121.85  124.37   -2.52 5.60e-01 3.19e+00 2.02e+01
  angle pdb=" CG  ARG B 346 "
        pdb=" CD  ARG B 346 "
        pdb=" NE  ARG B 346 "
      ideal   model   delta    sigma   weight residual
     112.00  120.75   -8.75 2.20e+00 2.07e-01 1.58e+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  117.91   -4.75 1.42e+00 4.96e-01 1.12e+01
  ... (remaining 9113 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 3652
       17.64 -    35.27: 302
       35.27 -    52.91: 57
       52.91 -    70.54: 8
       70.54 -    88.18: 5
  Dihedral angle restraints: 4024
    sinusoidal: 1685
      harmonic: 2339
  Sorted by residual:
  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  159.52   20.48     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  TRP E 606 "
           pdb=" C   TRP E 606 "
           pdb=" N   SER E 607 "
           pdb=" CA  SER E 607 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.99   20.01     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  ILE E 233 "
           pdb=" C   ILE E 233 "
           pdb=" N   LYS E 234 "
           pdb=" CA  LYS E 234 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.38  -18.62     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 4021 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 710
       0.049 -    0.097: 176
       0.097 -    0.146: 67
       0.146 -    0.195: 10
       0.195 -    0.243: 5
  Chirality restraints: 968
  Sorted by residual:
  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   -2.39   -0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CB  VAL E 447 "
            pdb=" CA  VAL E 447 "
            pdb=" CG1 VAL E 447 "
            pdb=" CG2 VAL E 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CG  LEU E 520 "
            pdb=" CB  LEU E 520 "
            pdb=" CD1 LEU E 520 "
            pdb=" CD2 LEU E 520 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 965 not shown)

  Planarity restraints: 1180
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 462 "    0.036 5.00e-02 4.00e+02   5.40e-02 4.67e+00
        pdb=" N   PRO B 463 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B 463 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 463 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 467 "   -0.009 2.00e-02 2.50e+03   1.87e-02 3.49e+00
        pdb=" CG  ASP B 467 "    0.032 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 467 "   -0.012 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 467 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN E 134 "   -0.031 5.00e-02 4.00e+02   4.64e-02 3.45e+00
        pdb=" N   PRO E 135 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO E 135 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO E 135 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1177 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1922
        2.82 -     3.34: 6061
        3.34 -     3.86: 10993
        3.86 -     4.38: 12649
        4.38 -     4.90: 21926
  Nonbonded interactions: 53551
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OD1 ASP E 494 "
            pdb=" OG1 THR E 496 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OH  TYR E 215 "
            pdb=" OE1 GLU E 571 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OG  SER B 383 "
            pdb=" OG1 THR B 385 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   PHE E 314 "
            pdb=" OG  SER E 317 "
     model   vdw
     2.378 3.040
  ... (remaining 53546 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:             4.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.740
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
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   0.053   6720  Z= 0.222
  Angle     :  0.858   9.434   9145  Z= 0.465
  Chirality :  0.053   0.243    968
  Planarity :  0.007   0.054   1175
  Dihedral  : 13.379  88.178   2506
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.27), residues: 793
  helix: -0.80 (0.23), residues: 374
  sheet:  0.98 (0.78), residues: 51
  loop : -1.07 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E 115 
 TYR   0.015   0.002   TYR E 237 
 PHE   0.016   0.002   PHE E 369 
 TRP   0.019   0.002   TRP E 165 
 HIS   0.006   0.002   HIS E 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 6709)
  covalent geometry    : angle       0.84420 ( 9118)
  SS BOND              : bond        0.00376 (    6)
  SS BOND              : angle       1.14367 (   12)
  hydrogen bonds       : bond        0.16856 (  309)
  hydrogen bonds       : angle       6.97752 (  891)
  link_NAG-ASN         : bond        0.00610 (    5)
  link_NAG-ASN         : angle       3.76346 (   15)

*********************** 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
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.224 
Fit side-chains
REVERT: B  506 GLN cc_start: 0.8870 (mt0) cc_final: 0.8656 (mt0)
REVERT: E  123 MET cc_start: 0.9504 (mmt) cc_final: 0.9288 (mmt)
REVERT: E  190 MET cc_start: 0.9238 (tmm) cc_final: 0.9037 (tmm)
REVERT: E  249 MET cc_start: 0.9160 (mmm) cc_final: 0.8745 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.0756
  time to fit residues: 6.0751
Evaluate side-chains
  41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.2980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
E 378 HIS
E 599 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.057072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.042693 restraints weight = 28299.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.2750 rms_B_bonded: 4.14
r_work: 0.2612 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.1141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6720  Z= 0.140
  Angle     :  0.548   8.424   9145  Z= 0.281
  Chirality :  0.041   0.168    968
  Planarity :  0.004   0.036   1175
  Dihedral  :  5.753  58.262    971
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  4.86 %
    Favored  : 94.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.29), residues: 793
  helix:  0.56 (0.25), residues: 392
  sheet:  0.77 (0.82), residues: 48
  loop : -0.65 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 115 
 TYR   0.015   0.001   TYR B 451 
 PHE   0.011   0.001   PHE E 369 
 TRP   0.018   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6709)
  covalent geometry    : angle       0.53972 ( 9118)
  SS BOND              : bond        0.00273 (    6)
  SS BOND              : angle       0.69853 (   12)
  hydrogen bonds       : bond        0.04638 (  309)
  hydrogen bonds       : angle       4.77688 (  891)
  link_NAG-ASN         : bond        0.00412 (    5)
  link_NAG-ASN         : angle       2.41585 (   15)

*********************** 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
  50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.214 
Fit side-chains
REVERT: B  386 LYS cc_start: 0.9387 (mtmm) cc_final: 0.9170 (mtmt)
REVERT: E  123 MET cc_start: 0.9458 (mmt) cc_final: 0.9236 (mmt)
REVERT: E  190 MET cc_start: 0.9262 (tmm) cc_final: 0.9058 (tmm)
REVERT: E  249 MET cc_start: 0.9143 (mmm) cc_final: 0.8697 (mmt)
REVERT: E  462 MET cc_start: 0.9296 (mmm) cc_final: 0.8976 (mtm)
  outliers start: 3
  outliers final: 1
  residues processed: 48
  average time/residue: 0.0740
  time to fit residues: 5.0988
Evaluate side-chains
  42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  248 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3144 r_free = 0.3144 target = 0.056045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.041663 restraints weight = 28214.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.2744 rms_B_bonded: 4.11
r_work: 0.2606 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6720  Z= 0.150
  Angle     :  0.529   9.049   9145  Z= 0.266
  Chirality :  0.041   0.169    968
  Planarity :  0.004   0.031   1175
  Dihedral  :  4.802  56.126    971
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  6.43 %
    Favored  : 92.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.30), residues: 793
  helix:  1.28 (0.27), residues: 386
  sheet:  0.20 (0.79), residues: 48
  loop : -0.34 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 115 
 TYR   0.012   0.001   TYR B 369 
 PHE   0.012   0.001   PHE E 369 
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6709)
  covalent geometry    : angle       0.52164 ( 9118)
  SS BOND              : bond        0.00286 (    6)
  SS BOND              : angle       0.73385 (   12)
  hydrogen bonds       : bond        0.04175 (  309)
  hydrogen bonds       : angle       4.41141 (  891)
  link_NAG-ASN         : bond        0.00336 (    5)
  link_NAG-ASN         : angle       2.16788 (   15)

*********************** 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
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.264 
Fit side-chains
REVERT: E  190 MET cc_start: 0.9297 (tmm) cc_final: 0.9096 (tmm)
REVERT: E  249 MET cc_start: 0.9136 (mmm) cc_final: 0.8651 (mmt)
REVERT: E  323 MET cc_start: 0.9457 (mmp) cc_final: 0.9175 (mmp)
REVERT: E  332 MET cc_start: 0.8191 (ppp) cc_final: 0.7948 (ppp)
REVERT: E  462 MET cc_start: 0.9357 (mmm) cc_final: 0.9086 (mtm)
  outliers start: 6
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0736
  time to fit residues: 5.0376
Evaluate side-chains
  39 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 60 optimal weight:    0.4980
   chunk 18 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 35 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3136 r_free = 0.3136 target = 0.055597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.041419 restraints weight = 28931.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.2733 rms_B_bonded: 4.01
r_work: 0.2598 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6720  Z= 0.165
  Angle     :  0.530   8.398   9145  Z= 0.266
  Chirality :  0.041   0.160    968
  Planarity :  0.003   0.035   1175
  Dihedral  :  4.616  56.022    971
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  8.43 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.30), residues: 793
  helix:  1.51 (0.27), residues: 386
  sheet: -0.07 (0.77), residues: 48
  loop : -0.21 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 115 
 TYR   0.011   0.001   TYR E 515 
 PHE   0.012   0.001   PHE E 369 
 TRP   0.011   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6709)
  covalent geometry    : angle       0.52381 ( 9118)
  SS BOND              : bond        0.00335 (    6)
  SS BOND              : angle       0.69711 (   12)
  hydrogen bonds       : bond        0.04117 (  309)
  hydrogen bonds       : angle       4.34123 (  891)
  link_NAG-ASN         : bond        0.00317 (    5)
  link_NAG-ASN         : angle       2.08696 (   15)

*********************** 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
  44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.266 
Fit side-chains
REVERT: B  378 LYS cc_start: 0.9229 (mmtm) cc_final: 0.8955 (mptt)
REVERT: E  190 MET cc_start: 0.9311 (tmm) cc_final: 0.9088 (tmm)
REVERT: E  249 MET cc_start: 0.9103 (mmm) cc_final: 0.8636 (mmt)
REVERT: E  323 MET cc_start: 0.9449 (mmp) cc_final: 0.9207 (mmp)
REVERT: E  332 MET cc_start: 0.8209 (ppp) cc_final: 0.7990 (ppp)
REVERT: E  462 MET cc_start: 0.9367 (mmm) cc_final: 0.9074 (mtm)
  outliers start: 3
  outliers final: 2
  residues processed: 43
  average time/residue: 0.0609
  time to fit residues: 3.9529
Evaluate side-chains
  40 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain E residue  143 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0040
   chunk 71 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.6394

-------------------------------------------------------------------------------
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 = 0.3153 r_free = 0.3153 target = 0.056284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.042032 restraints weight = 28810.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 4.05
r_work: 0.2623 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.2623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6720  Z= 0.119
  Angle     :  0.505   9.330   9145  Z= 0.252
  Chirality :  0.040   0.163    968
  Planarity :  0.003   0.037   1175
  Dihedral  :  4.405  55.627    971
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  9.00 %
    Favored  : 90.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.30), residues: 793
  helix:  1.62 (0.27), residues: 386
  sheet: -0.01 (0.78), residues: 48
  loop : -0.16 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 115 
 TYR   0.015   0.001   TYR B 369 
 PHE   0.011   0.001   PHE E 369 
 TRP   0.010   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 6709)
  covalent geometry    : angle       0.49902 ( 9118)
  SS BOND              : bond        0.00276 (    6)
  SS BOND              : angle       0.68075 (   12)
  hydrogen bonds       : bond        0.03821 (  309)
  hydrogen bonds       : angle       4.21787 (  891)
  link_NAG-ASN         : bond        0.00357 (    5)
  link_NAG-ASN         : angle       1.99802 (   15)

*********************** 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
  48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.217 
Fit side-chains
REVERT: B  378 LYS cc_start: 0.9221 (mmtm) cc_final: 0.9007 (mmtm)
REVERT: B  406 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8317 (pm20)
REVERT: E  190 MET cc_start: 0.9320 (tmm) cc_final: 0.9087 (tmm)
REVERT: E  249 MET cc_start: 0.9103 (mmm) cc_final: 0.8631 (mmt)
REVERT: E  323 MET cc_start: 0.9420 (mmp) cc_final: 0.9204 (mmp)
REVERT: E  411 SER cc_start: 0.9216 (m) cc_final: 0.8816 (p)
REVERT: E  462 MET cc_start: 0.9367 (mmm) cc_final: 0.9087 (mtm)
  outliers start: 4
  outliers final: 2
  residues processed: 46
  average time/residue: 0.0691
  time to fit residues: 4.6285
Evaluate side-chains
  43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  406 GLU
Chi-restraints excluded: chain E residue  143 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 78 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0370
   chunk 47 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    1.4064

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

Flipped N/Q/H residues before XYZ refinement:
B 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.054758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.040620 restraints weight = 29127.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.2707 rms_B_bonded: 3.96
r_work: 0.2571 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6720  Z= 0.209
  Angle     :  0.564   7.823   9145  Z= 0.282
  Chirality :  0.042   0.147    968
  Planarity :  0.003   0.039   1175
  Dihedral  :  4.526  55.658    971
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  9.43 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.30), residues: 793
  helix:  1.56 (0.27), residues: 395
  sheet: -0.10 (0.77), residues: 48
  loop : -0.14 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 115 
 TYR   0.016   0.001   TYR B 369 
 PHE   0.013   0.001   PHE E 523 
 TRP   0.010   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 6709)
  covalent geometry    : angle       0.55823 ( 9118)
  SS BOND              : bond        0.00382 (    6)
  SS BOND              : angle       0.70392 (   12)
  hydrogen bonds       : bond        0.04201 (  309)
  hydrogen bonds       : angle       4.29231 (  891)
  link_NAG-ASN         : bond        0.00333 (    5)
  link_NAG-ASN         : angle       2.09877 (   15)

*********************** 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
  44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.248 
Fit side-chains
REVERT: E  190 MET cc_start: 0.9328 (tmm) cc_final: 0.9055 (tmm)
REVERT: E  249 MET cc_start: 0.9089 (mmm) cc_final: 0.8628 (mmt)
REVERT: E  270 MET cc_start: 0.9357 (tpp) cc_final: 0.8419 (tpp)
REVERT: E  462 MET cc_start: 0.9390 (mmm) cc_final: 0.9077 (mtm)
  outliers start: 5
  outliers final: 4
  residues processed: 42
  average time/residue: 0.0599
  time to fit residues: 3.6965
Evaluate side-chains
  41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  406 GLU
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain E residue  143 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0040
   chunk 77 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 32 optimal weight:    5.9990
   chunk 49 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.8996

-------------------------------------------------------------------------------
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 = 0.3126 r_free = 0.3126 target = 0.055635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.041190 restraints weight = 28350.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.2725 rms_B_bonded: 4.10
r_work: 0.2585 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.2585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6720  Z= 0.148
  Angle     :  0.553  10.159   9145  Z= 0.270
  Chirality :  0.041   0.154    968
  Planarity :  0.003   0.039   1175
  Dihedral  :  4.439  55.355    971
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.86 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.31), residues: 793
  helix:  1.58 (0.27), residues: 396
  sheet: -0.14 (0.77), residues: 48
  loop : -0.10 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 115 
 TYR   0.014   0.001   TYR B 369 
 PHE   0.012   0.001   PHE E 523 
 TRP   0.010   0.001   TRP E  69 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6709)
  covalent geometry    : angle       0.54680 ( 9118)
  SS BOND              : bond        0.00307 (    6)
  SS BOND              : angle       0.66451 (   12)
  hydrogen bonds       : bond        0.03949 (  309)
  hydrogen bonds       : angle       4.21252 (  891)
  link_NAG-ASN         : bond        0.00316 (    5)
  link_NAG-ASN         : angle       2.01641 (   15)

*********************** 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
  49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.220 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8318 (pm20)
REVERT: E  152 MET cc_start: 0.9088 (mmm) cc_final: 0.8820 (mmt)
REVERT: E  190 MET cc_start: 0.9336 (tmm) cc_final: 0.9065 (tmm)
REVERT: E  249 MET cc_start: 0.9090 (mmm) cc_final: 0.8624 (mmt)
REVERT: E  270 MET cc_start: 0.9257 (tpp) cc_final: 0.8256 (tpp)
REVERT: E  462 MET cc_start: 0.9392 (mmm) cc_final: 0.9079 (mtm)
  outliers start: 9
  outliers final: 4
  residues processed: 47
  average time/residue: 0.0663
  time to fit residues: 4.6649
Evaluate side-chains
  43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  406 GLU
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain E residue  143 LEU
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 28 optimal weight:    0.4980
   chunk 23 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3138 r_free = 0.3138 target = 0.055951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.041559 restraints weight = 28404.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.2745 rms_B_bonded: 4.08
r_work: 0.2605 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6720  Z= 0.127
  Angle     :  0.553  11.624   9145  Z= 0.268
  Chirality :  0.041   0.159    968
  Planarity :  0.003   0.039   1175
  Dihedral  :  4.332  55.164    971
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.43 %
    Favored  : 88.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.31), residues: 793
  helix:  1.71 (0.27), residues: 394
  sheet: -0.14 (0.77), residues: 48
  loop : -0.01 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 115 
 TYR   0.013   0.001   TYR B 369 
 PHE   0.012   0.001   PHE E 523 
 TRP   0.009   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6709)
  covalent geometry    : angle       0.54443 ( 9118)
  SS BOND              : bond        0.00194 (    6)
  SS BOND              : angle       1.67856 (   12)
  hydrogen bonds       : bond        0.03813 (  309)
  hydrogen bonds       : angle       4.16858 (  891)
  link_NAG-ASN         : bond        0.00339 (    5)
  link_NAG-ASN         : angle       1.98230 (   15)

*********************** 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
  47 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.247 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8302 (pm20)
REVERT: E  190 MET cc_start: 0.9336 (tmm) cc_final: 0.9089 (tmm)
REVERT: E  249 MET cc_start: 0.9076 (mmm) cc_final: 0.8613 (mmt)
REVERT: E  270 MET cc_start: 0.9160 (tpp) cc_final: 0.8062 (tpp)
REVERT: E  462 MET cc_start: 0.9383 (mmm) cc_final: 0.9082 (mtm)
  outliers start: 6
  outliers final: 4
  residues processed: 44
  average time/residue: 0.0714
  time to fit residues: 4.6297
Evaluate side-chains
  42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  406 GLU
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain E residue  143 LEU
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0970
   chunk 18 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 0 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3130 r_free = 0.3130 target = 0.055762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.041344 restraints weight = 28574.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.2709 rms_B_bonded: 4.10
r_work: 0.2569 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.2569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6720  Z= 0.147
  Angle     :  0.565  12.246   9145  Z= 0.273
  Chirality :  0.041   0.155    968
  Planarity :  0.003   0.039   1175
  Dihedral  :  4.335  55.264    971
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.71 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.31), residues: 793
  helix:  1.67 (0.27), residues: 397
  sheet: -0.13 (0.77), residues: 48
  loop : -0.01 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 115 
 TYR   0.013   0.001   TYR B 369 
 PHE   0.012   0.001   PHE E 369 
 TRP   0.009   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6709)
  covalent geometry    : angle       0.55813 ( 9118)
  SS BOND              : bond        0.00230 (    6)
  SS BOND              : angle       1.22517 (   12)
  hydrogen bonds       : bond        0.03878 (  309)
  hydrogen bonds       : angle       4.18860 (  891)
  link_NAG-ASN         : bond        0.00324 (    5)
  link_NAG-ASN         : angle       2.02144 (   15)

*********************** 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
  46 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.214 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8335 (pm20)
REVERT: E  152 MET cc_start: 0.8774 (mmt) cc_final: 0.8562 (mmm)
REVERT: E  190 MET cc_start: 0.9315 (tmm) cc_final: 0.9044 (tmm)
REVERT: E  249 MET cc_start: 0.9060 (mmm) cc_final: 0.8604 (mmt)
REVERT: E  270 MET cc_start: 0.9146 (tpp) cc_final: 0.8330 (tpp)
REVERT: E  462 MET cc_start: 0.9375 (mmm) cc_final: 0.9072 (mtm)
  outliers start: 6
  outliers final: 3
  residues processed: 44
  average time/residue: 0.0692
  time to fit residues: 4.4478
Evaluate side-chains
  41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  406 GLU
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3135 r_free = 0.3135 target = 0.056010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.041581 restraints weight = 28333.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.2717 rms_B_bonded: 4.08
r_work: 0.2576 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6720  Z= 0.145
  Angle     :  0.576  12.024   9145  Z= 0.280
  Chirality :  0.042   0.156    968
  Planarity :  0.003   0.039   1175
  Dihedral  :  4.389  55.201    971
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 11.29 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.31), residues: 793
  helix:  1.68 (0.27), residues: 396
  sheet: -0.20 (0.78), residues: 48
  loop :  0.02 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 115 
 TYR   0.013   0.001   TYR B 369 
 PHE   0.018   0.001   PHE E 314 
 TRP   0.010   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6709)
  covalent geometry    : angle       0.56961 ( 9118)
  SS BOND              : bond        0.00228 (    6)
  SS BOND              : angle       1.22031 (   12)
  hydrogen bonds       : bond        0.03908 (  309)
  hydrogen bonds       : angle       4.24259 (  891)
  link_NAG-ASN         : bond        0.00325 (    5)
  link_NAG-ASN         : angle       1.99871 (   15)

********************** 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
  44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.240 
Fit side-chains
REVERT: E  152 MET cc_start: 0.8727 (mmt) cc_final: 0.8496 (mmm)
REVERT: E  190 MET cc_start: 0.9321 (tmm) cc_final: 0.9073 (tmm)
REVERT: E  249 MET cc_start: 0.9080 (mmm) cc_final: 0.8641 (mmt)
REVERT: E  270 MET cc_start: 0.9073 (tpp) cc_final: 0.8278 (tpp)
REVERT: E  462 MET cc_start: 0.9373 (mmm) cc_final: 0.9068 (mtm)
  outliers start: 5
  outliers final: 4
  residues processed: 42
  average time/residue: 0.0657
  time to fit residues: 4.1576
Evaluate side-chains
  42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  406 GLU
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 72 optimal weight:    0.1980
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 78 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3129 r_free = 0.3129 target = 0.055749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.041439 restraints weight = 28375.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.2715 rms_B_bonded: 4.04
r_work: 0.2574 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.2574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6720  Z= 0.156
  Angle     :  0.581  11.839   9145  Z= 0.284
  Chirality :  0.041   0.154    968
  Planarity :  0.003   0.039   1175
  Dihedral  :  4.437  55.199    971
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.14 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 11.29 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.31), residues: 793
  helix:  1.71 (0.27), residues: 395
  sheet: -0.33 (0.78), residues: 48
  loop :  0.02 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 115 
 TYR   0.013   0.001   TYR B 369 
 PHE   0.013   0.001   PHE E 314 
 TRP   0.010   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6709)
  covalent geometry    : angle       0.57520 ( 9118)
  SS BOND              : bond        0.00254 (    6)
  SS BOND              : angle       1.08591 (   12)
  hydrogen bonds       : bond        0.03927 (  309)
  hydrogen bonds       : angle       4.24768 (  891)
  link_NAG-ASN         : bond        0.00320 (    5)
  link_NAG-ASN         : angle       2.01842 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1640.21 seconds
wall clock time: 28 minutes 47.96 seconds (1727.96 seconds total)