Starting phenix.real_space_refine
on Thu Jul 24 21:53:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mjn_23879/07_2025/7mjn_23879.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mjn_23879/07_2025/7mjn_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_23879/07_2025/7mjn_23879.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mjn_23879/07_2025/7mjn_23879.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mjn_23879/07_2025/7mjn_23879.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mjn_23879/07_2025/7mjn_23879.cif"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.33, per 1000 atoms: 0.82
  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: 1.52
  Conformation dependent library (CDL) restraints added in 964.5 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: 0.65
  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: 1.74

  Time building geometry restraints manager: 1.83 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:             3.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.910
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.570
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (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
 TRP   0.019   0.002   TRP E 165 
 HIS   0.006   0.002   HIS E 378 
 PHE   0.016   0.002   PHE E 369 
 TYR   0.015   0.002   TYR E 237 
 ARG   0.013   0.001   ARG E 115 

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

*********************** 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  : 0.745 
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: 0.9287 (mmt)
REVERT: E  190 MET cc_start: 0.9238 (tmm) cc_final: 0.9036 (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: 0.1774
  time to fit residues: 14.2891
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  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0570
   overall best weight:    1.1302

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.056152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.042069 restraints weight = 27619.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.2730 rms_B_bonded: 3.99
r_work: 0.2592 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.2592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.1207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6720  Z= 0.178
  Angle     :  0.571   8.599   9145  Z= 0.294
  Chirality :  0.041   0.166    968
  Planarity :  0.004   0.036   1175
  Dihedral  :  5.778  58.093    971
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  4.71 %
    Favored  : 94.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.29), residues: 793
  helix:  0.60 (0.25), residues: 392
  sheet:  0.12 (0.74), residues: 58
  loop : -0.60 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.012   0.001   PHE E 369 
 TYR   0.017   0.001   TYR B 451 
 ARG   0.004   0.000   ARG E 115 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00312 (    5)
  link_NAG-ASN         : angle       2.43571 (   15)
  hydrogen bonds       : bond        0.04742 (  309)
  hydrogen bonds       : angle       4.79142 (  891)
  SS BOND              : bond        0.00326 (    6)
  SS BOND              : angle       0.74296 (   12)
  covalent geometry    : bond        0.00383 ( 6709)
  covalent geometry    : angle       0.56297 ( 9118)

*********************** 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  : 0.764 
Fit side-chains
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.9392 (mtmm) cc_final: 0.9177 (mtmt)
REVERT: E  123 MET cc_start: 0.9455 (mmt) cc_final: 0.9237 (mmt)
REVERT: E  249 MET cc_start: 0.9126 (mmm) cc_final: 0.8678 (mmt)
REVERT: E  332 MET cc_start: 0.8066 (ppp) cc_final: 0.7833 (ppp)
  outliers start: 3
  outliers final: 1
  residues processed: 48
  average time/residue: 0.1808
  time to fit residues: 12.4986
Evaluate side-chains
  43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
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 32 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0030
   chunk 73 optimal weight:    0.5980
   chunk 67 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.8392

-------------------------------------------------------------------------------
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 = 0.3147 r_free = 0.3147 target = 0.056318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.042003 restraints weight = 28351.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.2725 rms_B_bonded: 4.12
r_work: 0.2586 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6720  Z= 0.141
  Angle     :  0.519   8.775   9145  Z= 0.262
  Chirality :  0.040   0.167    968
  Planarity :  0.004   0.032   1175
  Dihedral  :  4.901  56.595    971
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  6.00 %
    Favored  : 93.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.30), residues: 793
  helix:  1.24 (0.26), residues: 386
  sheet:  0.27 (0.79), residues: 48
  loop : -0.39 (0.32), residues: 359

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

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00354 (    5)
  link_NAG-ASN         : angle       2.20103 (   15)
  hydrogen bonds       : bond        0.04179 (  309)
  hydrogen bonds       : angle       4.46362 (  891)
  SS BOND              : bond        0.00263 (    6)
  SS BOND              : angle       0.67999 (   12)
  covalent geometry    : bond        0.00308 ( 6709)
  covalent geometry    : angle       0.51151 ( 9118)

*********************** 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
  53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.786 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.8891 (pm20) cc_final: 0.8631 (mp0)
REVERT: E  249 MET cc_start: 0.9116 (mmm) cc_final: 0.8660 (mmt)
REVERT: E  323 MET cc_start: 0.9454 (mmp) cc_final: 0.9168 (mmp)
REVERT: E  332 MET cc_start: 0.8211 (ppp) cc_final: 0.7993 (ppp)
REVERT: E  462 MET cc_start: 0.9295 (mmm) cc_final: 0.9042 (mtm)
  outliers start: 5
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1749
  time to fit residues: 12.5988
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  : 0.801 
-------------------------------------------------------------------------------
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 22 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0870
   chunk 77 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 43 optimal weight:    0.4980
   chunk 32 optimal weight:    0.0070
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.3976

-------------------------------------------------------------------------------
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 = 0.3173 r_free = 0.3173 target = 0.057425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.042926 restraints weight = 28176.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.2757 rms_B_bonded: 4.17
r_work: 0.2620 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6720  Z= 0.100
  Angle     :  0.504   9.458   9145  Z= 0.249
  Chirality :  0.040   0.174    968
  Planarity :  0.003   0.034   1175
  Dihedral  :  4.488  56.146    971
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  7.43 %
    Favored  : 91.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.30), residues: 793
  helix:  1.43 (0.27), residues: 392
  sheet:  0.06 (0.78), residues: 48
  loop : -0.35 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.002   0.001   HIS E 505 
 PHE   0.011   0.001   PHE E 369 
 TYR   0.010   0.001   TYR B 369 
 ARG   0.002   0.000   ARG E 115 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00407 (    5)
  link_NAG-ASN         : angle       2.02445 (   15)
  hydrogen bonds       : bond        0.03792 (  309)
  hydrogen bonds       : angle       4.28009 (  891)
  SS BOND              : bond        0.00240 (    6)
  SS BOND              : angle       0.64612 (   12)
  covalent geometry    : bond        0.00218 ( 6709)
  covalent geometry    : angle       0.49756 ( 9118)

*********************** 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
  50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.760 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8580 (mp0)
REVERT: E  249 MET cc_start: 0.9110 (mmm) cc_final: 0.8655 (mmt)
REVERT: E  332 MET cc_start: 0.8314 (ppp) cc_final: 0.8089 (ppp)
REVERT: E  411 SER cc_start: 0.9206 (m) cc_final: 0.8773 (p)
REVERT: E  462 MET cc_start: 0.9274 (mmm) cc_final: 0.9047 (mtm)
REVERT: E  474 MET cc_start: 0.8323 (mmp) cc_final: 0.7670 (mmm)
  outliers start: 5
  outliers final: 0
  residues processed: 47
  average time/residue: 0.1660
  time to fit residues: 11.5458
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  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  406 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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 = 0.056332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.041901 restraints weight = 28071.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.2724 rms_B_bonded: 4.10
r_work: 0.2586 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6720  Z= 0.148
  Angle     :  0.511   7.427   9145  Z= 0.255
  Chirality :  0.041   0.162    968
  Planarity :  0.003   0.037   1175
  Dihedral  :  4.421  55.841    971
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  9.00 %
    Favored  : 90.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.30), residues: 793
  helix:  1.69 (0.27), residues: 386
  sheet:  0.00 (0.79), residues: 48
  loop : -0.18 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E  34 
 PHE   0.011   0.001   PHE E 369 
 TYR   0.010   0.001   TYR E 515 
 ARG   0.002   0.000   ARG E 115 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00339 (    5)
  link_NAG-ASN         : angle       2.03390 (   15)
  hydrogen bonds       : bond        0.03894 (  309)
  hydrogen bonds       : angle       4.24459 (  891)
  SS BOND              : bond        0.00276 (    6)
  SS BOND              : angle       0.54503 (   12)
  covalent geometry    : bond        0.00328 ( 6709)
  covalent geometry    : angle       0.50418 ( 9118)

*********************** 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
  44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.775 
Fit side-chains
REVERT: B  378 LYS cc_start: 0.9193 (mmtm) cc_final: 0.8978 (mmtm)
REVERT: B  406 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8487 (mp0)
REVERT: E  249 MET cc_start: 0.9113 (mmm) cc_final: 0.8658 (mmt)
REVERT: E  462 MET cc_start: 0.9291 (mmm) cc_final: 0.9044 (mtm)
  outliers start: 3
  outliers final: 1
  residues processed: 42
  average time/residue: 0.1624
  time to fit residues: 10.2542
Evaluate side-chains
  42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 72 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 27 optimal weight:    0.4980
   chunk 52 optimal weight:    7.9990
   chunk 30 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3154 r_free = 0.3154 target = 0.056240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.042070 restraints weight = 28000.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.2756 rms_B_bonded: 3.99
r_work: 0.2622 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6720  Z= 0.127
  Angle     :  0.505   8.040   9145  Z= 0.251
  Chirality :  0.040   0.161    968
  Planarity :  0.003   0.038   1175
  Dihedral  :  4.329  55.593    971
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  8.71 %
    Favored  : 90.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.30), residues: 793
  helix:  1.72 (0.27), residues: 388
  sheet: -0.00 (0.79), residues: 48
  loop : -0.12 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E  34 
 PHE   0.011   0.001   PHE E 369 
 TYR   0.017   0.001   TYR B 369 
 ARG   0.002   0.000   ARG E 115 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00344 (    5)
  link_NAG-ASN         : angle       1.97818 (   15)
  hydrogen bonds       : bond        0.03809 (  309)
  hydrogen bonds       : angle       4.14766 (  891)
  SS BOND              : bond        0.00269 (    6)
  SS BOND              : angle       0.53507 (   12)
  covalent geometry    : bond        0.00283 ( 6709)
  covalent geometry    : angle       0.49861 ( 9118)

*********************** 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
  48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.749 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8474 (mp0)
REVERT: E  249 MET cc_start: 0.9097 (mmm) cc_final: 0.8627 (mmt)
REVERT: E  270 MET cc_start: 0.9312 (tpp) cc_final: 0.8271 (tpp)
REVERT: E  323 MET cc_start: 0.9409 (mmp) cc_final: 0.9144 (mmp)
REVERT: E  462 MET cc_start: 0.9291 (mmm) cc_final: 0.9043 (mtm)
  outliers start: 5
  outliers final: 2
  residues processed: 45
  average time/residue: 0.1763
  time to fit residues: 11.6202
Evaluate side-chains
  42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 1.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 69 optimal weight:    0.9980
   chunk 33 optimal weight:    7.9990
   chunk 49 optimal weight:    0.3980
   chunk 16 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   chunk 35 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 13 optimal weight:    0.3980
   chunk 36 optimal weight:    0.8980
   chunk 31 optimal weight:    8.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3164 r_free = 0.3164 target = 0.056663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.042498 restraints weight = 28336.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.2772 rms_B_bonded: 4.00
r_work: 0.2637 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.2087

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= 0.115
  Angle     :  0.520   8.187   9145  Z= 0.253
  Chirality :  0.040   0.164    968
  Planarity :  0.003   0.038   1175
  Dihedral  :  4.254  55.451    971
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  9.86 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.31), residues: 793
  helix:  1.61 (0.27), residues: 400
  sheet: -0.06 (0.78), residues: 48
  loop : -0.12 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E  34 
 PHE   0.010   0.001   PHE E 369 
 TYR   0.017   0.001   TYR B 369 
 ARG   0.002   0.000   ARG E 115 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00348 (    5)
  link_NAG-ASN         : angle       1.91739 (   15)
  hydrogen bonds       : bond        0.03705 (  309)
  hydrogen bonds       : angle       4.10385 (  891)
  SS BOND              : bond        0.00262 (    6)
  SS BOND              : angle       0.56292 (   12)
  covalent geometry    : bond        0.00257 ( 6709)
  covalent geometry    : angle       0.51435 ( 9118)

*********************** 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
  46 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.696 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8465 (mp0)
REVERT: E  249 MET cc_start: 0.9072 (mmm) cc_final: 0.8607 (mmt)
REVERT: E  270 MET cc_start: 0.9147 (tpp) cc_final: 0.8363 (tpp)
REVERT: E  408 MET cc_start: 0.9621 (mmm) cc_final: 0.9351 (mmm)
REVERT: E  411 SER cc_start: 0.9230 (m) cc_final: 0.8700 (p)
REVERT: E  462 MET cc_start: 0.9286 (mmm) cc_final: 0.9057 (mtm)
  outliers start: 4
  outliers final: 2
  residues processed: 45
  average time/residue: 0.1579
  time to fit residues: 10.7340
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  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0370
   chunk 3 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.7058

-------------------------------------------------------------------------------
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 = 0.3156 r_free = 0.3156 target = 0.056366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.042169 restraints weight = 28414.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.2759 rms_B_bonded: 4.01
r_work: 0.2622 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.2147

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= 0.125
  Angle     :  0.521   8.696   9145  Z= 0.254
  Chirality :  0.040   0.161    968
  Planarity :  0.003   0.038   1175
  Dihedral  :  4.243  55.478    971
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 10.00 %
    Favored  : 89.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.31), residues: 793
  helix:  1.75 (0.27), residues: 394
  sheet: -0.06 (0.79), residues: 48
  loop : -0.01 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E  34 
 PHE   0.010   0.001   PHE E 369 
 TYR   0.017   0.001   TYR B 369 
 ARG   0.002   0.000   ARG E 115 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00328 (    5)
  link_NAG-ASN         : angle       1.93422 (   15)
  hydrogen bonds       : bond        0.03725 (  309)
  hydrogen bonds       : angle       4.12372 (  891)
  SS BOND              : bond        0.00274 (    6)
  SS BOND              : angle       0.56386 (   12)
  covalent geometry    : bond        0.00280 ( 6709)
  covalent geometry    : angle       0.51528 ( 9118)

*********************** 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
  48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.740 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8542 (mp0)
REVERT: E  249 MET cc_start: 0.9080 (mmm) cc_final: 0.8629 (mmt)
REVERT: E  270 MET cc_start: 0.9103 (tpp) cc_final: 0.8341 (tpp)
REVERT: E  462 MET cc_start: 0.9286 (mmm) cc_final: 0.9056 (mtm)
  outliers start: 4
  outliers final: 2
  residues processed: 47
  average time/residue: 0.1541
  time to fit residues: 10.9231
Evaluate side-chains
  42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 69 optimal weight:    0.5980
   chunk 75 optimal weight:    0.0470
   chunk 57 optimal weight:    0.3980
   chunk 6 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 52 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    0.5680

-------------------------------------------------------------------------------
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 = 0.3166 r_free = 0.3166 target = 0.056782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.042551 restraints weight = 28612.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.2772 rms_B_bonded: 4.04
r_work: 0.2638 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6720  Z= 0.115
  Angle     :  0.542   9.304   9145  Z= 0.261
  Chirality :  0.041   0.165    968
  Planarity :  0.003   0.038   1175
  Dihedral  :  4.206  55.327    971
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.31), residues: 793
  helix:  1.70 (0.27), residues: 400
  sheet: -0.12 (0.79), residues: 48
  loop : -0.07 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E  34 
 PHE   0.009   0.001   PHE E 523 
 TYR   0.016   0.001   TYR B 369 
 ARG   0.002   0.000   ARG E 115 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00349 (    5)
  link_NAG-ASN         : angle       1.92366 (   15)
  hydrogen bonds       : bond        0.03649 (  309)
  hydrogen bonds       : angle       4.08216 (  891)
  SS BOND              : bond        0.00272 (    6)
  SS BOND              : angle       0.58734 (   12)
  covalent geometry    : bond        0.00264 ( 6709)
  covalent geometry    : angle       0.53655 ( 9118)

*********************** 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
  45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8477 (mp0)
REVERT: E  249 MET cc_start: 0.9077 (mmm) cc_final: 0.8620 (mmt)
REVERT: E  270 MET cc_start: 0.8964 (tpp) cc_final: 0.8219 (tpp)
REVERT: E  462 MET cc_start: 0.9275 (mmm) cc_final: 0.9047 (mtm)
  outliers start: 6
  outliers final: 4
  residues processed: 42
  average time/residue: 0.1525
  time to fit residues: 9.6711
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  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  366 MET
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 16 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0870
   chunk 7 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 78 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.3174 r_free = 0.3174 target = 0.057007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.042805 restraints weight = 28382.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 4.03
r_work: 0.2649 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2294

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= 0.114
  Angle     :  0.550  10.918   9145  Z= 0.265
  Chirality :  0.040   0.166    968
  Planarity :  0.003   0.038   1175
  Dihedral  :  4.207  55.360    971
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.77 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 11.14 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.31), residues: 793
  helix:  1.74 (0.27), residues: 400
  sheet: -0.12 (0.79), residues: 48
  loop : -0.06 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 165 
 HIS   0.002   0.001   HIS E 505 
 PHE   0.010   0.001   PHE E 523 
 TYR   0.016   0.001   TYR B 369 
 ARG   0.002   0.000   ARG E 115 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00345 (    5)
  link_NAG-ASN         : angle       1.91016 (   15)
  hydrogen bonds       : bond        0.03653 (  309)
  hydrogen bonds       : angle       4.13397 (  891)
  SS BOND              : bond        0.00283 (    6)
  SS BOND              : angle       0.59168 (   12)
  covalent geometry    : bond        0.00262 ( 6709)
  covalent geometry    : angle       0.54467 ( 9118)

********************** 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: 4
    poor density    : 40
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8438 (mp0)
REVERT: E  152 MET cc_start: 0.8866 (mmt) cc_final: 0.8334 (mmm)
REVERT: E  249 MET cc_start: 0.9076 (mmm) cc_final: 0.8630 (mmt)
REVERT: E  462 MET cc_start: 0.9277 (mmm) cc_final: 0.9058 (mtm)
  outliers start: 4
  outliers final: 3
  residues processed: 41
  average time/residue: 0.1628
  time to fit residues: 9.9146
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  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  406 GLU
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain E residue  366 MET
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 23 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 50 optimal weight:    0.2980
   chunk 58 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    1.4386

-------------------------------------------------------------------------------
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 = 0.3120 r_free = 0.3120 target = 0.055029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.040828 restraints weight = 29069.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.2721 rms_B_bonded: 3.97
r_work: 0.2586 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6720  Z= 0.219
  Angle     :  0.624  11.633   9145  Z= 0.303
  Chirality :  0.043   0.157    968
  Planarity :  0.003   0.039   1175
  Dihedral  :  4.439  55.790    971
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.40 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.29 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.31), residues: 793
  helix:  1.79 (0.27), residues: 393
  sheet: -0.21 (0.80), residues: 48
  loop :  0.03 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.015   0.001   PHE E 523 
 TYR   0.017   0.001   TYR B 369 
 ARG   0.002   0.000   ARG B 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00353 (    5)
  link_NAG-ASN         : angle       2.06505 (   15)
  hydrogen bonds       : bond        0.04189 (  309)
  hydrogen bonds       : angle       4.32524 (  891)
  SS BOND              : bond        0.00419 (    6)
  SS BOND              : angle       0.60376 (   12)
  covalent geometry    : bond        0.00487 ( 6709)
  covalent geometry    : angle       0.61889 ( 9118)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3840.26 seconds
wall clock time: 66 minutes 48.61 seconds (4008.61 seconds total)