Starting phenix.real_space_refine
on Sat May 10 13:21:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iup_60911/05_2025/9iup_60911.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iup_60911/05_2025/9iup_60911.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iup_60911/05_2025/9iup_60911.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iup_60911/05_2025/9iup_60911.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iup_60911/05_2025/9iup_60911.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iup_60911/05_2025/9iup_60911.cif"
  }
  resolution = 3.3
  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=   0.002 sd=   0.086
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    4115      2.51       5
     N    1064      2.21       5
     O    1204      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6420
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 594, 4845
          Classifications: {'peptide': 594}
          Link IDs: {'PTRANS': 27, 'TRANS': 566}
    Chain: "B"
      Number of atoms: 1547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1547
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 13, 'TRANS': 179}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.36, per 1000 atoms: 0.68
  Number of scatterers: 6420
  At special positions: 0
  Unit cell: (73.528, 81.608, 118.776, 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    1204      8.00
     N    1064      7.00
     C    4115      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    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=2.05
    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

  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 B 601 " - " ASN B 343 "
      " NAG B 602 " - " ASN B 354 "
  Time building additional restraints: 1.54
  Conformation dependent library (CDL) restraints added in 905.9 milliseconds
  

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1484

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 8 sheets defined
      56.3% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.531A  pdb=" N   LYS A  26 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   THR A  27 " --> pdb=" O   GLU A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 80
    Processing helix  chain 'A' and resid 81 through 83
      No H-bonds generated for 'chain 'A' and resid 81 through 83'
    Processing helix  chain 'A' and resid 90 through 101
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.995A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU A 108 " --> pdb=" O   SER A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 147 through 154
      removed outlier: 3.895A  pdb=" N   ASN A 154 " --> pdb=" O   GLU A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.621A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 218 through 252
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 3.520A  pdb=" N   TYR A 279 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   SER A 280 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 319
      removed outlier: 3.907A  pdb=" N   PHE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 330
      removed outlier: 3.823A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 386
      removed outlier: 3.558A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 388
      No H-bonds generated for 'chain 'A' and resid 387 through 388'
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 400 through 413
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 446
      removed outlier: 3.820A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 473 through 484
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 532
      removed outlier: 4.508A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.580A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.803A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.967A  pdb=" N   GLU A 571 " --> pdb=" O   THR A 567 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'B' and resid 337 through 344
    Processing helix  chain 'B' and resid 364 through 370
      removed outlier: 3.729A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 389
      removed outlier: 4.130A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 410
      removed outlier: 3.502A  pdb=" N   VAL B 407 " --> pdb=" O   GLY B 404 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER B 408 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 421
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.749A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA4, first strand: chain 'B' and resid 357 through 358
    Processing sheet with id=AA5, first strand: chain 'B' and resid 357 through 358
    Processing sheet with id=AA6, first strand: chain 'B' and resid 391 through 392
      removed outlier: 3.561A  pdb=" N   VAL B 524 " --> pdb=" O   PHE B 392 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474

    314 hydrogen bonds defined for protein.
    888 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: 2.01

  Time building geometry restraints manager: 1.84 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 1066
        1.31 -     1.44: 1927
        1.44 -     1.58: 3556
        1.58 -     1.72: 0
        1.72 -     1.86: 58
  Bond restraints: 6607
  Sorted by residual:
  bond pdb=" C   PHE A  32 "
       pdb=" O   PHE A  32 "
    ideal  model  delta    sigma   weight residual
    1.236  1.167  0.069 1.16e-02 7.43e+03 3.52e+01
  bond pdb=" CA  ALA A  36 "
       pdb=" CB  ALA A  36 "
    ideal  model  delta    sigma   weight residual
    1.528  1.438  0.090 1.59e-02 3.96e+03 3.21e+01
  bond pdb=" CA  TYR B 495 "
       pdb=" C   TYR B 495 "
    ideal  model  delta    sigma   weight residual
    1.526  1.457  0.069 1.22e-02 6.72e+03 3.20e+01
  bond pdb=" CA  SER B 494 "
       pdb=" CB  SER B 494 "
    ideal  model  delta    sigma   weight residual
    1.529  1.441  0.089 1.58e-02 4.01e+03 3.14e+01
  bond pdb=" CA  TYR A  41 "
       pdb=" C   TYR A  41 "
    ideal  model  delta    sigma   weight residual
    1.523  1.448  0.075 1.35e-02 5.49e+03 3.11e+01
  ... (remaining 6602 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.41: 8906
        3.41 -     6.81: 65
        6.81 -    10.22: 6
       10.22 -    13.63: 2
       13.63 -    17.04: 1
  Bond angle restraints: 8980
  Sorted by residual:
  angle pdb=" C   TYR A  41 "
        pdb=" CA  TYR A  41 "
        pdb=" CB  TYR A  41 "
      ideal   model   delta    sigma   weight residual
     110.67   93.63   17.04 1.92e+00 2.71e-01 7.87e+01
  angle pdb=" CA  TYR B 495 "
        pdb=" CB  TYR B 495 "
        pdb=" CG  TYR B 495 "
      ideal   model   delta    sigma   weight residual
     113.90  127.41  -13.51 1.80e+00 3.09e-01 5.64e+01
  angle pdb=" CA  CYS B 379 "
        pdb=" CB  CYS B 379 "
        pdb=" SG  CYS B 379 "
      ideal   model   delta    sigma   weight residual
     114.40  127.64  -13.24 2.30e+00 1.89e-01 3.31e+01
  angle pdb=" C   HIS A  34 "
        pdb=" CA  HIS A  34 "
        pdb=" CB  HIS A  34 "
      ideal   model   delta    sigma   weight residual
     110.96  102.19    8.77 1.54e+00 4.22e-01 3.24e+01
  angle pdb=" C   ASN A  33 "
        pdb=" CA  ASN A  33 "
        pdb=" CB  ASN A  33 "
      ideal   model   delta    sigma   weight residual
     110.84  120.26   -9.42 1.66e+00 3.63e-01 3.22e+01
  ... (remaining 8975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 3282
       15.94 -    31.88: 455
       31.88 -    47.81: 145
       47.81 -    63.75: 31
       63.75 -    79.69: 13
  Dihedral angle restraints: 3926
    sinusoidal: 1615
      harmonic: 2311
  Sorted by residual:
  dihedral pdb=" C   TYR A  41 "
           pdb=" N   TYR A  41 "
           pdb=" CA  TYR A  41 "
           pdb=" CB  TYR A  41 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -102.81  -19.79     0      2.50e+00 1.60e-01 6.26e+01
  dihedral pdb=" CB  CYS B 379 "
           pdb=" SG  CYS B 379 "
           pdb=" SG  CYS B 432 "
           pdb=" CB  CYS B 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   28.69   64.31     1      1.00e+01 1.00e-02 5.44e+01
  dihedral pdb=" CB  CYS A 344 "
           pdb=" SG  CYS A 344 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  155.72  -62.72     1      1.00e+01 1.00e-02 5.20e+01
  ... (remaining 3923 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 812
       0.062 -    0.124: 116
       0.124 -    0.186: 6
       0.186 -    0.248: 2
       0.248 -    0.310: 3
  Chirality restraints: 939
  Sorted by residual:
  chirality pdb=" C1  NAG B 601 "
            pdb=" ND2 ASN B 343 "
            pdb=" C2  NAG B 601 "
            pdb=" O5  NAG B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" CA  GLU B 493 "
            pdb=" N   GLU B 493 "
            pdb=" C   GLU B 493 "
            pdb=" CB  GLU B 493 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CA  ASN A  33 "
            pdb=" N   ASN A  33 "
            pdb=" C   ASN A  33 "
            pdb=" CB  ASN A  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.59e+00
  ... (remaining 936 not shown)

  Planarity restraints: 1163
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 495 "    0.014 2.00e-02 2.50e+03   2.86e-02 8.18e+00
        pdb=" C   TYR B 495 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   TYR B 495 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLY B 496 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 493 "    0.013 2.00e-02 2.50e+03   2.71e-02 7.37e+00
        pdb=" C   GLU B 493 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   GLU B 493 "    0.017 2.00e-02 2.50e+03
        pdb=" N   SER B 494 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  37 "    0.012 2.00e-02 2.50e+03   2.35e-02 5.51e+00
        pdb=" C   GLU A  37 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   GLU A  37 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASP A  38 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1160 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 139
        2.69 -     3.24: 6180
        3.24 -     3.79: 10243
        3.79 -     4.35: 13276
        4.35 -     4.90: 22740
  Nonbonded interactions: 52578
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  41 "
            pdb=" OG1 THR B 500 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" OH  TYR A  41 "
            pdb=" OD2 ASP A 355 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OE1 GLU B 406 "
            pdb=" OH  TYR B 495 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OH  TYR A 183 "
            pdb=" OD1 ASP A 509 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OG  SER B 438 "
            pdb=" OD2 ASP B 442 "
     model   vdw
     2.280 3.040
  ... (remaining 52573 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:                  0.010
  Normalize map: mean=0, sd=1:             0.750
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     18.720
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  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:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
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   0.090   6616  Z= 0.314
  Angle     :  0.740  17.037   9000  Z= 0.449
  Chirality :  0.046   0.310    939
  Planarity :  0.004   0.037   1161
  Dihedral  : 16.868  79.689   2421
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 19.08 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.40 %
  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:  0.54 (0.31), residues: 783
  helix:  1.40 (0.27), residues: 393
  sheet: -1.37 (0.89), residues: 45
  loop : -0.57 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 594 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.019   0.001   PHE A  40 
 TYR   0.038   0.002   TYR B 495 
 ARG   0.002   0.000   ARG A 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00832 (    2)
  link_NAG-ASN         : angle       3.07390 (    6)
  hydrogen bonds       : bond        0.15698 (  308)
  hydrogen bonds       : angle       6.12297 (  888)
  SS BOND              : bond        0.00672 (    7)
  SS BOND              : angle       1.93483 (   14)
  covalent geometry    : bond        0.00471 ( 6607)
  covalent geometry    : angle       0.73285 ( 8980)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8036 (mmtt)
REVERT: A  325 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7106 (tp-100)
  outliers start: 1
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1881
  time to fit residues: 21.1171
Evaluate side-chains
  79 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0970
   chunk 32 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    0.1980
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 374 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.176897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.139397 restraints weight = 7177.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.33
r_work: 0.3153 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.0775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6616  Z= 0.115
  Angle     :  0.511   7.464   9000  Z= 0.263
  Chirality :  0.040   0.233    939
  Planarity :  0.004   0.037   1161
  Dihedral  :  4.251  56.047    899
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 17.05 %
    Favored  : 81.50 %
  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:  0.58 (0.31), residues: 783
  helix:  1.38 (0.26), residues: 405
  sheet: -1.47 (0.86), residues: 44
  loop : -0.55 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 436 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.012   0.001   PHE A 327 
 TYR   0.017   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00728 (    2)
  link_NAG-ASN         : angle       2.16185 (    6)
  hydrogen bonds       : bond        0.04413 (  308)
  hydrogen bonds       : angle       4.25217 (  888)
  SS BOND              : bond        0.00441 (    7)
  SS BOND              : angle       1.01545 (   14)
  covalent geometry    : bond        0.00244 ( 6607)
  covalent geometry    : angle       0.50743 ( 8980)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7961 (mmtt)
REVERT: A  465 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7365 (ttmm)
REVERT: A  482 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.8122 (mmm-85)
  outliers start: 10
  outliers final: 6
  residues processed: 92
  average time/residue: 0.1737
  time to fit residues: 21.8732
Evaluate side-chains
  83 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  516 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 24 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    1.6984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.171097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.132740 restraints weight = 7278.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.43
r_work: 0.3043 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6616  Z= 0.201
  Angle     :  0.569   6.889   9000  Z= 0.291
  Chirality :  0.042   0.224    939
  Planarity :  0.004   0.036   1161
  Dihedral  :  4.412  55.899    899
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.47 %
    Favored  : 80.78 %
  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:  0.27 (0.30), residues: 783
  helix:  1.15 (0.26), residues: 410
  sheet: -1.73 (0.78), residues: 54
  loop : -0.66 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 436 
 HIS   0.005   0.001   HIS A 535 
 PHE   0.014   0.001   PHE A 523 
 TYR   0.023   0.002   TYR A 385 
 ARG   0.003   0.000   ARG A 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00575 (    2)
  link_NAG-ASN         : angle       1.94537 (    6)
  hydrogen bonds       : bond        0.04788 (  308)
  hydrogen bonds       : angle       4.20896 (  888)
  SS BOND              : bond        0.00420 (    7)
  SS BOND              : angle       1.08437 (   14)
  covalent geometry    : bond        0.00473 ( 6607)
  covalent geometry    : angle       0.56562 ( 8980)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8140 (mmtt)
REVERT: A  149 ASN cc_start: 0.7524 (m-40) cc_final: 0.7323 (m-40)
REVERT: A  465 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7406 (ttmm)
REVERT: A  482 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.8147 (mmm-85)
REVERT: A  489 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6388 (mp0)
REVERT: B  394 ASN cc_start: 0.7688 (m-40) cc_final: 0.7404 (m-40)
  outliers start: 19
  outliers final: 13
  residues processed: 91
  average time/residue: 0.1643
  time to fit residues: 20.6634
Evaluate side-chains
  90 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  489 GLU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  516 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.4208 r_free = 0.4208 target = 0.201888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.158549 restraints weight = 7524.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 2.18
r_work: 0.3374 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6616  Z= 0.152
  Angle     :  0.534   6.890   9000  Z= 0.272
  Chirality :  0.041   0.203    939
  Planarity :  0.004   0.037   1161
  Dihedral  :  4.297  54.585    899
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 16.47 %
    Favored  : 80.35 %
  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:  0.33 (0.30), residues: 783
  helix:  1.18 (0.26), residues: 410
  sheet: -1.66 (0.79), residues: 54
  loop : -0.63 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 436 
 HIS   0.006   0.001   HIS A 535 
 PHE   0.012   0.001   PHE A 523 
 TYR   0.020   0.002   TYR A 385 
 ARG   0.002   0.000   ARG A 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00457 (    2)
  link_NAG-ASN         : angle       1.56616 (    6)
  hydrogen bonds       : bond        0.04442 (  308)
  hydrogen bonds       : angle       4.06261 (  888)
  SS BOND              : bond        0.00443 (    7)
  SS BOND              : angle       1.01290 (   14)
  covalent geometry    : bond        0.00353 ( 6607)
  covalent geometry    : angle       0.53107 ( 8980)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8163 (mmtt)
REVERT: A  145 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7408 (tm-30)
REVERT: A  149 ASN cc_start: 0.7629 (m-40) cc_final: 0.7340 (m-40)
REVERT: A  189 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7834 (tm-30)
REVERT: A  366 MET cc_start: 0.8020 (tpt) cc_final: 0.7479 (tpp)
REVERT: A  465 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7385 (ttmm)
REVERT: A  474 MET cc_start: 0.7836 (mmp) cc_final: 0.7606 (mmp)
REVERT: A  482 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.8216 (mmm-85)
REVERT: A  489 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6423 (mp0)
REVERT: B  394 ASN cc_start: 0.7672 (m-40) cc_final: 0.7432 (m-40)
  outliers start: 22
  outliers final: 13
  residues processed: 95
  average time/residue: 0.1674
  time to fit residues: 21.7744
Evaluate side-chains
  92 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  480 MET
Chi-restraints excluded: chain A residue  489 GLU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 52 optimal weight:    7.9990
   chunk 11 optimal weight:    0.7980
   chunk 4 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 445 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.173139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.133328 restraints weight = 7177.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.29
r_work: 0.3098 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6616  Z= 0.120
  Angle     :  0.500   6.800   9000  Z= 0.255
  Chirality :  0.040   0.191    939
  Planarity :  0.003   0.037   1161
  Dihedral  :  4.145  53.893    899
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 16.47 %
    Favored  : 80.06 %
  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:  0.57 (0.31), residues: 783
  helix:  1.37 (0.26), residues: 404
  sheet: -1.49 (0.78), residues: 54
  loop : -0.47 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 436 
 HIS   0.006   0.001   HIS A 535 
 PHE   0.011   0.001   PHE A 523 
 TYR   0.018   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00381 (    2)
  link_NAG-ASN         : angle       1.34238 (    6)
  hydrogen bonds       : bond        0.04137 (  308)
  hydrogen bonds       : angle       3.94469 (  888)
  SS BOND              : bond        0.00444 (    7)
  SS BOND              : angle       0.89353 (   14)
  covalent geometry    : bond        0.00270 ( 6607)
  covalent geometry    : angle       0.49801 ( 8980)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8194 (mmtt)
REVERT: A  145 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7396 (tm-30)
REVERT: A  149 ASN cc_start: 0.7576 (m-40) cc_final: 0.7236 (m-40)
REVERT: A  189 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7817 (tm-30)
REVERT: A  216 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7543 (p0)
REVERT: A  366 MET cc_start: 0.8068 (tpt) cc_final: 0.7542 (tpp)
REVERT: A  465 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7436 (ttmm)
REVERT: A  482 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.8159 (mmm-85)
REVERT: B  394 ASN cc_start: 0.7700 (m-40) cc_final: 0.7443 (m-40)
  outliers start: 24
  outliers final: 14
  residues processed: 98
  average time/residue: 0.1728
  time to fit residues: 23.4039
Evaluate side-chains
  93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue  216 ASP
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  480 MET
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 27 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.4138 r_free = 0.4138 target = 0.193868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.152252 restraints weight = 7320.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 2.38
r_work: 0.3310 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   6616  Z= 0.232
  Angle     :  0.591   7.863   9000  Z= 0.301
  Chirality :  0.043   0.190    939
  Planarity :  0.004   0.037   1161
  Dihedral  :  4.470  54.245    899
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 17.49 %
    Favored  : 79.34 %
  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:  0.32 (0.30), residues: 783
  helix:  1.16 (0.26), residues: 402
  sheet: -1.64 (0.74), residues: 54
  loop : -0.58 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 271 
 HIS   0.006   0.001   HIS A 535 
 PHE   0.016   0.001   PHE A 523 
 TYR   0.021   0.002   TYR A 385 
 ARG   0.004   0.001   ARG A 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00552 (    2)
  link_NAG-ASN         : angle       1.59606 (    6)
  hydrogen bonds       : bond        0.04929 (  308)
  hydrogen bonds       : angle       4.08633 (  888)
  SS BOND              : bond        0.00394 (    7)
  SS BOND              : angle       1.18694 (   14)
  covalent geometry    : bond        0.00553 ( 6607)
  covalent geometry    : angle       0.58811 ( 8980)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8228 (mmtt)
REVERT: A  145 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7379 (tm-30)
REVERT: A  149 ASN cc_start: 0.7607 (m-40) cc_final: 0.7255 (m-40)
REVERT: A  154 ASN cc_start: 0.8875 (p0) cc_final: 0.8551 (p0)
REVERT: A  189 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7935 (tm-30)
REVERT: A  216 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7717 (p0)
REVERT: A  465 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7403 (ttmm)
REVERT: B  394 ASN cc_start: 0.7702 (m-40) cc_final: 0.7420 (m-40)
  outliers start: 22
  outliers final: 15
  residues processed: 98
  average time/residue: 0.1586
  time to fit residues: 21.8125
Evaluate side-chains
  94 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  216 ASP
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 64 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 43 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4178 r_free = 0.4178 target = 0.197872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.156453 restraints weight = 7320.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 2.15
r_work: 0.3397 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6616  Z= 0.129
  Angle     :  0.527   6.926   9000  Z= 0.267
  Chirality :  0.041   0.185    939
  Planarity :  0.003   0.037   1161
  Dihedral  :  4.231  53.260    899
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.50 %
    Favored  : 78.47 %
  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:  0.43 (0.30), residues: 783
  helix:  1.17 (0.26), residues: 407
  sheet: -1.42 (0.74), residues: 54
  loop : -0.46 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 353 
 HIS   0.005   0.001   HIS A 535 
 PHE   0.011   0.001   PHE A 523 
 TYR   0.018   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00361 (    2)
  link_NAG-ASN         : angle       1.33240 (    6)
  hydrogen bonds       : bond        0.04259 (  308)
  hydrogen bonds       : angle       3.96371 (  888)
  SS BOND              : bond        0.00505 (    7)
  SS BOND              : angle       1.19446 (   14)
  covalent geometry    : bond        0.00293 ( 6607)
  covalent geometry    : angle       0.52396 ( 8980)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8201 (mmtt)
REVERT: A  145 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7319 (tm-30)
REVERT: A  149 ASN cc_start: 0.7644 (m-40) cc_final: 0.7286 (m-40)
REVERT: A  154 ASN cc_start: 0.8831 (p0) cc_final: 0.8515 (p0)
REVERT: A  189 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7782 (tm-30)
REVERT: A  366 MET cc_start: 0.7924 (tpt) cc_final: 0.7649 (tpp)
REVERT: A  465 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7348 (ttmm)
REVERT: A  474 MET cc_start: 0.7835 (mmp) cc_final: 0.7604 (mmp)
REVERT: B  394 ASN cc_start: 0.7685 (m-40) cc_final: 0.7421 (m-40)
  outliers start: 21
  outliers final: 16
  residues processed: 97
  average time/residue: 0.1668
  time to fit residues: 22.1801
Evaluate side-chains
  96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0570
   chunk 12 optimal weight:    0.0970
   chunk 36 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.5296

-------------------------------------------------------------------------------
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 = 0.3859 r_free = 0.3859 target = 0.172945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.134755 restraints weight = 7303.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.28
r_work: 0.3105 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6616  Z= 0.114
  Angle     :  0.511   6.837   9000  Z= 0.260
  Chirality :  0.040   0.179    939
  Planarity :  0.003   0.037   1161
  Dihedral  :  4.086  52.840    899
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.35 %
    Favored  : 79.05 %
  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:  0.58 (0.31), residues: 783
  helix:  1.29 (0.26), residues: 407
  sheet: -1.22 (0.75), residues: 54
  loop : -0.40 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 353 
 HIS   0.001   0.000   HIS A 540 
 PHE   0.012   0.001   PHE A 523 
 TYR   0.017   0.001   TYR A 385 
 ARG   0.004   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00325 (    2)
  link_NAG-ASN         : angle       1.19055 (    6)
  hydrogen bonds       : bond        0.04089 (  308)
  hydrogen bonds       : angle       3.90861 (  888)
  SS BOND              : bond        0.00495 (    7)
  SS BOND              : angle       1.06175 (   14)
  covalent geometry    : bond        0.00252 ( 6607)
  covalent geometry    : angle       0.50921 ( 8980)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7273 (tm-30)
REVERT: A  149 ASN cc_start: 0.7685 (m-40) cc_final: 0.7335 (m-40)
REVERT: A  154 ASN cc_start: 0.8745 (p0) cc_final: 0.8398 (p0)
REVERT: A  189 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7719 (tm-30)
REVERT: A  366 MET cc_start: 0.7844 (tpt) cc_final: 0.7593 (tpp)
REVERT: A  465 LYS cc_start: 0.7915 (ttmt) cc_final: 0.7407 (ttmm)
REVERT: B  394 ASN cc_start: 0.7554 (m-40) cc_final: 0.7270 (m-40)
  outliers start: 18
  outliers final: 16
  residues processed: 93
  average time/residue: 0.1633
  time to fit residues: 21.1092
Evaluate side-chains
  90 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0570
   overall best weight:    0.7498

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.172243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.134065 restraints weight = 7356.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.24
r_work: 0.3096 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6616  Z= 0.128
  Angle     :  0.535   7.747   9000  Z= 0.275
  Chirality :  0.041   0.176    939
  Planarity :  0.004   0.037   1161
  Dihedral  :  3.762  18.036    895
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 17.77 %
    Favored  : 78.90 %
  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:  0.54 (0.30), residues: 783
  helix:  1.25 (0.26), residues: 407
  sheet: -1.18 (0.75), residues: 54
  loop : -0.42 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 302 
 HIS   0.008   0.001   HIS A 535 
 PHE   0.012   0.001   PHE A 523 
 TYR   0.026   0.001   TYR A 279 
 ARG   0.005   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00344 (    2)
  link_NAG-ASN         : angle       1.18117 (    6)
  hydrogen bonds       : bond        0.04147 (  308)
  hydrogen bonds       : angle       3.92495 (  888)
  SS BOND              : bond        0.00474 (    7)
  SS BOND              : angle       1.04961 (   14)
  covalent geometry    : bond        0.00290 ( 6607)
  covalent geometry    : angle       0.53351 ( 8980)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7264 (tm-30)
REVERT: A  149 ASN cc_start: 0.7678 (m-40) cc_final: 0.7319 (m-40)
REVERT: A  154 ASN cc_start: 0.8741 (p0) cc_final: 0.8399 (p0)
REVERT: A  189 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: A  216 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7270 (p0)
REVERT: A  465 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7388 (ttmm)
REVERT: A  482 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8223 (mmm-85)
REVERT: B  394 ASN cc_start: 0.7555 (m-40) cc_final: 0.7267 (m-40)
  outliers start: 23
  outliers final: 20
  residues processed: 92
  average time/residue: 0.1579
  time to fit residues: 20.4959
Evaluate side-chains
  96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  216 ASP
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  599 ASN
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0030
   chunk 22 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   chunk 63 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 75 optimal weight:    0.1980
   chunk 54 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.5790

-------------------------------------------------------------------------------
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 = 0.3865 r_free = 0.3865 target = 0.173565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.134841 restraints weight = 7363.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.44
r_work: 0.3116 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6616  Z= 0.118
  Angle     :  0.535   9.133   9000  Z= 0.271
  Chirality :  0.041   0.174    939
  Planarity :  0.004   0.037   1161
  Dihedral  :  3.730  17.433    895
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.64 %
    Favored  : 78.76 %
  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:  0.52 (0.31), residues: 783
  helix:  1.21 (0.26), residues: 410
  sheet: -1.18 (0.74), residues: 54
  loop : -0.41 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 353 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.012   0.001   PHE A 523 
 TYR   0.017   0.001   TYR A 385 
 ARG   0.005   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00328 (    2)
  link_NAG-ASN         : angle       1.14602 (    6)
  hydrogen bonds       : bond        0.04030 (  308)
  hydrogen bonds       : angle       3.93309 (  888)
  SS BOND              : bond        0.00461 (    7)
  SS BOND              : angle       0.96555 (   14)
  covalent geometry    : bond        0.00261 ( 6607)
  covalent geometry    : angle       0.53358 ( 8980)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7264 (tm-30)
REVERT: A  149 ASN cc_start: 0.7672 (m-40) cc_final: 0.7310 (m-40)
REVERT: A  154 ASN cc_start: 0.8746 (p0) cc_final: 0.8413 (p0)
REVERT: A  189 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7707 (tm-30)
REVERT: A  465 LYS cc_start: 0.7916 (ttmt) cc_final: 0.7410 (ttmm)
REVERT: A  482 ARG cc_start: 0.8581 (mmm-85) cc_final: 0.8223 (mmm-85)
REVERT: B  394 ASN cc_start: 0.7522 (m-40) cc_final: 0.7240 (m-40)
  outliers start: 18
  outliers final: 17
  residues processed: 88
  average time/residue: 0.1557
  time to fit residues: 19.2357
Evaluate side-chains
  89 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 11 optimal weight:   40.0000
   chunk 12 optimal weight:    8.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.4140 r_free = 0.4140 target = 0.194005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.153323 restraints weight = 7598.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3729 rms_B_bonded: 2.22
r_work: 0.3318 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6616  Z= 0.210
  Angle     :  0.608   7.789   9000  Z= 0.311
  Chirality :  0.043   0.174    939
  Planarity :  0.004   0.036   1161
  Dihedral  :  4.123  20.917    895
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.21 %
    Favored  : 78.76 %
  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:  0.36 (0.30), residues: 783
  helix:  1.09 (0.26), residues: 402
  sheet: -1.21 (0.74), residues: 54
  loop : -0.49 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 271 
 HIS   0.010   0.001   HIS A 535 
 PHE   0.014   0.001   PHE A 523 
 TYR   0.020   0.002   TYR A 385 
 ARG   0.005   0.001   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00542 (    2)
  link_NAG-ASN         : angle       1.48738 (    6)
  hydrogen bonds       : bond        0.04838 (  308)
  hydrogen bonds       : angle       4.10423 (  888)
  SS BOND              : bond        0.00582 (    7)
  SS BOND              : angle       1.30742 (   14)
  covalent geometry    : bond        0.00498 ( 6607)
  covalent geometry    : angle       0.60476 ( 8980)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3059.71 seconds
wall clock time: 53 minutes 50.01 seconds (3230.01 seconds total)