Starting phenix.real_space_refine
on Sat May 10 13:38:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xyo_38779/05_2025/8xyo_38779.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xyo_38779/05_2025/8xyo_38779.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xyo_38779/05_2025/8xyo_38779.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xyo_38779/05_2025/8xyo_38779.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xyo_38779/05_2025/8xyo_38779.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xyo_38779/05_2025/8xyo_38779.cif"
  }
  resolution = 3.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      35      5.16       5
     C    4074      2.51       5
     N    1047      2.21       5
     O    1212      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 6369
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4739
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 578, 4729
          Classifications: {'peptide': 578}
          Link IDs: {'PTRANS': 24, 'TRANS': 553}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 578, 4729
          Classifications: {'peptide': 578}
          Link IDs: {'PTRANS': 24, 'TRANS': 553}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4850
    Chain: "B"
      Number of atoms: 1531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1531
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
    Chain: "A"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 85
          Unusual residues: {' ZN': 1, 'NAG': 6}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    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
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS A  34 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A  34 " occ=0.50
  Time building chain proxies: 5.96, per 1000 atoms: 0.94
  Number of scatterers: 6369
  At special positions: 0
  Unit cell: (73.95, 93.5, 124.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      35     16.00
     O    1212      8.00
     N    1047      7.00
     C    4074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, 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

  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 A 701 " - " ASN A 546 "
      " NAG A 702 " - " ASN A  90 "
      " NAG A 703 " - " ASN A 103 "
      " NAG A 704 " - " ASN A  53 "
      " NAG A 705 " - " ASN A 322 "
      " NAG A 706 " - " ASN A 432 "
      " NAG B1301 " - " ASN B 343 "
  Time building additional restraints: 1.35
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 707 "
        pdb="ZN    ZN A 707 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 707 " - pdb=" NE2 HIS A 374 "


  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1452

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 6 sheets defined
      58.0% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.703A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.783A  pdb=" N   GLN A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.919A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.835A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.765A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 220 through 252
      removed outlier: 4.023A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 3.611A  pdb=" N   ASN A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
    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 281
      removed outlier: 4.162A  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
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.735A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   SER A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 385
      removed outlier: 3.850A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    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 420
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.686A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 4.055A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ALA A 528 " --> pdb=" O   GLN A 524 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ALA A 532 " --> pdb=" O   ALA A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.524A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.882A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.716A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 599
      removed outlier: 3.543A  pdb=" N   LEU A 585 " --> pdb=" O   VAL A 581 " (cutoff:3.500A)
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 389
      removed outlier: 4.156A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'B' and resid 502 through 506
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.344A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 357
    Processing sheet with id=AA4, first strand: chain 'B' and resid 361 through 362
      removed outlier: 6.711A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474

    313 hydrogen bonds defined for protein.
    874 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: 1.68

  Time building geometry restraints manager: 1.61 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2025
        1.34 -     1.46: 1534
        1.46 -     1.58: 2932
        1.58 -     1.70: 0
        1.70 -     1.81: 56
  Bond restraints: 6547
  Sorted by residual:
  bond pdb=" C1  NAG A 704 "
       pdb=" O5  NAG A 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.22e+00
  bond pdb=" C   TYR B 495 "
       pdb=" N   GLY B 496 "
    ideal  model  delta    sigma   weight residual
    1.332  1.325  0.007 5.00e-03 4.00e+04 2.13e+00
  bond pdb=" C1  NAG A 703 "
       pdb=" O5  NAG A 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.73e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.70e+00
  bond pdb=" C1  NAG A 706 "
       pdb=" O5  NAG A 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.69e+00
  ... (remaining 6542 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 8478
        1.25 -     2.49: 327
        2.49 -     3.74: 71
        3.74 -     4.99: 19
        4.99 -     6.23: 2
  Bond angle restraints: 8897
  Sorted by residual:
  angle pdb=" C   THR A 334 "
        pdb=" N   ASP A 335 "
        pdb=" CA  ASP A 335 "
      ideal   model   delta    sigma   weight residual
     121.20  125.70   -4.50 1.40e+00 5.10e-01 1.03e+01
  angle pdb=" N   LYS A 234 "
        pdb=" CA  LYS A 234 "
        pdb=" C   LYS A 234 "
      ideal   model   delta    sigma   weight residual
     113.25  116.69   -3.44 1.30e+00 5.92e-01 7.02e+00
  angle pdb=" C   PRO A  84 "
        pdb=" N   LEU A  85 "
        pdb=" CA  LEU A  85 "
      ideal   model   delta    sigma   weight residual
     121.54  126.24   -4.70 1.91e+00 2.74e-01 6.06e+00
  angle pdb=" C   TYR B 495 "
        pdb=" N   GLY B 496 "
        pdb=" CA  GLY B 496 "
      ideal   model   delta    sigma   weight residual
     122.29  120.31    1.98 8.90e-01 1.26e+00 4.93e+00
  angle pdb=" CA  TRP A 165 "
        pdb=" CB  TRP A 165 "
        pdb=" CG  TRP A 165 "
      ideal   model   delta    sigma   weight residual
     113.60  117.33   -3.73 1.90e+00 2.77e-01 3.86e+00
  ... (remaining 8892 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 3590
       17.79 -    35.57: 271
       35.57 -    53.36: 48
       53.36 -    71.14: 12
       71.14 -    88.93: 14
  Dihedral angle restraints: 3935
    sinusoidal: 1669
      harmonic: 2266
  Sorted by residual:
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.04  -80.04     1      1.00e+01 1.00e-02 7.94e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -48.28  -37.72     1      1.00e+01 1.00e-02 2.01e+01
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  129.30  -36.30     1      1.00e+01 1.00e-02 1.86e+01
  ... (remaining 3932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 508
       0.028 -    0.056: 292
       0.056 -    0.085: 91
       0.085 -    0.113: 47
       0.113 -    0.141: 11
  Chirality restraints: 949
  Sorted by residual:
  chirality pdb=" CA  ILE B 434 "
            pdb=" N   ILE B 434 "
            pdb=" C   ILE B 434 "
            pdb=" CB  ILE B 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.98e-01
  chirality pdb=" CA  PRO B 491 "
            pdb=" N   PRO B 491 "
            pdb=" C   PRO B 491 "
            pdb=" CB  PRO B 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.72e-01
  chirality pdb=" C1  NAG A 702 "
            pdb=" ND2 ASN A  90 "
            pdb=" C2  NAG A 702 "
            pdb=" O5  NAG A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 946 not shown)

  Planarity restraints: 1148
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 475 "    0.008 2.00e-02 2.50e+03   1.57e-02 2.46e+00
        pdb=" C   LYS A 475 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   LYS A 475 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LYS A 476 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 473 "   -0.007 2.00e-02 2.50e+03   1.50e-02 2.24e+00
        pdb=" C   TRP A 473 "    0.026 2.00e-02 2.50e+03
        pdb=" O   TRP A 473 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   MET A 474 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 335 "    0.024 5.00e-02 4.00e+02   3.60e-02 2.07e+00
        pdb=" N   PRO A 336 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 336 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 336 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1145 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 69
        2.66 -     3.22: 5794
        3.22 -     3.78: 9374
        3.78 -     4.34: 12820
        4.34 -     4.90: 21900
  Nonbonded interactions: 49957
  Sorted by model distance:
  nonbonded pdb=" CD  GLU A 402 "
            pdb="ZN    ZN A 707 "
     model   vdw
     2.097 2.460
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 707 "
     model   vdw
     2.098 2.230
  nonbonded pdb=" OE1 GLU A 402 "
            pdb="ZN    ZN A 707 "
     model   vdw
     2.105 2.230
  nonbonded pdb=" OD1 ASP B 442 "
            pdb=" OH  TYR B 451 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   ASP A 431 "
            pdb=" OG1 THR A 434 "
     model   vdw
     2.227 3.040
  ... (remaining 49952 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=0.50 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:             2.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     20.620
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.040
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
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   0.202   6560  Z= 0.225
  Angle     :  0.607   7.932   8926  Z= 0.323
  Chirality :  0.042   0.141    949
  Planarity :  0.004   0.037   1141
  Dihedral  : 13.686  88.931   2471
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.35 (0.30), residues: 768
  helix:  1.20 (0.27), residues: 395
  sheet:  0.42 (0.66), residues: 60
  loop : -1.05 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 165 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.017   0.002   PHE A 512 
 TYR   0.016   0.001   TYR A 158 
 ARG   0.003   0.000   ARG A 204 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00335 (    7)
  link_NAG-ASN         : angle       2.73806 (   21)
  hydrogen bonds       : bond        0.16064 (  313)
  hydrogen bonds       : angle       5.81376 (  874)
  metal coordination   : bond        0.20153 (    2)
  SS BOND              : bond        0.00285 (    4)
  SS BOND              : angle       0.60120 (    8)
  covalent geometry    : bond        0.00416 ( 6547)
  covalent geometry    : angle       0.59324 ( 8897)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7343 (tt0) cc_final: 0.7074 (tt0)
REVERT: A  231 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7858 (mm-30)
REVERT: A  243 TYR cc_start: 0.7578 (t80) cc_final: 0.7359 (t80)
REVERT: A  299 ASP cc_start: 0.8028 (m-30) cc_final: 0.7727 (m-30)
REVERT: A  435 GLU cc_start: 0.7294 (mp0) cc_final: 0.6706 (mp0)
REVERT: A  491 VAL cc_start: 0.8438 (t) cc_final: 0.8130 (p)
REVERT: A  512 PHE cc_start: 0.8588 (t80) cc_final: 0.8384 (t80)
REVERT: A  515 TYR cc_start: 0.8382 (m-80) cc_final: 0.7475 (m-80)
REVERT: A  564 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7257 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1768
  time to fit residues: 37.2587
Evaluate side-chains
  137 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 57 optimal weight:    0.2980
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 522 GLN
A 524 GLN
B 354 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.112119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.101768 restraints weight = 19447.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.47
r_work: 0.3176 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6560  Z= 0.205
  Angle     :  0.617   8.300   8926  Z= 0.319
  Chirality :  0.045   0.206    949
  Planarity :  0.004   0.038   1141
  Dihedral  :  6.178  55.037    988
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  6.78 %
    Favored  : 92.18 %
  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:  0.41 (0.30), residues: 768
  helix:  1.39 (0.27), residues: 386
  sheet:  0.27 (0.66), residues: 61
  loop : -1.12 (0.32), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 165 
 HIS   0.008   0.002   HIS A 401 
 PHE   0.020   0.002   PHE A 512 
 TYR   0.015   0.002   TYR A 158 
 ARG   0.006   0.001   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00299 (    7)
  link_NAG-ASN         : angle       3.23584 (   21)
  hydrogen bonds       : bond        0.06893 (  313)
  hydrogen bonds       : angle       4.46984 (  874)
  metal coordination   : bond        0.00357 (    2)
  SS BOND              : bond        0.00614 (    4)
  SS BOND              : angle       1.45079 (    8)
  covalent geometry    : bond        0.00482 ( 6547)
  covalent geometry    : angle       0.59660 ( 8897)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 151
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8286 (tttt) cc_final: 0.8069 (tttt)
REVERT: A   75 GLU cc_start: 0.7728 (tt0) cc_final: 0.7469 (tt0)
REVERT: A  202 TYR cc_start: 0.8473 (t80) cc_final: 0.8111 (t80)
REVERT: A  231 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7951 (mm-30)
REVERT: A  243 TYR cc_start: 0.7491 (t80) cc_final: 0.7208 (t80)
REVERT: A  299 ASP cc_start: 0.7879 (m-30) cc_final: 0.7616 (m-30)
REVERT: A  435 GLU cc_start: 0.7321 (mp0) cc_final: 0.6828 (mp0)
REVERT: A  474 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7211 (mpp)
REVERT: A  491 VAL cc_start: 0.8409 (t) cc_final: 0.8084 (p)
REVERT: B  395 VAL cc_start: 0.8245 (p) cc_final: 0.7872 (t)
  outliers start: 7
  outliers final: 4
  residues processed: 153
  average time/residue: 0.1673
  time to fit residues: 34.5556
Evaluate side-chains
  141 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 136
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
B 354 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.108514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.097809 restraints weight = 20402.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.69
r_work: 0.3106 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3103
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3103
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   6560  Z= 0.245
  Angle     :  0.640   9.270   8926  Z= 0.331
  Chirality :  0.046   0.234    949
  Planarity :  0.005   0.071   1141
  Dihedral  :  5.667  55.394    988
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  8.41 %
    Favored  : 89.38 %
  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:  0.31 (0.30), residues: 768
  helix:  1.33 (0.27), residues: 383
  sheet:  0.61 (0.69), residues: 56
  loop : -1.25 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 165 
 HIS   0.009   0.002   HIS A 401 
 PHE   0.018   0.002   PHE A 369 
 TYR   0.018   0.002   TYR A 158 
 ARG   0.010   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00343 (    7)
  link_NAG-ASN         : angle       3.45705 (   21)
  hydrogen bonds       : bond        0.07411 (  313)
  hydrogen bonds       : angle       4.43982 (  874)
  metal coordination   : bond        0.00308 (    2)
  SS BOND              : bond        0.00164 (    4)
  SS BOND              : angle       1.67478 (    8)
  covalent geometry    : bond        0.00583 ( 6547)
  covalent geometry    : angle       0.61663 ( 8897)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.7636 (tt0) cc_final: 0.7334 (tt0)
REVERT: A  231 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8034 (mm-30)
REVERT: A  243 TYR cc_start: 0.7525 (t80) cc_final: 0.7174 (t80)
REVERT: A  299 ASP cc_start: 0.7968 (m-30) cc_final: 0.7731 (m-30)
REVERT: A  435 GLU cc_start: 0.7358 (mp0) cc_final: 0.6784 (mp0)
REVERT: A  491 VAL cc_start: 0.8461 (t) cc_final: 0.8100 (p)
REVERT: A  564 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7403 (mm-30)
REVERT: B  395 VAL cc_start: 0.8239 (p) cc_final: 0.8008 (t)
  outliers start: 15
  outliers final: 10
  residues processed: 155
  average time/residue: 0.1610
  time to fit residues: 33.5810
Evaluate side-chains
  158 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 148
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  534 LYS
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 56 optimal weight:    0.1980
   chunk 60 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3424 r_free = 0.3424 target = 0.109672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.098926 restraints weight = 20069.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.66
r_work: 0.3124 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6560  Z= 0.188
  Angle     :  0.589   8.185   8926  Z= 0.305
  Chirality :  0.044   0.239    949
  Planarity :  0.005   0.067   1141
  Dihedral  :  5.242  56.055    988
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.73 %
    Favored  : 88.20 %
  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: 768
  helix:  1.44 (0.27), residues: 383
  sheet:  0.48 (0.68), residues: 59
  loop : -1.17 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 165 
 HIS   0.007   0.001   HIS A 401 
 PHE   0.015   0.001   PHE A 369 
 TYR   0.016   0.002   TYR A 158 
 ARG   0.016   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00262 (    7)
  link_NAG-ASN         : angle       3.05012 (   21)
  hydrogen bonds       : bond        0.06546 (  313)
  hydrogen bonds       : angle       4.33077 (  874)
  metal coordination   : bond        0.00172 (    2)
  SS BOND              : bond        0.00335 (    4)
  SS BOND              : angle       1.80402 (    8)
  covalent geometry    : bond        0.00440 ( 6547)
  covalent geometry    : angle       0.56824 ( 8897)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 153
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.7585 (tt0) cc_final: 0.7288 (tt0)
REVERT: A  231 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8043 (mm-30)
REVERT: A  243 TYR cc_start: 0.7453 (t80) cc_final: 0.7088 (t80)
REVERT: A  299 ASP cc_start: 0.7928 (m-30) cc_final: 0.7699 (m-30)
REVERT: A  435 GLU cc_start: 0.7378 (mp0) cc_final: 0.6789 (mp0)
REVERT: A  474 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.7031 (mpp)
REVERT: A  491 VAL cc_start: 0.8417 (t) cc_final: 0.8042 (p)
REVERT: A  564 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7366 (mm-30)
REVERT: B  395 VAL cc_start: 0.8220 (p) cc_final: 0.7964 (t)
REVERT: B  433 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8135 (t)
  outliers start: 14
  outliers final: 9
  residues processed: 159
  average time/residue: 0.1767
  time to fit residues: 37.9584
Evaluate side-chains
  157 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  514 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 17 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0870
   chunk 50 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.3423 r_free = 0.3423 target = 0.109644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.099805 restraints weight = 15399.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.25
r_work: 0.3158 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3003
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3003
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6560  Z= 0.183
  Angle     :  0.581   7.820   8926  Z= 0.301
  Chirality :  0.044   0.248    949
  Planarity :  0.004   0.039   1141
  Dihedral  :  5.079  55.137    988
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 10.32 %
    Favored  : 87.32 %
  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:  0.48 (0.30), residues: 768
  helix:  1.45 (0.27), residues: 383
  sheet:  0.49 (0.68), residues: 59
  loop : -1.11 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 165 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.015   0.001   PHE A 369 
 TYR   0.015   0.002   TYR B 396 
 ARG   0.003   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00245 (    7)
  link_NAG-ASN         : angle       2.92189 (   21)
  hydrogen bonds       : bond        0.06475 (  313)
  hydrogen bonds       : angle       4.30225 (  874)
  metal coordination   : bond        0.00162 (    2)
  SS BOND              : bond        0.00247 (    4)
  SS BOND              : angle       1.72466 (    8)
  covalent geometry    : bond        0.00428 ( 6547)
  covalent geometry    : angle       0.56235 ( 8897)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7802 (tt0) cc_final: 0.7501 (tt0)
REVERT: A  231 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8259 (mm-30)
REVERT: A  243 TYR cc_start: 0.7553 (t80) cc_final: 0.7219 (t80)
REVERT: A  299 ASP cc_start: 0.8054 (m-30) cc_final: 0.7833 (m-30)
REVERT: A  424 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7957 (mp)
REVERT: A  474 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7236 (mpp)
REVERT: A  491 VAL cc_start: 0.8493 (t) cc_final: 0.8119 (p)
REVERT: A  564 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7549 (mm-30)
REVERT: B  395 VAL cc_start: 0.8285 (p) cc_final: 0.7986 (t)
REVERT: B  433 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8242 (t)
  outliers start: 16
  outliers final: 11
  residues processed: 156
  average time/residue: 0.1682
  time to fit residues: 35.2784
Evaluate side-chains
  161 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  514 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 25 optimal weight:    0.0870
   chunk 10 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0570
   chunk 62 optimal weight:    0.6980
   chunk 6 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0030
   chunk 73 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.2486

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

Flipped N/Q/H residues before XYZ refinement:
A 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.112384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.101186 restraints weight = 22240.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 2.85
r_work: 0.3144 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6560  Z= 0.120
  Angle     :  0.520   6.533   8926  Z= 0.270
  Chirality :  0.041   0.256    949
  Planarity :  0.004   0.036   1141
  Dihedral  :  4.779  54.499    988
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.36 %
    Favored  : 86.43 %
  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:  0.71 (0.30), residues: 768
  helix:  1.65 (0.27), residues: 380
  sheet:  0.51 (0.68), residues: 59
  loop : -0.95 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 165 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.011   0.001   PHE A 369 
 TYR   0.014   0.001   TYR A 202 
 ARG   0.002   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00239 (    7)
  link_NAG-ASN         : angle       2.38343 (   21)
  hydrogen bonds       : bond        0.05150 (  313)
  hydrogen bonds       : angle       4.17445 (  874)
  metal coordination   : bond        0.00030 (    2)
  SS BOND              : bond        0.00195 (    4)
  SS BOND              : angle       1.05620 (    8)
  covalent geometry    : bond        0.00256 ( 6547)
  covalent geometry    : angle       0.50727 ( 8897)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7618 (tt0) cc_final: 0.7302 (tt0)
REVERT: A  299 ASP cc_start: 0.7936 (m-30) cc_final: 0.7712 (m-30)
REVERT: A  474 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7074 (mpp)
REVERT: A  491 VAL cc_start: 0.8336 (t) cc_final: 0.7963 (p)
REVERT: A  564 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7388 (mm-30)
REVERT: B  395 VAL cc_start: 0.8104 (p) cc_final: 0.7705 (t)
REVERT: B  433 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8112 (t)
  outliers start: 15
  outliers final: 8
  residues processed: 148
  average time/residue: 0.1684
  time to fit residues: 33.4402
Evaluate side-chains
  148 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 138
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 54 optimal weight:    0.2980
   chunk 41 optimal weight:    0.8980
   chunk 23 optimal weight:    0.4980
   chunk 32 optimal weight:    0.7980
   chunk 72 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3428 r_free = 0.3428 target = 0.110067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.099603 restraints weight = 18348.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.52
r_work: 0.3141 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6560  Z= 0.177
  Angle     :  0.567   7.404   8926  Z= 0.293
  Chirality :  0.043   0.260    949
  Planarity :  0.004   0.038   1141
  Dihedral  :  4.876  54.673    988
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.39 %
    Favored  : 85.84 %
  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:  0.71 (0.30), residues: 768
  helix:  1.62 (0.27), residues: 383
  sheet:  0.55 (0.68), residues: 59
  loop : -0.95 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 165 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.015   0.001   PHE A 369 
 TYR   0.015   0.002   TYR A 587 
 ARG   0.003   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00214 (    7)
  link_NAG-ASN         : angle       2.76115 (   21)
  hydrogen bonds       : bond        0.06117 (  313)
  hydrogen bonds       : angle       4.24913 (  874)
  metal coordination   : bond        0.00034 (    2)
  SS BOND              : bond        0.00194 (    4)
  SS BOND              : angle       1.18220 (    8)
  covalent geometry    : bond        0.00415 ( 6547)
  covalent geometry    : angle       0.55097 ( 8897)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7557 (tt0) cc_final: 0.7240 (tt0)
REVERT: A  299 ASP cc_start: 0.7933 (m-30) cc_final: 0.7703 (m-30)
REVERT: A  424 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7841 (mp)
REVERT: A  474 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7212 (mpp)
REVERT: A  475 LYS cc_start: 0.7685 (ptmm) cc_final: 0.7435 (tttm)
REVERT: A  491 VAL cc_start: 0.8372 (t) cc_final: 0.8001 (p)
REVERT: A  564 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7307 (mm-30)
REVERT: B  433 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8130 (t)
  outliers start: 12
  outliers final: 8
  residues processed: 153
  average time/residue: 0.1768
  time to fit residues: 36.2378
Evaluate side-chains
  157 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0980
   chunk 72 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3415 r_free = 0.3415 target = 0.109191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.098446 restraints weight = 20486.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.70
r_work: 0.3113 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3112
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3112
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6560  Z= 0.207
  Angle     :  0.594   7.927   8926  Z= 0.307
  Chirality :  0.044   0.270    949
  Planarity :  0.004   0.039   1141
  Dihedral  :  4.986  54.837    988
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 12.54 %
    Favored  : 85.25 %
  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:  0.60 (0.30), residues: 768
  helix:  1.53 (0.27), residues: 383
  sheet:  0.57 (0.68), residues: 59
  loop : -1.02 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 165 
 HIS   0.007   0.001   HIS A 241 
 PHE   0.016   0.002   PHE A 369 
 TYR   0.015   0.002   TYR A 158 
 ARG   0.004   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00248 (    7)
  link_NAG-ASN         : angle       2.96912 (   21)
  hydrogen bonds       : bond        0.06602 (  313)
  hydrogen bonds       : angle       4.30178 (  874)
  metal coordination   : bond        0.00065 (    2)
  SS BOND              : bond        0.00226 (    4)
  SS BOND              : angle       1.20868 (    8)
  covalent geometry    : bond        0.00490 ( 6547)
  covalent geometry    : angle       0.57591 ( 8897)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 147
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7581 (tt0) cc_final: 0.7279 (tt0)
REVERT: A  299 ASP cc_start: 0.7960 (m-30) cc_final: 0.7746 (m-30)
REVERT: A  424 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7931 (mp)
REVERT: A  474 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7202 (mpp)
REVERT: A  475 LYS cc_start: 0.7704 (ptmm) cc_final: 0.7456 (tttm)
REVERT: A  491 VAL cc_start: 0.8405 (t) cc_final: 0.8034 (p)
REVERT: A  564 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7317 (mm-30)
REVERT: B  433 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8137 (t)
  outliers start: 15
  outliers final: 9
  residues processed: 154
  average time/residue: 0.1824
  time to fit residues: 37.9263
Evaluate side-chains
  158 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 57 optimal weight:    0.2980
   chunk 9 optimal weight:    0.0170
   chunk 10 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 18 optimal weight:    0.1980
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.3618

-------------------------------------------------------------------------------
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 = 0.3441 r_free = 0.3441 target = 0.110910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.100083 restraints weight = 20091.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 2.68
r_work: 0.3143 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3144
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3144
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6560  Z= 0.146
  Angle     :  0.551   7.444   8926  Z= 0.285
  Chirality :  0.042   0.271    949
  Planarity :  0.004   0.037   1141
  Dihedral  :  4.846  54.478    988
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.13 %
    Favored  : 84.96 %
  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:  0.71 (0.30), residues: 768
  helix:  1.64 (0.27), residues: 380
  sheet:  0.58 (0.69), residues: 59
  loop : -0.96 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.012   0.001   PHE A 369 
 TYR   0.015   0.002   TYR A 202 
 ARG   0.003   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00230 (    7)
  link_NAG-ASN         : angle       2.65391 (   21)
  hydrogen bonds       : bond        0.05722 (  313)
  hydrogen bonds       : angle       4.23513 (  874)
  metal coordination   : bond        0.00021 (    2)
  SS BOND              : bond        0.00206 (    4)
  SS BOND              : angle       0.93979 (    8)
  covalent geometry    : bond        0.00331 ( 6547)
  covalent geometry    : angle       0.53546 ( 8897)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7554 (tt0) cc_final: 0.7226 (tt0)
REVERT: A  299 ASP cc_start: 0.7895 (m-30) cc_final: 0.7680 (m-30)
REVERT: A  474 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7081 (mpp)
REVERT: A  491 VAL cc_start: 0.8354 (t) cc_final: 0.7974 (p)
REVERT: A  564 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7365 (mm-30)
REVERT: B  433 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8112 (t)
  outliers start: 13
  outliers final: 9
  residues processed: 150
  average time/residue: 0.1894
  time to fit residues: 38.1555
Evaluate side-chains
  155 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 40 optimal weight:    0.1980
   chunk 46 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0370
   chunk 58 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0670
   chunk 73 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.2996

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

Flipped N/Q/H residues before XYZ refinement:
A 524 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.111685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.099923 restraints weight = 25981.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 3.13
r_work: 0.3126 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6560  Z= 0.133
  Angle     :  0.539   6.938   8926  Z= 0.279
  Chirality :  0.042   0.267    949
  Planarity :  0.004   0.036   1141
  Dihedral  :  4.743  54.378    988
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.57 %
    Favored  : 84.37 %
  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 (0.31), residues: 768
  helix:  1.70 (0.27), residues: 380
  sheet:  0.60 (0.68), residues: 60
  loop : -0.88 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.011   0.001   PHE A 369 
 TYR   0.014   0.001   TYR A 587 
 ARG   0.003   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00219 (    7)
  link_NAG-ASN         : angle       2.48593 (   21)
  hydrogen bonds       : bond        0.05432 (  313)
  hydrogen bonds       : angle       4.19912 (  874)
  metal coordination   : bond        0.00052 (    2)
  SS BOND              : bond        0.00212 (    4)
  SS BOND              : angle       0.83938 (    8)
  covalent geometry    : bond        0.00294 ( 6547)
  covalent geometry    : angle       0.52513 ( 8897)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 136
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7614 (tt0) cc_final: 0.7293 (tt0)
REVERT: A  299 ASP cc_start: 0.7950 (m-30) cc_final: 0.7736 (m-30)
REVERT: A  474 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7098 (mpp)
REVERT: A  491 VAL cc_start: 0.8355 (t) cc_final: 0.7976 (p)
REVERT: A  564 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7440 (mm-30)
REVERT: B  433 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.8138 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 144
  average time/residue: 0.1739
  time to fit residues: 33.4250
Evaluate side-chains
  146 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  514 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0470
   chunk 5 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0670
   chunk 2 optimal weight:    0.2980
   chunk 65 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0770
   overall best weight:    0.2174

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

Flipped N/Q/H residues before XYZ refinement:
A 522 GLN
A 524 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.113008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.101483 restraints weight = 24222.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 3.00
r_work: 0.3153 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3151
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3151
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6560  Z= 0.117
  Angle     :  0.517   5.975   8926  Z= 0.269
  Chirality :  0.041   0.262    949
  Planarity :  0.004   0.035   1141
  Dihedral  :  4.579  54.064    988
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.72 %
    Favored  : 84.22 %
  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:  0.91 (0.31), residues: 768
  helix:  1.76 (0.27), residues: 380
  sheet:  0.51 (0.69), residues: 59
  loop : -0.77 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 401 
 PHE   0.010   0.001   PHE A 369 
 TYR   0.014   0.001   TYR A 202 
 ARG   0.002   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00215 (    7)
  link_NAG-ASN         : angle       2.16392 (   21)
  hydrogen bonds       : bond        0.04925 (  313)
  hydrogen bonds       : angle       4.14050 (  874)
  metal coordination   : bond        0.00203 (    2)
  SS BOND              : bond        0.00219 (    4)
  SS BOND              : angle       0.73423 (    8)
  covalent geometry    : bond        0.00250 ( 6547)
  covalent geometry    : angle       0.50684 ( 8897)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3565.76 seconds
wall clock time: 62 minutes 56.14 seconds (3776.14 seconds total)