Starting phenix.real_space_refine
on Thu Jul 24 15:06:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ddp_30653/07_2025/7ddp_30653.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ddp_30653/07_2025/7ddp_30653.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ddp_30653/07_2025/7ddp_30653.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ddp_30653/07_2025/7ddp_30653.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ddp_30653/07_2025/7ddp_30653.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ddp_30653/07_2025/7ddp_30653.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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      37      5.16       5
     C    4143      2.51       5
     N    1065      2.21       5
     O    1231      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6477
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4877
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 27, 'TRANS': 569}
      Conformer: "B"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 27, 'TRANS': 569}
          bond proxies already assigned to first conformer: 4998
    Chain: "C"
      Number of atoms: 1529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1529
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "A"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 57
          Unusual residues: {' ZN': 1, 'NAG': 4}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      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
  Time building chain proxies: 6.81, per 1000 atoms: 1.05
  Number of scatterers: 6477
  At special positions: 0
  Unit cell: (102.356, 97.3875, 105.338, 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      37     16.00
     O    1231      8.00
     N    1065      7.00
     C    4143      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 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 902 " - " ASN A 546 "
      " NAG A 903 " - " ASN A  90 "
      " NAG A 904 " - " ASN A 322 "
      " NAG A 905 " - " ASN A  53 "
      " NAG C 601 " - " ASN C 343 "
  Time building additional restraints: 1.60
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 374 "


  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1488

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 5 sheets defined
      56.8% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 4.030A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 81
    Processing helix  chain 'A' and resid 82 through 83
      No H-bonds generated for 'chain 'A' and resid 82 through 83'
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.596A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.529A  pdb=" N   GLN A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 108
      removed outlier: 3.806A  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 147 through 155
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 4.205A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 219 through 252
      removed outlier: 4.122A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.775A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.623A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.708A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 400 through 414
      removed outlier: 3.557A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 447
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 472 through 484
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 532
      removed outlier: 4.283A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 4.098A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.726A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 364 through 370
      removed outlier: 4.335A  pdb=" N   LEU C 368 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 388
      removed outlier: 3.680A  pdb=" N   ASN C 388 " --> pdb=" O   PRO C 384 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 410
    Processing helix  chain 'C' and resid 438 through 443
    Processing helix  chain 'C' and resid 502 through 506
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.784A  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 'C' and resid 354 through 358
      removed outlier: 3.523A  pdb=" N   LYS C 356 " --> pdb=" O   ALA C 397 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   VAL C 433 " --> pdb=" O   LYS C 378 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LYS C 378 " --> pdb=" O   VAL C 433 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 448 through 454
      removed outlier: 5.328A  pdb=" N   TYR C 449 " --> pdb=" O   PHE C 497 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   PHE C 497 " --> pdb=" O   TYR C 449 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   TYR C 451 " --> pdb=" O   TYR C 495 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 473 through 474
      removed outlier: 3.540A  pdb=" N   TYR C 473 " --> pdb=" O   TYR C 489 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR C 489 " --> pdb=" O   TYR C 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    310 hydrogen bonds defined for protein.
    881 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: 1.63

  Time building geometry restraints manager: 1.89 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2071
        1.35 -     1.46: 1708
        1.46 -     1.58: 2820
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6657
  Sorted by residual:
  bond pdb=" N   TYR C 489 "
       pdb=" CA  TYR C 489 "
    ideal  model  delta    sigma   weight residual
    1.455  1.492 -0.037 1.21e-02 6.83e+03 9.23e+00
  bond pdb=" N   PHE C 456 "
       pdb=" CA  PHE C 456 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.23e-02 6.61e+03 6.41e+00
  bond pdb=" C1  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.03e+00
  bond pdb=" C1  NAG A 904 "
       pdb=" O5  NAG A 904 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.12e+00
  bond pdb=" C1  NAG A 903 "
       pdb=" O5  NAG A 903 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.98e+00
  ... (remaining 6652 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 8793
        1.42 -     2.83: 209
        2.83 -     4.25: 32
        4.25 -     5.67: 14
        5.67 -     7.09: 2
  Bond angle restraints: 9050
  Sorted by residual:
  angle pdb=" N   VAL A 318 "
        pdb=" CA  VAL A 318 "
        pdb=" C   VAL A 318 "
      ideal   model   delta    sigma   weight residual
     112.80  109.72    3.08 1.15e+00 7.56e-01 7.19e+00
  angle pdb=" C   LEU A 144 "
        pdb=" N   GLU A 145 "
        pdb=" CA  GLU A 145 "
      ideal   model   delta    sigma   weight residual
     120.44  123.89   -3.45 1.30e+00 5.92e-01 7.05e+00
  angle pdb=" N   CYS C 432 "
        pdb=" CA  CYS C 432 "
        pdb=" C   CYS C 432 "
      ideal   model   delta    sigma   weight residual
     108.38  111.77   -3.39 1.35e+00 5.49e-01 6.29e+00
  angle pdb=" CA  CYS C 432 "
        pdb=" CB  CYS C 432 "
        pdb=" SG  CYS C 432 "
      ideal   model   delta    sigma   weight residual
     114.40  119.69   -5.29 2.30e+00 1.89e-01 5.28e+00
  angle pdb=" N   ILE A 421 "
        pdb=" CA  ILE A 421 "
        pdb=" C   ILE A 421 "
      ideal   model   delta    sigma   weight residual
     112.98  110.18    2.80 1.25e+00 6.40e-01 5.03e+00
  ... (remaining 9045 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3599
       17.97 -    35.94: 318
       35.94 -    53.91: 53
       53.91 -    71.88: 12
       71.88 -    89.85: 11
  Dihedral angle restraints: 3993
    sinusoidal: 1671
      harmonic: 2322
  Sorted by residual:
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    8.59   84.41     1      1.00e+01 1.00e-02 8.67e+01
  dihedral pdb=" CB  CYS C 379 "
           pdb=" SG  CYS C 379 "
           pdb=" SG  CYS C 432 "
           pdb=" CB  CYS C 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   15.94   77.06     1      1.00e+01 1.00e-02 7.45e+01
  dihedral pdb=" CB  CYS C 391 "
           pdb=" SG  CYS C 391 "
           pdb=" SG  CYS C 525 "
           pdb=" CB  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   23.03   69.97     1      1.00e+01 1.00e-02 6.31e+01
  ... (remaining 3990 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 578
       0.029 -    0.058: 260
       0.058 -    0.087: 72
       0.087 -    0.115: 51
       0.115 -    0.144: 4
  Chirality restraints: 965
  Sorted by residual:
  chirality pdb=" CA  PHE C 456 "
            pdb=" N   PHE C 456 "
            pdb=" C   PHE C 456 "
            pdb=" CB  PHE C 456 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 5.21e-01
  chirality pdb=" CA  ILE A 468 "
            pdb=" N   ILE A 468 "
            pdb=" C   ILE A 468 "
            pdb=" CB  ILE A 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  chirality pdb=" CA  PRO A 253 "
            pdb=" N   PRO A 253 "
            pdb=" C   PRO A 253 "
            pdb=" CB  PRO A 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.40e-01
  ... (remaining 962 not shown)

  Planarity restraints: 1170
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS C 488 "    0.012 2.00e-02 2.50e+03   2.48e-02 6.17e+00
        pdb=" C   CYS C 488 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   CYS C 488 "    0.016 2.00e-02 2.50e+03
        pdb=" N   TYR C 489 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 499 "    0.024 5.00e-02 4.00e+02   3.62e-02 2.10e+00
        pdb=" N   PRO A 500 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 500 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 500 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 582 "    0.023 5.00e-02 4.00e+02   3.50e-02 1.96e+00
        pdb=" N   PRO A 583 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 583 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 583 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1167 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 103
        2.66 -     3.22: 6014
        3.22 -     3.78: 10236
        3.78 -     4.34: 14322
        4.34 -     4.90: 23151
  Nonbonded interactions: 53826
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 901 "
     model   vdw
     2.100 2.230
  nonbonded pdb=" OH  TYR A 237 "
            pdb=" O   VAL A 485 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OD1 ASP C 442 "
            pdb=" OH  TYR C 451 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   SER A 254 "
            pdb=" OG  SER A 254 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" NH1 ARG A 177 "
            pdb=" O   GLU A 495 "
     model   vdw
     2.302 3.120
  ... (remaining 53821 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:                  0.000
  Normalize map: mean=0, sd=1:             2.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.920
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
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      :  0.004   0.201   6671  Z= 0.189
  Angle     :  0.576   8.657   9079  Z= 0.315
  Chirality :  0.040   0.144    965
  Planarity :  0.003   0.036   1165
  Dihedral  : 14.105  89.849   2484
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  2.73 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.27), residues: 788
  helix: -0.20 (0.24), residues: 395
  sheet: -2.05 (0.62), residues: 56
  loop : -1.70 (0.29), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 302 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.016   0.001   PHE A 369 
 TYR   0.015   0.001   TYR A 381 
 ARG   0.002   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00270 (    5)
  link_NAG-ASN         : angle       3.05573 (   15)
  hydrogen bonds       : bond        0.14992 (  310)
  hydrogen bonds       : angle       5.38033 (  881)
  metal coordination   : bond        0.19010 (    2)
  SS BOND              : bond        0.00264 (    7)
  SS BOND              : angle       2.46969 (   14)
  covalent geometry    : bond        0.00292 ( 6657)
  covalent geometry    : angle       0.55504 ( 9050)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7258 (pttt)
REVERT: A  195 HIS cc_start: 0.8245 (m90) cc_final: 0.8040 (m170)
REVERT: A  202 TYR cc_start: 0.7367 (t80) cc_final: 0.7158 (t80)
REVERT: A  474 MET cc_start: 0.7289 (mmp) cc_final: 0.6871 (mmt)
  outliers start: 2
  outliers final: 1
  residues processed: 128
  average time/residue: 0.2132
  time to fit residues: 35.9332
Evaluate side-chains
  98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  489 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:   10.0000
   chunk 59 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 45 optimal weight:    7.9990
   chunk 70 optimal weight:    7.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.151758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.120395 restraints weight = 17332.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 4.01
r_work: 0.2958 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2964
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2964
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6671  Z= 0.190
  Angle     :  0.619   8.078   9079  Z= 0.311
  Chirality :  0.043   0.150    965
  Planarity :  0.004   0.052   1165
  Dihedral  :  5.307  56.208    967
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.08 %
    Favored  : 87.19 %
  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: -0.56 (0.28), residues: 788
  helix:  0.58 (0.25), residues: 401
  sheet: -1.69 (0.61), residues: 60
  loop : -1.24 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 302 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.018   0.002   PHE A 369 
 TYR   0.030   0.002   TYR A 381 
 ARG   0.003   0.001   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00301 (    5)
  link_NAG-ASN         : angle       2.91705 (   15)
  hydrogen bonds       : bond        0.05027 (  310)
  hydrogen bonds       : angle       4.52030 (  881)
  metal coordination   : bond        0.01742 (    2)
  SS BOND              : bond        0.00336 (    7)
  SS BOND              : angle       2.78151 (   14)
  covalent geometry    : bond        0.00447 ( 6657)
  covalent geometry    : angle       0.59891 ( 9050)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7180 (pttt)
REVERT: A  474 MET cc_start: 0.7615 (mmp) cc_final: 0.7058 (mmp)
REVERT: A  495 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7220 (mm-30)
REVERT: C  378 LYS cc_start: 0.6806 (mtpt) cc_final: 0.5882 (ptmm)
REVERT: C  492 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7018 (mp)
  outliers start: 12
  outliers final: 6
  residues processed: 108
  average time/residue: 0.1884
  time to fit residues: 27.7055
Evaluate side-chains
  98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain C residue  432 CYS
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  492 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 67 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
A 373 HIS
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.153275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.121523 restraints weight = 10777.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.18
r_work: 0.3101 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2962
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6671  Z= 0.139
  Angle     :  0.562   7.017   9079  Z= 0.282
  Chirality :  0.041   0.136    965
  Planarity :  0.004   0.032   1165
  Dihedral  :  4.917  51.077    967
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.53 %
    Favored  : 84.32 %
  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: -0.01 (0.29), residues: 788
  helix:  1.03 (0.26), residues: 402
  sheet: -1.67 (0.64), residues: 60
  loop : -0.92 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.018   0.001   PHE A 369 
 TYR   0.018   0.001   TYR A 381 
 ARG   0.003   0.000   ARG A 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00241 (    5)
  link_NAG-ASN         : angle       2.57269 (   15)
  hydrogen bonds       : bond        0.04536 (  310)
  hydrogen bonds       : angle       4.35939 (  881)
  metal coordination   : bond        0.00431 (    2)
  SS BOND              : bond        0.00292 (    7)
  SS BOND              : angle       2.52168 (   14)
  covalent geometry    : bond        0.00320 ( 6657)
  covalent geometry    : angle       0.54437 ( 9050)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 1.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7222 (pttt)
REVERT: A  190 MET cc_start: 0.8013 (ttt) cc_final: 0.7549 (ttp)
REVERT: A  474 MET cc_start: 0.7630 (mmp) cc_final: 0.7100 (mmp)
REVERT: A  495 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7285 (mm-30)
REVERT: C  378 LYS cc_start: 0.6778 (mtpt) cc_final: 0.5838 (ptmm)
REVERT: C  452 LEU cc_start: 0.7988 (mp) cc_final: 0.7677 (mm)
REVERT: C  492 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7104 (mp)
  outliers start: 15
  outliers final: 11
  residues processed: 108
  average time/residue: 0.1999
  time to fit residues: 28.9869
Evaluate side-chains
  104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  432 CYS
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  480 CYS
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  504 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 9 optimal weight:    0.3980
   chunk 39 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.153093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.122480 restraints weight = 15911.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 3.58
r_work: 0.3020 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6671  Z= 0.139
  Angle     :  0.562   6.809   9079  Z= 0.283
  Chirality :  0.041   0.129    965
  Planarity :  0.004   0.032   1165
  Dihedral  :  4.771  45.102    967
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.11 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.30), residues: 788
  helix:  1.22 (0.26), residues: 401
  sheet: -1.67 (0.66), residues: 60
  loop : -0.71 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.014   0.001   PHE A 369 
 TYR   0.017   0.001   TYR A 381 
 ARG   0.004   0.000   ARG A 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00220 (    5)
  link_NAG-ASN         : angle       2.47462 (   15)
  hydrogen bonds       : bond        0.04497 (  310)
  hydrogen bonds       : angle       4.35887 (  881)
  metal coordination   : bond        0.00353 (    2)
  SS BOND              : bond        0.00341 (    7)
  SS BOND              : angle       2.40513 (   14)
  covalent geometry    : bond        0.00321 ( 6657)
  covalent geometry    : angle       0.54546 ( 9050)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 LYS cc_start: 0.8087 (mmmm) cc_final: 0.7192 (pttt)
REVERT: C  378 LYS cc_start: 0.6797 (mtpt) cc_final: 0.6117 (ptmm)
REVERT: C  409 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.7280 (mp10)
REVERT: C  452 LEU cc_start: 0.7938 (mp) cc_final: 0.7641 (mm)
REVERT: C  492 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7038 (mp)
  outliers start: 16
  outliers final: 11
  residues processed: 107
  average time/residue: 0.1780
  time to fit residues: 26.0452
Evaluate side-chains
  103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  432 CYS
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  480 CYS
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  492 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 3 optimal weight:    0.2980
   chunk 34 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A 121 ASN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.155511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.122252 restraints weight = 12804.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.45
r_work: 0.3094 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3103
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3103
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6671  Z= 0.110
  Angle     :  0.528   7.035   9079  Z= 0.265
  Chirality :  0.040   0.129    965
  Planarity :  0.003   0.027   1165
  Dihedral  :  4.408  41.130    967
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.40 %
    Favored  : 82.01 %
  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:  0.55 (0.30), residues: 788
  helix:  1.44 (0.26), residues: 402
  sheet: -1.61 (0.67), residues: 60
  loop : -0.54 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.013   0.001   PHE A 369 
 TYR   0.010   0.001   TYR A 381 
 ARG   0.004   0.000   ARG A 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    5)
  link_NAG-ASN         : angle       2.25122 (   15)
  hydrogen bonds       : bond        0.04059 (  310)
  hydrogen bonds       : angle       4.25601 (  881)
  metal coordination   : bond        0.00220 (    2)
  SS BOND              : bond        0.00279 (    7)
  SS BOND              : angle       2.27135 (   14)
  covalent geometry    : bond        0.00242 ( 6657)
  covalent geometry    : angle       0.51292 ( 9050)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 LYS cc_start: 0.8063 (mmmm) cc_final: 0.7190 (pttt)
REVERT: A  474 MET cc_start: 0.7615 (mmp) cc_final: 0.7243 (mmp)
REVERT: C  378 LYS cc_start: 0.6824 (mtpt) cc_final: 0.6184 (ptmm)
REVERT: C  391 CYS cc_start: 0.4973 (OUTLIER) cc_final: 0.4592 (t)
REVERT: C  409 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.7304 (mp10)
REVERT: C  452 LEU cc_start: 0.7872 (mp) cc_final: 0.7564 (mm)
  outliers start: 18
  outliers final: 15
  residues processed: 111
  average time/residue: 0.1960
  time to fit residues: 29.7391
Evaluate side-chains
  112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  432 CYS
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  480 CYS
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  504 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 62 optimal weight:    9.9990
   chunk 60 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 77 optimal weight:    8.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A 121 ASN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.152020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.120656 restraints weight = 8713.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 1.94
r_work: 0.3076 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2944
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2944
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6671  Z= 0.171
  Angle     :  0.587   9.273   9079  Z= 0.294
  Chirality :  0.042   0.131    965
  Planarity :  0.004   0.037   1165
  Dihedral  :  4.796  37.470    967
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 15.97 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.30), residues: 788
  helix:  1.25 (0.26), residues: 401
  sheet: -1.48 (0.68), residues: 61
  loop : -0.57 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.016   0.002   PHE A 369 
 TYR   0.021   0.001   TYR A 381 
 ARG   0.006   0.001   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00214 (    5)
  link_NAG-ASN         : angle       2.38557 (   15)
  hydrogen bonds       : bond        0.04818 (  310)
  hydrogen bonds       : angle       4.38889 (  881)
  metal coordination   : bond        0.00493 (    2)
  SS BOND              : bond        0.00291 (    7)
  SS BOND              : angle       2.34594 (   14)
  covalent geometry    : bond        0.00402 ( 6657)
  covalent geometry    : angle       0.57221 ( 9050)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.683 
Fit side-chains
REVERT: A  114 LYS cc_start: 0.8211 (mmmm) cc_final: 0.7301 (pttt)
REVERT: A  335 ASP cc_start: 0.6031 (t0) cc_final: 0.5823 (t0)
REVERT: C  378 LYS cc_start: 0.7019 (mtpt) cc_final: 0.6169 (ptmm)
REVERT: C  391 CYS cc_start: 0.5107 (OUTLIER) cc_final: 0.4710 (t)
REVERT: C  409 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.7317 (mp10)
REVERT: C  488 CYS cc_start: 0.6777 (m) cc_final: 0.6521 (m)
  outliers start: 19
  outliers final: 16
  residues processed: 107
  average time/residue: 0.1805
  time to fit residues: 26.3661
Evaluate side-chains
  108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  432 CYS
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  480 CYS
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  504 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0970
   chunk 73 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    0.2980
   chunk 25 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A 121 ASN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.156392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.124177 restraints weight = 10760.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.18
r_work: 0.3139 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3143
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3143
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6671  Z= 0.107
  Angle     :  0.528   7.304   9079  Z= 0.264
  Chirality :  0.040   0.125    965
  Planarity :  0.003   0.026   1165
  Dihedral  :  4.278  34.334    967
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.83 %
    Favored  : 80.43 %
  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:  0.75 (0.30), residues: 788
  helix:  1.53 (0.26), residues: 400
  sheet: -1.56 (0.67), residues: 60
  loop : -0.32 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.019   0.001   PHE A 315 
 TYR   0.008   0.001   TYR A 381 
 ARG   0.005   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    5)
  link_NAG-ASN         : angle       2.11396 (   15)
  hydrogen bonds       : bond        0.04013 (  310)
  hydrogen bonds       : angle       4.22956 (  881)
  metal coordination   : bond        0.00177 (    2)
  SS BOND              : bond        0.00247 (    7)
  SS BOND              : angle       2.15440 (   14)
  covalent geometry    : bond        0.00235 ( 6657)
  covalent geometry    : angle       0.51488 ( 9050)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A  114 LYS cc_start: 0.8078 (mmmm) cc_final: 0.7244 (pttt)
REVERT: C  378 LYS cc_start: 0.6867 (mtpt) cc_final: 0.6339 (ptmm)
REVERT: C  391 CYS cc_start: 0.4924 (OUTLIER) cc_final: 0.4503 (t)
REVERT: C  409 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.7288 (mp10)
  outliers start: 19
  outliers final: 16
  residues processed: 110
  average time/residue: 0.1748
  time to fit residues: 26.1074
Evaluate side-chains
  112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  432 CYS
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  480 CYS
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  504 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 59 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.156688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.125201 restraints weight = 8679.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 1.95
r_work: 0.3161 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3028
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3028 r_free = 0.3028    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3028 r_free = 0.3028    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3028
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6671  Z= 0.108
  Angle     :  0.521   7.320   9079  Z= 0.261
  Chirality :  0.040   0.127    965
  Planarity :  0.003   0.024   1165
  Dihedral  :  4.129  31.713    967
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.40 %
    Favored  : 80.72 %
  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:  0.86 (0.30), residues: 788
  helix:  1.62 (0.26), residues: 401
  sheet: -1.48 (0.67), residues: 60
  loop : -0.27 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.014   0.001   PHE A 315 
 TYR   0.009   0.001   TYR A 381 
 ARG   0.005   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00193 (    5)
  link_NAG-ASN         : angle       2.02857 (   15)
  hydrogen bonds       : bond        0.04000 (  310)
  hydrogen bonds       : angle       4.19432 (  881)
  metal coordination   : bond        0.00173 (    2)
  SS BOND              : bond        0.00249 (    7)
  SS BOND              : angle       2.04475 (   14)
  covalent geometry    : bond        0.00239 ( 6657)
  covalent geometry    : angle       0.50881 ( 9050)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.728 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 LYS cc_start: 0.8131 (mmmm) cc_final: 0.7256 (pttt)
REVERT: C  378 LYS cc_start: 0.6736 (mtpt) cc_final: 0.6292 (ptmm)
REVERT: C  391 CYS cc_start: 0.5000 (OUTLIER) cc_final: 0.4521 (t)
REVERT: C  409 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.7391 (mp10)
REVERT: C  452 LEU cc_start: 0.7851 (mp) cc_final: 0.7536 (mm)
  outliers start: 20
  outliers final: 16
  residues processed: 110
  average time/residue: 0.1860
  time to fit residues: 27.4186
Evaluate side-chains
  113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  432 CYS
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  480 CYS
Chi-restraints excluded: chain C residue  504 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 57 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 45 optimal weight:    0.4980
   chunk 55 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 42 optimal weight:    0.1980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.157462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.125900 restraints weight = 8803.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.04
r_work: 0.3205 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3029
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3029
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6671  Z= 0.104
  Angle     :  0.515   7.404   9079  Z= 0.257
  Chirality :  0.040   0.127    965
  Planarity :  0.003   0.024   1165
  Dihedral  :  3.905  29.466    965
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.83 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.30), residues: 788
  helix:  1.74 (0.26), residues: 399
  sheet: -1.07 (0.73), residues: 50
  loop : -0.23 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.013   0.001   PHE A 369 
 TYR   0.010   0.001   TYR A 215 
 ARG   0.005   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00200 (    5)
  link_NAG-ASN         : angle       1.96589 (   15)
  hydrogen bonds       : bond        0.03894 (  310)
  hydrogen bonds       : angle       4.17120 (  881)
  metal coordination   : bond        0.00181 (    2)
  SS BOND              : bond        0.00233 (    7)
  SS BOND              : angle       1.97212 (   14)
  covalent geometry    : bond        0.00229 ( 6657)
  covalent geometry    : angle       0.50315 ( 9050)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7237 (pttt)
REVERT: C  378 LYS cc_start: 0.6502 (mtpt) cc_final: 0.6139 (ptmm)
REVERT: C  391 CYS cc_start: 0.4972 (OUTLIER) cc_final: 0.4455 (t)
REVERT: C  409 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.7375 (mp10)
REVERT: C  452 LEU cc_start: 0.7827 (mp) cc_final: 0.7504 (mm)
  outliers start: 18
  outliers final: 16
  residues processed: 112
  average time/residue: 0.1720
  time to fit residues: 26.4643
Evaluate side-chains
  118 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  432 CYS
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  480 CYS
Chi-restraints excluded: chain C residue  504 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.0070
   chunk 23 optimal weight:    5.9990
   chunk 65 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 25 optimal weight:    0.1980
   chunk 67 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    1.0002

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.156457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.124662 restraints weight = 12874.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.48
r_work: 0.3116 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3093
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3093
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6671  Z= 0.117
  Angle     :  0.534   8.634   9079  Z= 0.265
  Chirality :  0.040   0.126    965
  Planarity :  0.003   0.024   1165
  Dihedral  :  3.994  28.641    965
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.41 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.30), residues: 788
  helix:  1.69 (0.26), residues: 401
  sheet: -1.02 (0.73), residues: 50
  loop : -0.25 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.014   0.001   PHE A 369 
 TYR   0.012   0.001   TYR A 215 
 ARG   0.005   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00200 (    5)
  link_NAG-ASN         : angle       1.99173 (   15)
  hydrogen bonds       : bond        0.04117 (  310)
  hydrogen bonds       : angle       4.20597 (  881)
  metal coordination   : bond        0.00235 (    2)
  SS BOND              : bond        0.00243 (    7)
  SS BOND              : angle       1.97760 (   14)
  covalent geometry    : bond        0.00267 ( 6657)
  covalent geometry    : angle       0.52339 ( 9050)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 LYS cc_start: 0.8109 (mmmm) cc_final: 0.7241 (pttt)
REVERT: A  557 MET cc_start: 0.8684 (tmm) cc_final: 0.8417 (tmm)
REVERT: C  378 LYS cc_start: 0.6533 (mtpt) cc_final: 0.6133 (ptmm)
REVERT: C  391 CYS cc_start: 0.4993 (OUTLIER) cc_final: 0.4525 (t)
  outliers start: 17
  outliers final: 16
  residues processed: 108
  average time/residue: 0.1850
  time to fit residues: 27.2513
Evaluate side-chains
  111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  432 CYS
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  480 CYS
Chi-restraints excluded: chain C residue  504 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    0.0070
   chunk 31 optimal weight:    0.0670
   chunk 37 optimal weight:    0.0470
   chunk 72 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0570
   overall best weight:    0.1752

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.161026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.128871 restraints weight = 11309.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 2.34
r_work: 0.3198 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3182
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6671  Z= 0.098
  Angle     :  0.514   9.364   9079  Z= 0.256
  Chirality :  0.039   0.126    965
  Planarity :  0.003   0.025   1165
  Dihedral  :  3.680  26.102    965
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.84 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.31), residues: 788
  helix:  1.87 (0.26), residues: 399
  sheet: -0.83 (0.74), residues: 50
  loop : -0.09 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 163 
 HIS   0.008   0.001   HIS A 374 
 PHE   0.014   0.001   PHE A 315 
 TYR   0.008   0.001   TYR A  50 
 ARG   0.004   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00217 (    5)
  link_NAG-ASN         : angle       1.81685 (   15)
  hydrogen bonds       : bond        0.03570 (  310)
  hydrogen bonds       : angle       4.11894 (  881)
  metal coordination   : bond        0.00046 (    2)
  SS BOND              : bond        0.00199 (    7)
  SS BOND              : angle       1.85275 (   14)
  covalent geometry    : bond        0.00206 ( 6657)
  covalent geometry    : angle       0.50433 ( 9050)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4222.72 seconds
wall clock time: 74 minutes 51.31 seconds (4491.31 seconds total)