Starting phenix.real_space_refine
on Wed Jul 23 20:21:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k6l_36922/07_2025/8k6l_36922.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k6l_36922/07_2025/8k6l_36922.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k6l_36922/07_2025/8k6l_36922.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k6l_36922/07_2025/8k6l_36922.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k6l_36922/07_2025/8k6l_36922.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k6l_36922/07_2025/8k6l_36922.cif"
  }
  resolution = 2.92
  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=   0.092
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
     S      34      5.16       5
     Cl      2      4.86       5
     C    2749      2.51       5
     N     651      2.21       5
     O     719      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4155
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 547, 4086
          Classifications: {'peptide': 547}
          Incomplete info: {'truncation_to_alanine': 58}
          Link IDs: {'PTRANS': 18, 'TRANS': 528}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 234
          Unresolved non-hydrogen dihedrals: 146
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 109
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Unusual residues: {'IOQ': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 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: 3.29, per 1000 atoms: 0.79
  Number of scatterers: 4155
  At special positions: 0
  Unit cell: (65.24, 100.656, 87.608, 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)
     Cl      2     17.00
     S      34     16.00
     O     719      8.00
     N     651      7.00
     C    2749      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 142 " - pdb=" SG  CYS A 463 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 430 " - pdb=" SG  CYS A 530 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 459 " - pdb=" SG  CYS A 506 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 465 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 524 " distance=1.71
    Simple disulfide: pdb=" SG  CYS A 489 " - pdb=" SG  CYS A 504 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 599 " - pdb=" SG  CYS A 613 " 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
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A 802 " - " ASN A 516 "
      " NAG B   1 " - " ASN A 503 "
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 519.1 milliseconds
  

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  996

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 3 sheets defined
      67.3% alpha, 2.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 51
      removed outlier: 3.662A  pdb=" N   PHE A  30 " --> pdb=" O   GLY A  26 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ALA A  33 " --> pdb=" O   MET A  29 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER A  35 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 60
    Processing helix  chain 'A' and resid 62 through 71
    Processing helix  chain 'A' and resid 71 through 88
      removed outlier: 3.577A  pdb=" N   ILE A  75 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU A  79 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL A  80 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   VAL A  82 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   PHE A  83 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 91
      No H-bonds generated for 'chain 'A' and resid 89 through 91'
    Processing helix  chain 'A' and resid 92 through 111
      removed outlier: 3.808A  pdb=" N   THR A 111 " --> pdb=" O   GLY A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 118
      removed outlier: 4.173A  pdb=" N   PHE A 116 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 185
    Processing helix  chain 'A' and resid 187 through 199
      removed outlier: 3.747A  pdb=" N   LEU A 191 " --> pdb=" O   PRO A 187 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   SER A 194 " --> pdb=" O   PRO A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 216
      removed outlier: 4.516A  pdb=" N   LEU A 207 " --> pdb=" O   GLY A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 231
      removed outlier: 3.844A  pdb=" N   ILE A 221 " --> pdb=" O   MET A 217 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   SER A 228 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 272
      removed outlier: 3.614A  pdb=" N   LEU A 263 " --> pdb=" O   TRP A 259 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   VAL A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER A 265 " --> pdb=" O   ASN A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 278
      removed outlier: 3.851A  pdb=" N   PHE A 276 " --> pdb=" O   SER A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 334
      removed outlier: 3.810A  pdb=" N   ILE A 332 " --> pdb=" O   SER A 328 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU A 333 " --> pdb=" O   PHE A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 367
      removed outlier: 5.301A  pdb=" N   PHE A 360 " --> pdb=" O   PHE A 356 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   LYS A 361 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 401
      removed outlier: 3.630A  pdb=" N   GLY A 379 " --> pdb=" O   ASN A 375 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL A 380 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ILE A 381 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      Proline residue:  A 384  - end of helix
      removed outlier: 3.514A  pdb=" N   ILE A 397 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LYS A 401 " --> pdb=" O   ILE A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 423
      removed outlier: 3.876A  pdb=" N   PHE A 421 " --> pdb=" O   MET A 417 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   TYR A 422 " --> pdb=" O   SER A 418 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU A 423 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 428
    Processing helix  chain 'A' and resid 457 through 461
    Processing helix  chain 'A' and resid 527 through 550
      removed outlier: 3.846A  pdb=" N   THR A 531 " --> pdb=" O   ASP A 527 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE A 536 " --> pdb=" O   ARG A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 560
    Processing helix  chain 'A' and resid 567 through 583
    Processing helix  chain 'A' and resid 586 through 596
    Processing helix  chain 'A' and resid 617 through 651
    Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436
    Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 502
      removed outlier: 3.594A  pdb=" N   PHE A 501 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 602
      removed outlier: 6.820A  pdb=" N   CYS A 599 " --> pdb=" O   TYR A 616 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   TYR A 616 " --> pdb=" O   CYS A 599 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   LYS A 601 " --> pdb=" O   ARG A 614 " (cutoff:3.500A)

    244 hydrogen bonds defined for protein.
    711 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: 1.09

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 881
        1.33 -     1.45: 1009
        1.45 -     1.57: 2315
        1.57 -     1.70: 0
        1.70 -     1.82: 53
  Bond restraints: 4258
  Sorted by residual:
  bond pdb=" C   THR A 186 "
       pdb=" N   PRO A 187 "
    ideal  model  delta    sigma   weight residual
    1.331  1.371 -0.039 7.90e-03 1.60e+04 2.44e+01
  bond pdb=" C   SER A 140 "
       pdb=" N   THR A 141 "
    ideal  model  delta    sigma   weight residual
    1.332  1.291  0.041 1.40e-02 5.10e+03 8.70e+00
  bond pdb=" C   PHE A 591 "
       pdb=" O   PHE A 591 "
    ideal  model  delta    sigma   weight residual
    1.237  1.210  0.026 1.17e-02 7.31e+03 5.05e+00
  bond pdb=" C   PRO A 588 "
       pdb=" O   PRO A 588 "
    ideal  model  delta    sigma   weight residual
    1.237  1.211  0.026 1.16e-02 7.43e+03 4.98e+00
  bond pdb=" C   ILE A 589 "
       pdb=" O   ILE A 589 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.025 1.13e-02 7.83e+03 4.97e+00
  ... (remaining 4253 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 5574
        2.40 -     4.79: 175
        4.79 -     7.19: 21
        7.19 -     9.59: 10
        9.59 -    11.98: 2
  Bond angle restraints: 5782
  Sorted by residual:
  angle pdb=" C   ILE A 585 "
        pdb=" CA  ILE A 585 "
        pdb=" CB  ILE A 585 "
      ideal   model   delta    sigma   weight residual
     111.30  101.87    9.43 9.60e-01 1.09e+00 9.65e+01
  angle pdb=" N   ILE A  52 "
        pdb=" CA  ILE A  52 "
        pdb=" C   ILE A  52 "
      ideal   model   delta    sigma   weight residual
     110.62  117.58   -6.96 1.02e+00 9.61e-01 4.65e+01
  angle pdb=" N   ASN A 375 "
        pdb=" CA  ASN A 375 "
        pdb=" C   ASN A 375 "
      ideal   model   delta    sigma   weight residual
     111.02  120.98   -9.96 1.52e+00 4.33e-01 4.30e+01
  angle pdb=" C   ALA A  32 "
        pdb=" N   ALA A  33 "
        pdb=" CA  ALA A  33 "
      ideal   model   delta    sigma   weight residual
     120.28  129.02   -8.74 1.34e+00 5.57e-01 4.25e+01
  angle pdb=" C   THR A 186 "
        pdb=" N   PRO A 187 "
        pdb=" CA  PRO A 187 "
      ideal   model   delta    sigma   weight residual
     121.00  113.85    7.15 1.16e+00 7.43e-01 3.80e+01
  ... (remaining 5777 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.07: 2317
       21.07 -    42.14: 131
       42.14 -    63.21: 43
       63.21 -    84.28: 4
       84.28 -   105.35: 16
  Dihedral angle restraints: 2511
    sinusoidal: 947
      harmonic: 1564
  Sorted by residual:
  dihedral pdb=" CB  CYS A 430 "
           pdb=" SG  CYS A 430 "
           pdb=" SG  CYS A 530 "
           pdb=" CB  CYS A 530 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.45   71.45     1      1.00e+01 1.00e-02 6.55e+01
  dihedral pdb=" CB  CYS A 599 "
           pdb=" SG  CYS A 599 "
           pdb=" SG  CYS A 613 "
           pdb=" CB  CYS A 613 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.91   69.91     1      1.00e+01 1.00e-02 6.30e+01
  dihedral pdb=" C   TYR A 590 "
           pdb=" N   TYR A 590 "
           pdb=" CA  TYR A 590 "
           pdb=" CB  TYR A 590 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.33   16.73     0      2.50e+00 1.60e-01 4.48e+01
  ... (remaining 2508 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.243: 672
       0.243 -    0.486: 2
       0.486 -    0.729: 2
       0.729 -    0.972: 1
       0.972 -    1.215: 1
  Chirality restraints: 678
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.19   -0.21 2.00e-02 2.50e+03 1.13e+02
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 503 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.18   -1.22 2.00e-01 2.50e+01 3.69e+01
  chirality pdb=" C1  NAG A 802 "
            pdb=" ND2 ASN A 516 "
            pdb=" C2  NAG A 802 "
            pdb=" O5  NAG A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.47   -0.93 2.00e-01 2.50e+01 2.16e+01
  ... (remaining 675 not shown)

  Planarity restraints: 702
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   1 "   -0.339 2.00e-02 2.50e+03   2.94e-01 1.08e+03
        pdb=" C7  NAG B   1 "    0.079 2.00e-02 2.50e+03
        pdb=" C8  NAG B   1 "   -0.094 2.00e-02 2.50e+03
        pdb=" N2  NAG B   1 "    0.524 2.00e-02 2.50e+03
        pdb=" O7  NAG B   1 "   -0.170 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   2 "   -0.310 2.00e-02 2.50e+03   2.61e-01 8.49e+02
        pdb=" C7  NAG B   2 "    0.081 2.00e-02 2.50e+03
        pdb=" C8  NAG B   2 "   -0.189 2.00e-02 2.50e+03
        pdb=" N2  NAG B   2 "    0.448 2.00e-02 2.50e+03
        pdb=" O7  NAG B   2 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 802 "    0.309 2.00e-02 2.50e+03   2.60e-01 8.48e+02
        pdb=" C7  NAG A 802 "   -0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG A 802 "    0.189 2.00e-02 2.50e+03
        pdb=" N2  NAG A 802 "   -0.448 2.00e-02 2.50e+03
        pdb=" O7  NAG A 802 "    0.030 2.00e-02 2.50e+03
  ... (remaining 699 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1278
        2.82 -     3.34: 3822
        3.34 -     3.86: 6400
        3.86 -     4.38: 7155
        4.38 -     4.90: 12360
  Nonbonded interactions: 31015
  Sorted by model distance:
  nonbonded pdb=" O   SER A  85 "
            pdb=" OG  SER A  89 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   GLY A 324 "
            pdb=" OG  SER A 328 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" O   LEU A 507 "
            pdb=" CD1 LEU A 507 "
     model   vdw
     2.400 3.460
  nonbonded pdb=" O   SER A 491 "
            pdb=" CD1 PHE A 501 "
     model   vdw
     2.463 3.340
  nonbonded pdb=" O   SER A 371 "
            pdb=" OG  SER A 371 "
     model   vdw
     2.475 3.040
  ... (remaining 31010 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     14.730
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
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      :  0.008   0.316   4268  Z= 0.450
  Angle     :  1.188  27.121   5805  Z= 0.698
  Chirality :  0.086   1.215    678
  Planarity :  0.019   0.294    700
  Dihedral  : 17.751 105.346   1494
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.98 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.20 %
  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: -2.44 (0.31), residues: 539
  helix: -0.93 (0.25), residues: 333
  sheet:  None (None), residues: 0
  loop : -2.71 (0.36), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A 575 
 PHE   0.012   0.001   PHE A 621 
 TYR   0.026   0.002   TYR A 625 
 ARG   0.002   0.000   ARG A 526 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.15759 (    2)
  link_NAG-ASN         : angle      17.33816 (    6)
  link_BETA1-4         : bond        0.00992 (    1)
  link_BETA1-4         : angle       4.76017 (    3)
  hydrogen bonds       : bond        0.20972 (  244)
  hydrogen bonds       : angle       6.62794 (  711)
  SS BOND              : bond        0.11957 (    7)
  SS BOND              : angle       5.91851 (   14)
  covalent geometry    : bond        0.00534 ( 4258)
  covalent geometry    : angle       1.00455 ( 5782)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.422 
Fit side-chains
REVERT: A  198 ASP cc_start: 0.8666 (m-30) cc_final: 0.8031 (m-30)
REVERT: A  253 ARG cc_start: 0.7701 (mtm180) cc_final: 0.6301 (mtp-110)
REVERT: A  580 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7566 (mtt90)
REVERT: A  623 ARG cc_start: 0.7437 (tpp80) cc_final: 0.7188 (mtm-85)
REVERT: A  648 LYS cc_start: 0.7736 (ttmt) cc_final: 0.6993 (ttpt)
  outliers start: 9
  outliers final: 3
  residues processed: 83
  average time/residue: 1.1828
  time to fit residues: 101.9497
Evaluate side-chains
  59 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  563 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.0000
   chunk 40 optimal weight:    0.0170
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0980
   chunk 27 optimal weight:    0.0070
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0770
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.0398

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

Flipped N/Q/H residues before XYZ refinement:
A 335 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.161307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.122346 restraints weight = 4988.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 2.41
r_work: 0.3246 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4268  Z= 0.146
  Angle     :  0.751  18.879   5805  Z= 0.346
  Chirality :  0.054   0.759    678
  Planarity :  0.004   0.052    700
  Dihedral  :  9.478  54.720    662
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 20.72 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.36), residues: 539
  helix:  0.93 (0.29), residues: 342
  sheet:  None (None), residues: 0
  loop : -2.28 (0.39), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.012   0.001   PHE A 501 
 TYR   0.026   0.001   TYR A 590 
 ARG   0.001   0.000   ARG A 246 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01607 (    2)
  link_NAG-ASN         : angle      11.58119 (    6)
  link_BETA1-4         : bond        0.01450 (    1)
  link_BETA1-4         : angle       4.74450 (    3)
  hydrogen bonds       : bond        0.06390 (  244)
  hydrogen bonds       : angle       4.23303 (  711)
  SS BOND              : bond        0.00187 (    7)
  SS BOND              : angle       0.85294 (   14)
  covalent geometry    : bond        0.00252 ( 4258)
  covalent geometry    : angle       0.64310 ( 5782)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.494 
Fit side-chains
REVERT: A   48 MET cc_start: 0.7364 (tpt) cc_final: 0.7101 (tpp)
REVERT: A   74 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7989 (mm-30)
REVERT: A  185 GLU cc_start: 0.8352 (pt0) cc_final: 0.8017 (pp20)
REVERT: A  198 ASP cc_start: 0.8334 (m-30) cc_final: 0.7731 (m-30)
REVERT: A  253 ARG cc_start: 0.7825 (mtm180) cc_final: 0.6032 (mtp-110)
REVERT: A  580 ARG cc_start: 0.8045 (mtp-110) cc_final: 0.7488 (mtm-85)
REVERT: A  648 LYS cc_start: 0.7457 (ttmt) cc_final: 0.6686 (ttpt)
  outliers start: 8
  outliers final: 2
  residues processed: 62
  average time/residue: 1.4804
  time to fit residues: 95.0835
Evaluate side-chains
  52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  560 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 38 optimal weight:    0.0770
   chunk 2 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN
A 178 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.153340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.114967 restraints weight = 4989.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.19
r_work: 0.3186 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4268  Z= 0.145
  Angle     :  0.683  16.925   5805  Z= 0.325
  Chirality :  0.052   0.689    678
  Planarity :  0.004   0.049    700
  Dihedral  :  7.025  57.838    660
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.52 %
    Favored  : 76.87 %
  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:  0.44 (0.37), residues: 539
  helix:  1.46 (0.29), residues: 344
  sheet:  None (None), residues: 0
  loop : -1.93 (0.40), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 258 
 HIS   0.002   0.001   HIS A 575 
 PHE   0.013   0.001   PHE A 621 
 TYR   0.024   0.002   TYR A 625 
 ARG   0.002   0.000   ARG A 623 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01320 (    2)
  link_NAG-ASN         : angle      10.39199 (    6)
  link_BETA1-4         : bond        0.01204 (    1)
  link_BETA1-4         : angle       3.45731 (    3)
  hydrogen bonds       : bond        0.07058 (  244)
  hydrogen bonds       : angle       3.93050 (  711)
  SS BOND              : bond        0.00647 (    7)
  SS BOND              : angle       0.80471 (   14)
  covalent geometry    : bond        0.00293 ( 4258)
  covalent geometry    : angle       0.59001 ( 5782)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 MET cc_start: 0.7585 (mmm) cc_final: 0.7367 (mmt)
REVERT: A  251 ASP cc_start: 0.6935 (m-30) cc_final: 0.6317 (m-30)
REVERT: A  253 ARG cc_start: 0.7810 (mtm180) cc_final: 0.5943 (mtp-110)
REVERT: A  348 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7277 (tp-100)
REVERT: A  433 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7011 (ptpp)
REVERT: A  482 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7739 (mt)
REVERT: A  623 ARG cc_start: 0.7399 (tpp80) cc_final: 0.7000 (mtt180)
REVERT: A  648 LYS cc_start: 0.7257 (ttmt) cc_final: 0.6523 (ttpt)
  outliers start: 15
  outliers final: 2
  residues processed: 60
  average time/residue: 1.5968
  time to fit residues: 99.3822
Evaluate side-chains
  53 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  433 LYS
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  560 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.149526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.110824 restraints weight = 4934.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.16
r_work: 0.3140 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4268  Z= 0.151
  Angle     :  0.663  16.219   5805  Z= 0.318
  Chirality :  0.050   0.660    678
  Planarity :  0.004   0.048    700
  Dihedral  :  6.684  53.716    660
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 20.96 %
    Favored  : 75.66 %
  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:  0.84 (0.37), residues: 539
  helix:  1.67 (0.29), residues: 345
  sheet:  None (None), residues: 0
  loop : -1.55 (0.42), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 254 
 HIS   0.002   0.001   HIS A 520 
 PHE   0.015   0.001   PHE A 621 
 TYR   0.023   0.002   TYR A 590 
 ARG   0.002   0.000   ARG A 633 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01301 (    2)
  link_NAG-ASN         : angle       9.67169 (    6)
  link_BETA1-4         : bond        0.00677 (    1)
  link_BETA1-4         : angle       2.99655 (    3)
  hydrogen bonds       : bond        0.07361 (  244)
  hydrogen bonds       : angle       3.89152 (  711)
  SS BOND              : bond        0.00272 (    7)
  SS BOND              : angle       0.75361 (   14)
  covalent geometry    : bond        0.00320 ( 4258)
  covalent geometry    : angle       0.58106 ( 5782)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A  176 MET cc_start: 0.7680 (mmm) cc_final: 0.7466 (mmt)
REVERT: A  185 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7861 (pp20)
REVERT: A  198 ASP cc_start: 0.8285 (m-30) cc_final: 0.7636 (m-30)
REVERT: A  253 ARG cc_start: 0.7826 (mtm180) cc_final: 0.5987 (mtp-110)
REVERT: A  348 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7360 (tp-100)
REVERT: A  623 ARG cc_start: 0.7456 (tpp80) cc_final: 0.7152 (mtm-85)
REVERT: A  648 LYS cc_start: 0.7323 (ttmt) cc_final: 0.6598 (ttpt)
  outliers start: 14
  outliers final: 5
  residues processed: 60
  average time/residue: 1.0248
  time to fit residues: 64.2762
Evaluate side-chains
  55 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  636 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 2 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 43 optimal weight:    0.1980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.152663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.113158 restraints weight = 5065.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.43
r_work: 0.3169 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4268  Z= 0.134
  Angle     :  0.632  15.832   5805  Z= 0.301
  Chirality :  0.049   0.630    678
  Planarity :  0.004   0.048    700
  Dihedral  :  6.660  55.281    660
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 21.69 %
    Favored  : 75.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.37), residues: 539
  helix:  2.02 (0.29), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.57 (0.41), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.012   0.001   PHE A 621 
 TYR   0.023   0.001   TYR A 590 
 ARG   0.002   0.000   ARG A 633 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01367 (    2)
  link_NAG-ASN         : angle       9.42954 (    6)
  link_BETA1-4         : bond        0.00673 (    1)
  link_BETA1-4         : angle       3.00824 (    3)
  hydrogen bonds       : bond        0.06636 (  244)
  hydrogen bonds       : angle       3.73322 (  711)
  SS BOND              : bond        0.00224 (    7)
  SS BOND              : angle       0.55815 (   14)
  covalent geometry    : bond        0.00272 ( 4258)
  covalent geometry    : angle       0.55055 ( 5782)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.465 
Fit side-chains
REVERT: A  198 ASP cc_start: 0.8436 (m-30) cc_final: 0.7814 (m-30)
REVERT: A  253 ARG cc_start: 0.7927 (mtm180) cc_final: 0.6094 (mtp-110)
REVERT: A  348 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7519 (tp-100)
REVERT: A  623 ARG cc_start: 0.7596 (tpp80) cc_final: 0.7224 (mtt180)
REVERT: A  648 LYS cc_start: 0.7209 (ttmt) cc_final: 0.6493 (ttpt)
  outliers start: 13
  outliers final: 8
  residues processed: 57
  average time/residue: 1.0031
  time to fit residues: 59.7618
Evaluate side-chains
  55 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  647 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0050
   chunk 10 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 42 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.6594

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.153101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.113692 restraints weight = 4948.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 2.38
r_work: 0.3169 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4268  Z= 0.139
  Angle     :  0.648  15.699   5805  Z= 0.311
  Chirality :  0.049   0.627    678
  Planarity :  0.004   0.048    700
  Dihedral  :  6.712  54.510    660
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 2.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 20.96 %
    Favored  : 75.66 %
  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:  1.19 (0.37), residues: 539
  helix:  2.09 (0.29), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.61 (0.41), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A 520 
 PHE   0.015   0.001   PHE A 386 
 TYR   0.023   0.001   TYR A 590 
 ARG   0.002   0.000   ARG A 633 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01363 (    2)
  link_NAG-ASN         : angle       9.30952 (    6)
  link_BETA1-4         : bond        0.00517 (    1)
  link_BETA1-4         : angle       2.86110 (    3)
  hydrogen bonds       : bond        0.06727 (  244)
  hydrogen bonds       : angle       3.73791 (  711)
  SS BOND              : bond        0.00226 (    7)
  SS BOND              : angle       1.79912 (   14)
  covalent geometry    : bond        0.00289 ( 4258)
  covalent geometry    : angle       0.56511 ( 5782)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A  198 ASP cc_start: 0.8603 (m-30) cc_final: 0.7981 (m-30)
REVERT: A  247 ILE cc_start: 0.8625 (pt) cc_final: 0.8341 (tp)
REVERT: A  253 ARG cc_start: 0.7975 (mtm180) cc_final: 0.6191 (mtp-110)
REVERT: A  348 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7758 (tp-100)
REVERT: A  623 ARG cc_start: 0.7776 (tpp80) cc_final: 0.7434 (mtt180)
REVERT: A  648 LYS cc_start: 0.7375 (ttmt) cc_final: 0.6656 (ttpt)
  outliers start: 14
  outliers final: 8
  residues processed: 60
  average time/residue: 1.2139
  time to fit residues: 75.6412
Evaluate side-chains
  57 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  647 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0970
   chunk 29 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0370
   chunk 10 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    0.5256

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.154249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.114837 restraints weight = 4949.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.39
r_work: 0.3180 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3050 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4268  Z= 0.126
  Angle     :  0.622  15.374   5805  Z= 0.296
  Chirality :  0.048   0.612    678
  Planarity :  0.004   0.048    700
  Dihedral  :  6.676  57.958    660
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 21.69 %
    Favored  : 74.94 %
  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:  1.38 (0.37), residues: 539
  helix:  2.23 (0.29), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.53 (0.41), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 258 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.014   0.001   PHE A 386 
 TYR   0.023   0.001   TYR A 590 
 ARG   0.001   0.000   ARG A 633 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01408 (    2)
  link_NAG-ASN         : angle       9.08256 (    6)
  link_BETA1-4         : bond        0.00512 (    1)
  link_BETA1-4         : angle       2.82227 (    3)
  hydrogen bonds       : bond        0.06155 (  244)
  hydrogen bonds       : angle       3.66786 (  711)
  SS BOND              : bond        0.00355 (    7)
  SS BOND              : angle       1.04756 (   14)
  covalent geometry    : bond        0.00251 ( 4258)
  covalent geometry    : angle       0.54393 ( 5782)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.523 
Fit side-chains
REVERT: A  198 ASP cc_start: 0.8572 (m-30) cc_final: 0.7946 (m-30)
REVERT: A  247 ILE cc_start: 0.8656 (pt) cc_final: 0.8369 (tp)
REVERT: A  253 ARG cc_start: 0.7949 (mtm180) cc_final: 0.6023 (mmm160)
REVERT: A  348 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7676 (tp-100)
REVERT: A  417 MET cc_start: 0.8881 (tpp) cc_final: 0.8603 (mmm)
REVERT: A  440 MET cc_start: 0.7991 (ptm) cc_final: 0.7758 (ptt)
REVERT: A  648 LYS cc_start: 0.7193 (ttmt) cc_final: 0.6471 (ttpt)
  outliers start: 14
  outliers final: 8
  residues processed: 59
  average time/residue: 0.9183
  time to fit residues: 56.9192
Evaluate side-chains
  56 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  647 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    0.0010
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.153871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.114540 restraints weight = 4888.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.37
r_work: 0.3176 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4268  Z= 0.132
  Angle     :  0.628  15.202   5805  Z= 0.300
  Chirality :  0.048   0.607    678
  Planarity :  0.004   0.047    700
  Dihedral  :  6.674  59.750    660
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 22.41 %
    Favored  : 74.70 %
  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:  1.44 (0.38), residues: 539
  helix:  2.28 (0.29), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.51 (0.41), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 258 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.015   0.001   PHE A 386 
 TYR   0.022   0.001   TYR A 590 
 ARG   0.001   0.000   ARG A 633 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01415 (    2)
  link_NAG-ASN         : angle       8.94887 (    6)
  link_BETA1-4         : bond        0.00580 (    1)
  link_BETA1-4         : angle       2.72553 (    3)
  hydrogen bonds       : bond        0.06313 (  244)
  hydrogen bonds       : angle       3.66378 (  711)
  SS BOND              : bond        0.00236 (    7)
  SS BOND              : angle       1.02933 (   14)
  covalent geometry    : bond        0.00268 ( 4258)
  covalent geometry    : angle       0.55328 ( 5782)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.463 
Fit side-chains
REVERT: A  198 ASP cc_start: 0.8585 (m-30) cc_final: 0.7954 (m-30)
REVERT: A  247 ILE cc_start: 0.8636 (pt) cc_final: 0.8366 (tp)
REVERT: A  253 ARG cc_start: 0.7960 (mtm180) cc_final: 0.6017 (mmm160)
REVERT: A  348 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7674 (tp-100)
REVERT: A  417 MET cc_start: 0.8883 (tpp) cc_final: 0.8614 (mmm)
REVERT: A  440 MET cc_start: 0.8119 (ptm) cc_final: 0.7900 (ptt)
REVERT: A  623 ARG cc_start: 0.7657 (tpp80) cc_final: 0.7306 (mtt180)
  outliers start: 12
  outliers final: 9
  residues processed: 53
  average time/residue: 1.0368
  time to fit residues: 57.3596
Evaluate side-chains
  56 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  647 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 34 optimal weight:    0.0670
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0000
   chunk 22 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.4522

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.155532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.116563 restraints weight = 4937.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.37
r_work: 0.3202 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.3268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4268  Z= 0.122
  Angle     :  0.613  15.067   5805  Z= 0.291
  Chirality :  0.048   0.606    678
  Planarity :  0.004   0.049    700
  Dihedral  :  6.494  54.295    660
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 22.89 %
    Favored  : 74.46 %
  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:  1.59 (0.38), residues: 539
  helix:  2.39 (0.29), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.43 (0.41), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 258 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.015   0.001   PHE A 386 
 TYR   0.023   0.001   TYR A 590 
 ARG   0.001   0.000   ARG A 181 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01457 (    2)
  link_NAG-ASN         : angle       8.78243 (    6)
  link_BETA1-4         : bond        0.00510 (    1)
  link_BETA1-4         : angle       2.69499 (    3)
  hydrogen bonds       : bond        0.05736 (  244)
  hydrogen bonds       : angle       3.58185 (  711)
  SS BOND              : bond        0.00167 (    7)
  SS BOND              : angle       0.81538 (   14)
  covalent geometry    : bond        0.00240 ( 4258)
  covalent geometry    : angle       0.54029 ( 5782)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A  198 ASP cc_start: 0.8517 (m-30) cc_final: 0.7925 (m-30)
REVERT: A  247 ILE cc_start: 0.8673 (pt) cc_final: 0.8402 (tp)
REVERT: A  253 ARG cc_start: 0.7963 (mtm180) cc_final: 0.6016 (mmm160)
REVERT: A  348 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7617 (tp-100)
REVERT: A  417 MET cc_start: 0.8773 (tpp) cc_final: 0.8507 (mmm)
  outliers start: 11
  outliers final: 7
  residues processed: 54
  average time/residue: 0.9383
  time to fit residues: 53.2091
Evaluate side-chains
  55 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  558 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0370
   chunk 43 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.6458

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.152844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.113410 restraints weight = 4975.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.38
r_work: 0.3165 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4268  Z= 0.135
  Angle     :  0.631  15.031   5805  Z= 0.303
  Chirality :  0.048   0.600    678
  Planarity :  0.004   0.048    700
  Dihedral  :  6.185  53.799    659
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 23.37 %
    Favored  : 74.70 %
  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:  1.48 (0.38), residues: 539
  helix:  2.22 (0.29), residues: 345
  sheet:  None (None), residues: 0
  loop : -1.41 (0.41), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 254 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.017   0.001   PHE A 386 
 TYR   0.022   0.001   TYR A 590 
 ARG   0.001   0.000   ARG A 633 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01405 (    2)
  link_NAG-ASN         : angle       8.70517 (    6)
  link_BETA1-4         : bond        0.00471 (    1)
  link_BETA1-4         : angle       2.52303 (    3)
  hydrogen bonds       : bond        0.06479 (  244)
  hydrogen bonds       : angle       3.66676 (  711)
  SS BOND              : bond        0.00210 (    7)
  SS BOND              : angle       0.83264 (   14)
  covalent geometry    : bond        0.00282 ( 4258)
  covalent geometry    : angle       0.56278 ( 5782)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.476 
Fit side-chains
REVERT: A  198 ASP cc_start: 0.8571 (m-30) cc_final: 0.7948 (m-30)
REVERT: A  247 ILE cc_start: 0.8694 (pt) cc_final: 0.8416 (tp)
REVERT: A  253 ARG cc_start: 0.7977 (mtm180) cc_final: 0.6036 (mmm160)
REVERT: A  348 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7709 (tp-100)
REVERT: A  417 MET cc_start: 0.8851 (tpp) cc_final: 0.8587 (mmm)
REVERT: A  623 ARG cc_start: 0.7736 (tpp80) cc_final: 0.7394 (mtt180)
  outliers start: 8
  outliers final: 7
  residues processed: 51
  average time/residue: 1.1008
  time to fit residues: 58.6862
Evaluate side-chains
  54 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  558 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 36 optimal weight:    0.0370
   chunk 32 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0980
   chunk 37 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 23 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.4258

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.155418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.116317 restraints weight = 4952.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.39
r_work: 0.3202 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4268  Z= 0.122
  Angle     :  0.611  14.967   5805  Z= 0.291
  Chirality :  0.047   0.599    678
  Planarity :  0.004   0.049    700
  Dihedral  :  6.081  53.451    659
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 23.13 %
    Favored  : 74.46 %
  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:  1.60 (0.38), residues: 539
  helix:  2.32 (0.29), residues: 345
  sheet:  None (None), residues: 0
  loop : -1.39 (0.41), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.018   0.001   PHE A 386 
 TYR   0.023   0.001   TYR A 590 
 ARG   0.001   0.000   ARG A 633 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01420 (    2)
  link_NAG-ASN         : angle       8.59153 (    6)
  link_BETA1-4         : bond        0.00491 (    1)
  link_BETA1-4         : angle       2.56797 (    3)
  hydrogen bonds       : bond        0.05711 (  244)
  hydrogen bonds       : angle       3.57061 (  711)
  SS BOND              : bond        0.00202 (    7)
  SS BOND              : angle       0.67606 (   14)
  covalent geometry    : bond        0.00238 ( 4258)
  covalent geometry    : angle       0.54187 ( 5782)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3496.33 seconds
wall clock time: 61 minutes 0.85 seconds (3660.85 seconds total)