Starting phenix.real_space_refine
on Fri May  9 23:37:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k6l_36922/05_2025/8k6l_36922.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k6l_36922/05_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_36922/05_2025/8k6l_36922.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k6l_36922/05_2025/8k6l_36922.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k6l_36922/05_2025/8k6l_36922.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k6l_36922/05_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-5687/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: 3.08, per 1000 atoms: 0.74
  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: 1.14
  Conformation dependent library (CDL) restraints added in 506.3 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: 0.43
  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: 1.05

  Time building geometry restraints manager: 1.28 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:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.760
  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:10.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.560
-------------------------------------------------------------------------------
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  : 0.411 
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: 1.0589
  time to fit residues: 91.5755
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  : 0.449 
-------------------------------------------------------------------------------
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 = 44)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.122358 restraints weight = 4988.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 2.41
r_work: 0.3245 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: 0.7746
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  : 0.423 
Fit side-chains
REVERT: A   48 MET cc_start: 0.7362 (tpt) cc_final: 0.7099 (tpp)
REVERT: A   74 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7989 (mm-30)
REVERT: A  185 GLU cc_start: 0.8351 (pt0) cc_final: 0.8014 (pp20)
REVERT: A  198 ASP cc_start: 0.8331 (m-30) cc_final: 0.7728 (m-30)
REVERT: A  253 ARG cc_start: 0.7825 (mtm180) cc_final: 0.6033 (mtp-110)
REVERT: A  580 ARG cc_start: 0.8043 (mtp-110) cc_final: 0.7485 (mtm-85)
REVERT: A  648 LYS cc_start: 0.7453 (ttmt) cc_final: 0.6683 (ttpt)
  outliers start: 8
  outliers final: 2
  residues processed: 62
  average time/residue: 1.0681
  time to fit residues: 68.8870
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  : 0.444 
-------------------------------------------------------------------------------
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:    0.6980
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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 = 0.3744 r_free = 0.3744 target = 0.153902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.115588 restraints weight = 4985.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.18
r_work: 0.3194 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.2309

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= 0.143
  Angle     :  0.678  16.796   5805  Z= 0.323
  Chirality :  0.051   0.686    678
  Planarity :  0.004   0.049    700
  Dihedral  :  7.001  58.099    660
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 19.04 %
    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:  0.48 (0.37), residues: 539
  helix:  1.49 (0.29), residues: 344
  sheet:  None (None), residues: 0
  loop : -1.90 (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 520 
 PHE   0.012   0.001   PHE A 621 
 TYR   0.024   0.002   TYR A 590 
 ARG   0.001   0.000   ARG A 633 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01323 (    2)
  link_NAG-ASN         : angle      10.27088 (    6)
  link_BETA1-4         : bond        0.00399 (    1)
  link_BETA1-4         : angle       3.35526 (    3)
  hydrogen bonds       : bond        0.06869 (  244)
  hydrogen bonds       : angle       3.90452 (  711)
  SS BOND              : bond        0.00657 (    7)
  SS BOND              : angle       0.85767 (   14)
  covalent geometry    : bond        0.00281 ( 4258)
  covalent geometry    : angle       0.58737 ( 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
  65 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 MET cc_start: 0.7566 (mmm) cc_final: 0.7358 (mmt)
REVERT: A  253 ARG cc_start: 0.7808 (mtm180) cc_final: 0.5940 (mtp-110)
REVERT: A  348 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7257 (tp-100)
REVERT: A  433 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7004 (ptpp)
REVERT: A  648 LYS cc_start: 0.7217 (ttmt) cc_final: 0.6492 (ttpt)
  outliers start: 17
  outliers final: 4
  residues processed: 60
  average time/residue: 0.9893
  time to fit residues: 62.2368
Evaluate side-chains
  53 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  433 LYS
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:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0060
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.5396

-------------------------------------------------------------------------------
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 = 0.3747 r_free = 0.3747 target = 0.154267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.116485 restraints weight = 4941.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.16
r_work: 0.3210 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.2634

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= 0.128
  Angle     :  0.637  16.250   5805  Z= 0.301
  Chirality :  0.049   0.656    678
  Planarity :  0.004   0.049    700
  Dihedral  :  6.568  52.900    660
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 20.96 %
    Favored  : 75.42 %
  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:  1.03 (0.37), residues: 539
  helix:  1.91 (0.29), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.58 (0.41), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 258 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.016   0.001   PHE A 501 
 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        0.01354 (    2)
  link_NAG-ASN         : angle       9.61926 (    6)
  link_BETA1-4         : bond        0.00636 (    1)
  link_BETA1-4         : angle       3.08302 (    3)
  hydrogen bonds       : bond        0.06173 (  244)
  hydrogen bonds       : angle       3.72843 (  711)
  SS BOND              : bond        0.00227 (    7)
  SS BOND              : angle       0.69345 (   14)
  covalent geometry    : bond        0.00255 ( 4258)
  covalent geometry    : angle       0.55296 ( 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: 15
    poor density    : 50
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A  185 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7929 (pp20)
REVERT: A  198 ASP cc_start: 0.8183 (m-30) cc_final: 0.7539 (m-30)
REVERT: A  253 ARG cc_start: 0.7842 (mtm180) cc_final: 0.5989 (mtp-110)
REVERT: A  348 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.7172 (tp-100)
REVERT: A  417 MET cc_start: 0.8624 (tpp) cc_final: 0.8394 (mmp)
REVERT: A  648 LYS cc_start: 0.6919 (ttmt) cc_final: 0.6203 (ttpt)
  outliers start: 15
  outliers final: 6
  residues processed: 61
  average time/residue: 0.9316
  time to fit residues: 59.5403
Evaluate side-chains
  56 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
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:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0870
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.7358

-------------------------------------------------------------------------------
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 = 0.3747 r_free = 0.3747 target = 0.152569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.113044 restraints weight = 5061.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.41
r_work: 0.3165 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4268  Z= 0.142
  Angle     :  0.643  15.742   5805  Z= 0.307
  Chirality :  0.049   0.636    678
  Planarity :  0.004   0.047    700
  Dihedral  :  6.613  55.106    660
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 22.17 %
    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:  1.18 (0.37), residues: 539
  helix:  2.03 (0.29), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.52 (0.42), 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 520 
 PHE   0.013   0.001   PHE A 621 
 TYR   0.023   0.001   TYR A 625 
 ARG   0.002   0.000   ARG A 633 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01361 (    2)
  link_NAG-ASN         : angle       9.38951 (    6)
  link_BETA1-4         : bond        0.00557 (    1)
  link_BETA1-4         : angle       2.92579 (    3)
  hydrogen bonds       : bond        0.06903 (  244)
  hydrogen bonds       : angle       3.75041 (  711)
  SS BOND              : bond        0.00246 (    7)
  SS BOND              : angle       0.60251 (   14)
  covalent geometry    : bond        0.00297 ( 4258)
  covalent geometry    : angle       0.56438 ( 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
  60 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.424 
Fit side-chains
REVERT: A  185 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8044 (pp20)
REVERT: A  198 ASP cc_start: 0.8280 (m-30) cc_final: 0.7622 (m-30)
REVERT: A  253 ARG cc_start: 0.7855 (mtm180) cc_final: 0.6008 (mtp-110)
REVERT: A  348 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7347 (tp-100)
REVERT: A  417 MET cc_start: 0.8710 (tpp) cc_final: 0.8487 (mmp)
REVERT: A  553 THR cc_start: 0.8380 (m) cc_final: 0.8169 (p)
REVERT: A  623 ARG cc_start: 0.7462 (tpp80) cc_final: 0.7078 (mtt180)
REVERT: A  648 LYS cc_start: 0.7021 (ttmt) cc_final: 0.6317 (ttpt)
  outliers start: 11
  outliers final: 6
  residues processed: 56
  average time/residue: 0.9813
  time to fit residues: 57.4233
Evaluate side-chains
  56 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
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  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:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3738 r_free = 0.3738 target = 0.150778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.110953 restraints weight = 4995.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.42
r_work: 0.3139 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.2753

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= 0.148
  Angle     :  0.644  15.534   5805  Z= 0.309
  Chirality :  0.049   0.627    678
  Planarity :  0.004   0.046    700
  Dihedral  :  6.637  54.616    660
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 2.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 21.20 %
    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:  1.20 (0.37), residues: 539
  helix:  2.05 (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   0.004   0.001   TRP A 258 
 HIS   0.002   0.001   HIS A 520 
 PHE   0.015   0.001   PHE A 501 
 TYR   0.023   0.002   TYR A 625 
 ARG   0.002   0.000   ARG A 633 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01331 (    2)
  link_NAG-ASN         : angle       9.20857 (    6)
  link_BETA1-4         : bond        0.00548 (    1)
  link_BETA1-4         : angle       2.70264 (    3)
  hydrogen bonds       : bond        0.07248 (  244)
  hydrogen bonds       : angle       3.80790 (  711)
  SS BOND              : bond        0.00260 (    7)
  SS BOND              : angle       0.61843 (   14)
  covalent geometry    : bond        0.00318 ( 4258)
  covalent geometry    : angle       0.56837 ( 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: 15
    poor density    : 48
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A  198 ASP cc_start: 0.8598 (m-30) cc_final: 0.7972 (m-30)
REVERT: A  247 ILE cc_start: 0.8649 (pt) cc_final: 0.8333 (tp)
REVERT: A  253 ARG cc_start: 0.7910 (mtm180) cc_final: 0.6123 (mtp-110)
REVERT: A  348 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7799 (tp-100)
REVERT: A  417 MET cc_start: 0.8921 (tpp) cc_final: 0.8674 (mmp)
REVERT: A  623 ARG cc_start: 0.7796 (tpp80) cc_final: 0.7440 (mtt180)
REVERT: A  640 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7518 (t80)
REVERT: A  648 LYS cc_start: 0.7454 (ttmt) cc_final: 0.6746 (ttpt)
  outliers start: 15
  outliers final: 8
  residues processed: 59
  average time/residue: 1.1072
  time to fit residues: 68.1230
Evaluate side-chains
  55 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  474 CYS
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  640 TYR
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:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    6.9990
   chunk 39 optimal weight:   10.0000
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3732 r_free = 0.3732 target = 0.150444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.110670 restraints weight = 4968.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.38
r_work: 0.3133 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.2821

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= 0.158
  Angle     :  0.665  15.487   5805  Z= 0.323
  Chirality :  0.050   0.621    678
  Planarity :  0.004   0.045    700
  Dihedral  :  6.795  54.789    660
  Min Nonbonded Distance : 2.563

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:  1.17 (0.37), residues: 539
  helix:  2.06 (0.29), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.59 (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   0.016   0.001   PHE A 386 
 TYR   0.022   0.002   TYR A 625 
 ARG   0.002   0.000   ARG A 633 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01348 (    2)
  link_NAG-ASN         : angle       9.13966 (    6)
  link_BETA1-4         : bond        0.00550 (    1)
  link_BETA1-4         : angle       2.68183 (    3)
  hydrogen bonds       : bond        0.07459 (  244)
  hydrogen bonds       : angle       3.83132 (  711)
  SS BOND              : bond        0.00277 (    7)
  SS BOND              : angle       1.86512 (   14)
  covalent geometry    : bond        0.00344 ( 4258)
  covalent geometry    : angle       0.58754 ( 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
  64 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A  198 ASP cc_start: 0.8596 (m-30) cc_final: 0.7965 (m-30)
REVERT: A  247 ILE cc_start: 0.8636 (pt) cc_final: 0.8327 (tp)
REVERT: A  348 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7820 (tp-100)
REVERT: A  417 MET cc_start: 0.8932 (tpp) cc_final: 0.8677 (mmp)
REVERT: A  623 ARG cc_start: 0.7801 (tpp80) cc_final: 0.7439 (mtt180)
REVERT: A  640 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.7539 (t80)
REVERT: A  648 LYS cc_start: 0.7526 (ttmt) cc_final: 0.6811 (ttpt)
  outliers start: 14
  outliers final: 7
  residues processed: 61
  average time/residue: 0.9847
  time to fit residues: 62.8237
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  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  640 TYR
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:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0020
   chunk 14 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.5988

-------------------------------------------------------------------------------
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 = 0.3758 r_free = 0.3758 target = 0.152661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.113043 restraints weight = 4896.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 2.39
r_work: 0.3161 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.3013

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= 0.134
  Angle     :  0.634  15.316   5805  Z= 0.304
  Chirality :  0.049   0.608    678
  Planarity :  0.004   0.047    700
  Dihedral  :  6.758  59.847    660
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 1.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 22.17 %
    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:  1.35 (0.37), residues: 539
  helix:  2.20 (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   0.004   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A 520 
 PHE   0.014   0.001   PHE A 386 
 TYR   0.022   0.001   TYR A 590 
 ARG   0.002   0.000   ARG A 526 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01389 (    2)
  link_NAG-ASN         : angle       8.98029 (    6)
  link_BETA1-4         : bond        0.00575 (    1)
  link_BETA1-4         : angle       2.73834 (    3)
  hydrogen bonds       : bond        0.06528 (  244)
  hydrogen bonds       : angle       3.72631 (  711)
  SS BOND              : bond        0.00214 (    7)
  SS BOND              : angle       1.31918 (   14)
  covalent geometry    : bond        0.00275 ( 4258)
  covalent geometry    : angle       0.55823 ( 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
  61 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.449 
Fit side-chains
REVERT: A  198 ASP cc_start: 0.8568 (m-30) cc_final: 0.7928 (m-30)
REVERT: A  247 ILE cc_start: 0.8638 (pt) cc_final: 0.8358 (tp)
REVERT: A  348 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7713 (tp-100)
REVERT: A  417 MET cc_start: 0.8896 (tpp) cc_final: 0.8649 (mmt)
REVERT: A  440 MET cc_start: 0.8117 (ptm) cc_final: 0.7877 (ptt)
REVERT: A  623 ARG cc_start: 0.7675 (tpp80) cc_final: 0.7308 (mtt180)
REVERT: A  648 LYS cc_start: 0.7314 (ttmt) cc_final: 0.6579 (ttpt)
  outliers start: 13
  outliers final: 9
  residues processed: 56
  average time/residue: 0.9732
  time to fit residues: 56.9719
Evaluate side-chains
  59 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   79 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 10 optimal weight:    9.9990
   chunk 33 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3733 r_free = 0.3733 target = 0.150478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.110642 restraints weight = 4954.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 2.38
r_work: 0.3123 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3036

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= 0.150
  Angle     :  0.648  15.096   5805  Z= 0.313
  Chirality :  0.049   0.604    678
  Planarity :  0.004   0.047    700
  Dihedral  :  6.747  59.909    660
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 2.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 22.17 %
    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:  1.28 (0.37), residues: 539
  helix:  2.06 (0.29), residues: 345
  sheet:  None (None), residues: 0
  loop : -1.47 (0.41), 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 115 
 PHE   0.015   0.001   PHE A 386 
 TYR   0.023   0.001   TYR A 625 
 ARG   0.002   0.000   ARG A 623 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01396 (    2)
  link_NAG-ASN         : angle       8.84802 (    6)
  link_BETA1-4         : bond        0.00473 (    1)
  link_BETA1-4         : angle       2.51617 (    3)
  hydrogen bonds       : bond        0.07268 (  244)
  hydrogen bonds       : angle       3.80351 (  711)
  SS BOND              : bond        0.00253 (    7)
  SS BOND              : angle       1.22963 (   14)
  covalent geometry    : bond        0.00321 ( 4258)
  covalent geometry    : angle       0.57687 ( 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
  61 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A  198 ASP cc_start: 0.8608 (m-30) cc_final: 0.7975 (m-30)
REVERT: A  247 ILE cc_start: 0.8690 (pt) cc_final: 0.8317 (tp)
REVERT: A  251 ASP cc_start: 0.7279 (m-30) cc_final: 0.6858 (m-30)
REVERT: A  348 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7805 (tp-100)
REVERT: A  417 MET cc_start: 0.8892 (tpp) cc_final: 0.8644 (mmt)
REVERT: A  440 MET cc_start: 0.8123 (ptm) cc_final: 0.7910 (ptt)
REVERT: A  623 ARG cc_start: 0.7720 (tpp80) cc_final: 0.7327 (mtt180)
REVERT: A  648 LYS cc_start: 0.7418 (ttmt) cc_final: 0.6707 (ttpt)
  outliers start: 13
  outliers final: 8
  residues processed: 57
  average time/residue: 1.0308
  time to fit residues: 61.4026
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  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0170
   chunk 2 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0070
   chunk 43 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.4636

-------------------------------------------------------------------------------
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 = 0.3776 r_free = 0.3776 target = 0.154354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.114984 restraints weight = 4956.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.40
r_work: 0.3184 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3200

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= 0.124
  Angle     :  0.619  15.220   5805  Z= 0.296
  Chirality :  0.048   0.604    678
  Planarity :  0.004   0.049    700
  Dihedral  :  6.518  53.666    660
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 23.13 %
    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:  1.48 (0.38), residues: 539
  helix:  2.21 (0.29), residues: 345
  sheet:  None (None), residues: 0
  loop : -1.40 (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   0.017   0.001   PHE A 386 
 TYR   0.023   0.001   TYR A 590 
 ARG   0.002   0.000   ARG A 526 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01436 (    2)
  link_NAG-ASN         : angle       8.78423 (    6)
  link_BETA1-4         : bond        0.00504 (    1)
  link_BETA1-4         : angle       2.68249 (    3)
  hydrogen bonds       : bond        0.05962 (  244)
  hydrogen bonds       : angle       3.63175 (  711)
  SS BOND              : bond        0.00301 (    7)
  SS BOND              : angle       0.99133 (   14)
  covalent geometry    : bond        0.00243 ( 4258)
  covalent geometry    : angle       0.54603 ( 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
  56 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A  198 ASP cc_start: 0.8515 (m-30) cc_final: 0.7900 (m-30)
REVERT: A  247 ILE cc_start: 0.8679 (pt) cc_final: 0.8358 (tp)
REVERT: A  251 ASP cc_start: 0.7243 (m-30) cc_final: 0.6896 (m-30)
REVERT: A  348 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7653 (tp-100)
REVERT: A  417 MET cc_start: 0.8829 (tpp) cc_final: 0.8541 (mmm)
REVERT: A  605 ASN cc_start: 0.6574 (t0) cc_final: 0.6360 (t0)
  outliers start: 8
  outliers final: 5
  residues processed: 54
  average time/residue: 0.9323
  time to fit residues: 52.8009
Evaluate side-chains
  53 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    0.1980
   chunk 22 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 37 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0070
   chunk 23 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0020
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0070
   overall best weight:    0.1224

-------------------------------------------------------------------------------
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 = 0.3880 r_free = 0.3880 target = 0.164647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.126611 restraints weight = 4944.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.42
r_work: 0.3335 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.3726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4268  Z= 0.107
  Angle     :  0.595  14.775   5805  Z= 0.279
  Chirality :  0.047   0.588    678
  Planarity :  0.004   0.052    700
  Dihedral  :  6.004  52.862    659
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 24.10 %
    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:  1.73 (0.38), residues: 539
  helix:  2.40 (0.29), residues: 346
  sheet:  None (None), residues: 0
  loop : -1.29 (0.42), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 602 
 HIS   0.001   0.000   HIS A 204 
 PHE   0.015   0.001   PHE A 386 
 TYR   0.026   0.001   TYR A 590 
 ARG   0.002   0.000   ARG A 181 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01456 (    2)
  link_NAG-ASN         : angle       8.45851 (    6)
  link_BETA1-4         : bond        0.00506 (    1)
  link_BETA1-4         : angle       2.85402 (    3)
  hydrogen bonds       : bond        0.04009 (  244)
  hydrogen bonds       : angle       3.37501 (  711)
  SS BOND              : bond        0.00188 (    7)
  SS BOND              : angle       0.94310 (   14)
  covalent geometry    : bond        0.00205 ( 4258)
  covalent geometry    : angle       0.52392 ( 5782)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3011.81 seconds
wall clock time: 52 minutes 34.39 seconds (3154.39 seconds total)