Starting phenix.real_space_refine
on Sat May 10 17:38:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vke_43315/05_2025/8vke_43315.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vke_43315/05_2025/8vke_43315.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vke_43315/05_2025/8vke_43315.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vke_43315/05_2025/8vke_43315.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vke_43315/05_2025/8vke_43315.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vke_43315/05_2025/8vke_43315.cif"
  }
  resolution = 3.1
  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=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    4218      2.51       5
     N    1114      2.21       5
     O    1290      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6652
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "H"
      Number of atoms: 991
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 991
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "L"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 825
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 7, 'TRANS': 105}
    Chain: "R"
      Number of atoms: 1496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 1496
          Classifications: {'peptide': 186}
          Link IDs: {'PTRANS': 10, 'TRANS': 175}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 991
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 991
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "B"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 825
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 7, 'TRANS': 105}
    Chain: "C"
      Number of atoms: 1496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 1496
          Classifications: {'peptide': 186}
          Link IDs: {'PTRANS': 10, 'TRANS': 175}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 8.47, per 1000 atoms: 1.27
  Number of scatterers: 6652
  At special positions: 0
  Unit cell: (81.78, 88.36, 103.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    1290      8.00
     N    1114      7.00
     C    4218      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 391 " - pdb=" SG  CYS R 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 480 " - pdb=" SG  CYS R 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG C1301 " - " ASN C 343 "
      " NAG R1301 " - " ASN R 343 "
  Time building additional restraints: 1.37
  Conformation dependent library (CDL) restraints added in 862.9 milliseconds
  

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1572

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 20 sheets defined
      12.2% alpha, 35.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'H' and resid 99 through 100A
      No H-bonds generated for 'chain 'H' and resid 99 through 100A'
    Processing helix  chain 'L' and resid 27A through 30
    Processing helix  chain 'R' and resid 338 through 343
    Processing helix  chain 'R' and resid 349 through 353
      removed outlier: 3.616A  pdb=" N   TRP R 353 " --> pdb=" O   VAL R 350 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 364 through 372
      removed outlier: 3.756A  pdb=" N   LEU R 368 " --> pdb=" O   ASP R 364 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 383 through 387
      removed outlier: 3.820A  pdb=" N   LEU R 387 " --> pdb=" O   PRO R 384 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 404 through 410
      removed outlier: 3.687A  pdb=" N   VAL R 407 " --> pdb=" O   GLY R 404 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ARG R 408 " --> pdb=" O   ASP R 405 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLN R 409 " --> pdb=" O   GLU R 406 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 416 through 422
    Processing helix  chain 'A' and resid 83 through 87
    Processing helix  chain 'A' and resid 99 through 100A
      No H-bonds generated for 'chain 'A' and resid 99 through 100A'
    Processing helix  chain 'B' and resid 27A through 30
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 349 through 353
      removed outlier: 3.575A  pdb=" N   TRP C 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 364 through 372
      removed outlier: 3.566A  pdb=" N   LEU C 368 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 387
      removed outlier: 3.796A  pdb=" N   LEU C 387 " --> pdb=" O   PRO C 384 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 408
      removed outlier: 3.751A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.981A  pdb=" N   VAL H  35A" --> pdb=" O   ASP H  50 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   ASP H  50 " --> pdb=" O   VAL H  35A" (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   TRP H  36 " --> pdb=" O   LEU H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 4.063A  pdb=" N   ASN H 102 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   ALA H  96 " --> pdb=" O   PHE H 100K" (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   PHE H 100K" --> pdb=" O   ALA H  96 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 100C through 100E
    Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 13
      removed outlier: 6.322A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13
    Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 24
    Processing sheet with id=AA8, first strand: chain 'R' and resid 391 through 392
      removed outlier: 3.861A  pdb=" N   PHE R 392 " --> pdb=" O   VAL R 524 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL R 524 " --> pdb=" O   PHE R 392 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AB1, first strand: chain 'R' and resid 473 through 474
    Processing sheet with id=AB2, first strand: chain 'A' and resid 3 through 6
    Processing sheet with id=AB3, first strand: chain 'A' and resid 10 through 12
      removed outlier: 6.915A  pdb=" N   VAL A  35A" --> pdb=" O   ASP A  50 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   ASP A  50 " --> pdb=" O   VAL A  35A" (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   TRP A  36 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 10 through 12
      removed outlier: 4.054A  pdb=" N   ASN A 102 " --> pdb=" O   ARG A  94 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   ALA A  96 " --> pdb=" O   PHE A 100K" (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   PHE A 100K" --> pdb=" O   ALA A  96 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 100C through 100E
    Processing sheet with id=AB6, first strand: chain 'B' and resid 9 through 13
      removed outlier: 6.330A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 9 through 13
    Processing sheet with id=AB8, first strand: chain 'B' and resid 19 through 24
    Processing sheet with id=AB9, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.766A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AC2, first strand: chain 'C' and resid 473 through 474

    248 hydrogen bonds defined for protein.
    558 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: 1.86

  Time building geometry restraints manager: 1.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2123
        1.35 -     1.48: 1885
        1.48 -     1.60: 2772
        1.60 -     1.72: 0
        1.72 -     1.85: 36
  Bond restraints: 6816
  Sorted by residual:
  bond pdb=" N   VAL B  11 "
       pdb=" CA  VAL B  11 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.040 1.11e-02 8.12e+03 1.28e+01
  bond pdb=" C   GLN B   6 "
       pdb=" N   PRO B   7 "
    ideal  model  delta    sigma   weight residual
    1.329  1.363 -0.034 1.18e-02 7.18e+03 8.35e+00
  bond pdb=" N   SER B   9 "
       pdb=" CA  SER B   9 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.23e-02 6.61e+03 5.97e+00
  bond pdb=" N   CYS R 480 "
       pdb=" CA  CYS R 480 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.029 1.21e-02 6.83e+03 5.84e+00
  bond pdb=" N   LYS R 478 "
       pdb=" CA  LYS R 478 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.030 1.45e-02 4.76e+03 4.34e+00
  ... (remaining 6811 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 8977
        1.49 -     2.98: 260
        2.98 -     4.47: 31
        4.47 -     5.95: 1
        5.95 -     7.44: 1
  Bond angle restraints: 9270
  Sorted by residual:
  angle pdb=" CA  VAL B  11 "
        pdb=" C   VAL B  11 "
        pdb=" O   VAL B  11 "
      ideal   model   delta    sigma   weight residual
     121.67  118.17    3.50 1.05e+00 9.07e-01 1.11e+01
  angle pdb=" CA  CYS R 391 "
        pdb=" CB  CYS R 391 "
        pdb=" SG  CYS R 391 "
      ideal   model   delta    sigma   weight residual
     114.40  121.84   -7.44 2.30e+00 1.89e-01 1.05e+01
  angle pdb=" CA  SER B   9 "
        pdb=" C   SER B   9 "
        pdb=" O   SER B   9 "
      ideal   model   delta    sigma   weight residual
     121.23  118.05    3.18 1.07e+00 8.73e-01 8.85e+00
  angle pdb=" N   PRO B   7 "
        pdb=" CA  PRO B   7 "
        pdb=" C   PRO B   7 "
      ideal   model   delta    sigma   weight residual
     110.70  107.15    3.55 1.22e+00 6.72e-01 8.48e+00
  angle pdb=" O   GLN B   6 "
        pdb=" C   GLN B   6 "
        pdb=" N   PRO B   7 "
      ideal   model   delta    sigma   weight residual
     121.55  119.38    2.17 7.80e-01 1.64e+00 7.76e+00
  ... (remaining 9265 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 3642
       17.11 -    34.22: 308
       34.22 -    51.33: 79
       51.33 -    68.45: 16
       68.45 -    85.56: 11
  Dihedral angle restraints: 4056
    sinusoidal: 1588
      harmonic: 2468
  Sorted by residual:
  dihedral pdb=" CB  CYS R 480 "
           pdb=" SG  CYS R 480 "
           pdb=" SG  CYS R 488 "
           pdb=" CB  CYS R 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.41  -75.41     1      1.00e+01 1.00e-02 7.18e+01
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.94  -68.94     1      1.00e+01 1.00e-02 6.15e+01
  dihedral pdb=" CB  CYS C 336 "
           pdb=" SG  CYS C 336 "
           pdb=" SG  CYS C 361 "
           pdb=" CB  CYS C 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -38.05  -47.95     1      1.00e+01 1.00e-02 3.17e+01
  ... (remaining 4053 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 693
       0.037 -    0.074: 217
       0.074 -    0.111: 78
       0.111 -    0.148: 31
       0.148 -    0.185: 3
  Chirality restraints: 1022
  Sorted by residual:
  chirality pdb=" CA  VAL B  11 "
            pdb=" N   VAL B  11 "
            pdb=" C   VAL B  11 "
            pdb=" CB  VAL B  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.18 2.00e-01 2.50e+01 8.52e-01
  chirality pdb=" CA  ILE B  48 "
            pdb=" N   ILE B  48 "
            pdb=" C   ILE B  48 "
            pdb=" CB  ILE B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.50e-01
  chirality pdb=" CA  ASN B  52 "
            pdb=" N   ASN B  52 "
            pdb=" C   ASN B  52 "
            pdb=" CB  ASN B  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.89e-01
  ... (remaining 1019 not shown)

  Planarity restraints: 1194
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 478 "   -0.052 5.00e-02 4.00e+02   7.77e-02 9.66e+00
        pdb=" N   PRO C 479 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO C 479 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO C 479 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 372 "    0.020 5.00e-02 4.00e+02   3.02e-02 1.46e+00
        pdb=" N   PRO C 373 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO C 373 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 373 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 362 "    0.006 2.00e-02 2.50e+03   1.17e-02 1.37e+00
        pdb=" C   VAL C 362 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   VAL C 362 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ALA C 363 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1191 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 111
        2.66 -     3.22: 5977
        3.22 -     3.78: 10000
        3.78 -     4.34: 14631
        4.34 -     4.90: 24437
  Nonbonded interactions: 55156
  Sorted by model distance:
  nonbonded pdb=" O   SER C 366 "
            pdb=" ND2 ASN C 370 "
     model   vdw
     2.103 3.120
  nonbonded pdb=" O   PHE R 486 "
            pdb=" ND2 ASN C 450 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" O   TRP R 353 "
            pdb=" NH1 ARG R 466 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" NH1 ARG H  71 "
            pdb=" OG1 THR H  73 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" N   GLN H 105 "
            pdb=" OE1 GLN H 105 "
     model   vdw
     2.294 3.120
  ... (remaining 55151 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'L'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'R'
}

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:             32.260
  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:             0.020
  Extract box with map and model:          2.080
  Check model and map are aligned:         0.040
  Set scattering table:                    0.110
  Process input model:                     22.440
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
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      :  0.003   0.050   6830  Z= 0.179
  Angle     :  0.595   7.443   9300  Z= 0.351
  Chirality :  0.045   0.185   1022
  Planarity :  0.004   0.078   1192
  Dihedral  : 14.192  85.558   2448
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 13.86 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.28), residues: 838
  helix: -3.52 (0.46), residues: 64
  sheet:  1.18 (0.33), residues: 276
  loop : -0.22 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.001   0.000   HIS C 505 
 PHE   0.013   0.001   PHE R 392 
 TYR   0.018   0.001   TYR L  49 
 ARG   0.004   0.000   ARG C 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00119 (    2)
  link_NAG-ASN         : angle       0.91710 (    6)
  hydrogen bonds       : bond        0.19375 (  224)
  hydrogen bonds       : angle       9.21471 (  558)
  SS BOND              : bond        0.00373 (   12)
  SS BOND              : angle       1.40294 (   24)
  covalent geometry    : bond        0.00349 ( 6816)
  covalent geometry    : angle       0.59123 ( 9270)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.740 
Fit side-chains
REVERT: L   17 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7062 (tt0)
REVERT: L   78 LEU cc_start: 0.7864 (tp) cc_final: 0.7593 (mt)
REVERT: R  466 ARG cc_start: 0.8088 (ptm160) cc_final: 0.7887 (ptt180)
  outliers start: 1
  outliers final: 1
  residues processed: 109
  average time/residue: 0.1897
  time to fit residues: 27.5315
Evaluate side-chains
  105 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  427 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
R 487 ASN
C 448 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.134764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.108886 restraints weight = 8277.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 1.93
r_work: 0.3066 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.0904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6830  Z= 0.216
  Angle     :  0.599   7.736   9300  Z= 0.324
  Chirality :  0.047   0.170   1022
  Planarity :  0.005   0.050   1192
  Dihedral  :  5.913  53.119    980
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.32 %
    Favored  : 84.65 %
  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: -0.37 (0.27), residues: 838
  helix: -3.91 (0.43), residues: 54
  sheet:  0.82 (0.32), residues: 278
  loop : -0.41 (0.25), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  47 
 HIS   0.002   0.001   HIS B  34 
 PHE   0.012   0.002   PHE R 392 
 TYR   0.026   0.002   TYR L  49 
 ARG   0.003   0.000   ARG C 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00075 (    2)
  link_NAG-ASN         : angle       1.32307 (    6)
  hydrogen bonds       : bond        0.03832 (  224)
  hydrogen bonds       : angle       6.72410 (  558)
  SS BOND              : bond        0.00340 (   12)
  SS BOND              : angle       1.29481 (   24)
  covalent geometry    : bond        0.00508 ( 6816)
  covalent geometry    : angle       0.59539 ( 9270)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.710 
Fit side-chains
REVERT: H   77 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.8028 (pt0)
REVERT: L   17 GLN cc_start: 0.7283 (mm-40) cc_final: 0.7054 (tt0)
REVERT: L   78 LEU cc_start: 0.7979 (tp) cc_final: 0.7612 (mt)
REVERT: A   56 GLU cc_start: 0.8636 (mp0) cc_final: 0.8389 (mt-10)
  outliers start: 15
  outliers final: 10
  residues processed: 110
  average time/residue: 0.1886
  time to fit residues: 27.6921
Evaluate side-chains
  111 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   77 GLN
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  470 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 79 optimal weight:    0.5980
   chunk 7 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 370 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.135109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.105973 restraints weight = 8251.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 1.98
r_work: 0.3010 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6830  Z= 0.205
  Angle     :  0.574   6.712   9300  Z= 0.310
  Chirality :  0.046   0.172   1022
  Planarity :  0.005   0.039   1192
  Dihedral  :  5.776  52.905    978
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.40 %
    Favored  : 82.88 %
  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: -0.59 (0.27), residues: 838
  helix: -3.85 (0.45), residues: 50
  sheet:  0.68 (0.31), residues: 278
  loop : -0.63 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  47 
 HIS   0.002   0.001   HIS B  34 
 PHE   0.010   0.001   PHE B  91 
 TYR   0.022   0.002   TYR L  49 
 ARG   0.005   0.000   ARG R 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00087 (    2)
  link_NAG-ASN         : angle       1.23864 (    6)
  hydrogen bonds       : bond        0.03358 (  224)
  hydrogen bonds       : angle       6.35150 (  558)
  SS BOND              : bond        0.00381 (   12)
  SS BOND              : angle       1.53628 (   24)
  covalent geometry    : bond        0.00486 ( 6816)
  covalent geometry    : angle       0.56915 ( 9270)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.786 
Fit side-chains
REVERT: L   17 GLN cc_start: 0.7280 (mm-40) cc_final: 0.6970 (tt0)
REVERT: L   69 THR cc_start: 0.9089 (t) cc_final: 0.8605 (m)
REVERT: L   78 LEU cc_start: 0.7860 (tp) cc_final: 0.7492 (mt)
REVERT: R  466 ARG cc_start: 0.8403 (ptm-80) cc_final: 0.8109 (ptt180)
REVERT: A   56 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8042 (mp0)
  outliers start: 20
  outliers final: 15
  residues processed: 114
  average time/residue: 0.2057
  time to fit residues: 30.8288
Evaluate side-chains
  118 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  415 THR
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  415 THR
Chi-restraints excluded: chain C residue  470 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 24 optimal weight:    0.0670
   chunk 71 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   chunk 18 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 = 0.3591 r_free = 0.3591 target = 0.136068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.106834 restraints weight = 8235.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.98
r_work: 0.3036 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6830  Z= 0.162
  Angle     :  0.534   6.138   9300  Z= 0.289
  Chirality :  0.045   0.170   1022
  Planarity :  0.004   0.032   1192
  Dihedral  :  5.663  52.791    978
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 14.13 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.27), residues: 838
  helix: -3.72 (0.48), residues: 50
  sheet:  0.63 (0.31), residues: 278
  loop : -0.65 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.002   0.001   HIS B  34 
 PHE   0.009   0.001   PHE B  91 
 TYR   0.019   0.002   TYR L  49 
 ARG   0.004   0.000   ARG C 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00100 (    2)
  link_NAG-ASN         : angle       1.18367 (    6)
  hydrogen bonds       : bond        0.02874 (  224)
  hydrogen bonds       : angle       6.11209 (  558)
  SS BOND              : bond        0.00376 (   12)
  SS BOND              : angle       1.15760 (   24)
  covalent geometry    : bond        0.00383 ( 6816)
  covalent geometry    : angle       0.53087 ( 9270)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.729 
Fit side-chains
REVERT: H   76 SER cc_start: 0.8416 (m) cc_final: 0.8041 (p)
REVERT: L   17 GLN cc_start: 0.7322 (mm-40) cc_final: 0.6964 (tt0)
REVERT: L   69 THR cc_start: 0.9111 (t) cc_final: 0.8631 (m)
REVERT: L   78 LEU cc_start: 0.7916 (tp) cc_final: 0.7601 (mt)
REVERT: A   56 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8204 (mt-10)
REVERT: C  501 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8270 (m-10)
  outliers start: 27
  outliers final: 19
  residues processed: 122
  average time/residue: 0.1936
  time to fit residues: 31.2163
Evaluate side-chains
  123 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   97 ASN
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  468 ILE
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   24 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  415 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  501 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0070
   chunk 61 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 39 optimal weight:    0.2980
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN
C 370 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.138132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.111019 restraints weight = 8114.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 2.05
r_work: 0.3134 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6830  Z= 0.136
  Angle     :  0.512   6.160   9300  Z= 0.276
  Chirality :  0.044   0.168   1022
  Planarity :  0.004   0.032   1192
  Dihedral  :  5.564  52.823    978
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 15.22 %
    Favored  : 81.66 %
  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: -0.63 (0.27), residues: 838
  helix: -3.82 (0.46), residues: 54
  sheet:  0.61 (0.32), residues: 278
  loop : -0.60 (0.24), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.010   0.001   PHE C 486 
 TYR   0.017   0.001   TYR L  49 
 ARG   0.003   0.000   ARG C 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00139 (    2)
  link_NAG-ASN         : angle       1.10338 (    6)
  hydrogen bonds       : bond        0.02696 (  224)
  hydrogen bonds       : angle       5.96996 (  558)
  SS BOND              : bond        0.00374 (   12)
  SS BOND              : angle       0.96086 (   24)
  covalent geometry    : bond        0.00319 ( 6816)
  covalent geometry    : angle       0.50995 ( 9270)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.788 
Fit side-chains
REVERT: H   76 SER cc_start: 0.8357 (m) cc_final: 0.8130 (p)
REVERT: L   17 GLN cc_start: 0.7378 (mm-40) cc_final: 0.7090 (tt0)
REVERT: L   69 THR cc_start: 0.9145 (t) cc_final: 0.8656 (m)
REVERT: L   78 LEU cc_start: 0.7947 (tp) cc_final: 0.7686 (mt)
REVERT: A   56 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8278 (mt-10)
REVERT: C  501 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8244 (m-10)
  outliers start: 23
  outliers final: 17
  residues processed: 120
  average time/residue: 0.2257
  time to fit residues: 36.0389
Evaluate side-chains
  121 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  389 ASP
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  501 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0770
   chunk 79 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0670
   overall best weight:    0.4676

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

Flipped N/Q/H residues before XYZ refinement:
R 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.137856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.109775 restraints weight = 8100.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 1.98
r_work: 0.3119 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6830  Z= 0.147
  Angle     :  0.518   5.336   9300  Z= 0.280
  Chirality :  0.044   0.168   1022
  Planarity :  0.004   0.041   1192
  Dihedral  :  5.550  52.748    978
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 14.40 %
    Favored  : 82.07 %
  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: -0.66 (0.27), residues: 838
  helix: -3.80 (0.46), residues: 54
  sheet:  0.74 (0.32), residues: 258
  loop : -0.67 (0.24), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.011   0.001   PHE C 486 
 TYR   0.019   0.002   TYR L  49 
 ARG   0.004   0.000   ARG H  71 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00111 (    2)
  link_NAG-ASN         : angle       1.12931 (    6)
  hydrogen bonds       : bond        0.02644 (  224)
  hydrogen bonds       : angle       5.91035 (  558)
  SS BOND              : bond        0.00315 (   12)
  SS BOND              : angle       0.93534 (   24)
  covalent geometry    : bond        0.00347 ( 6816)
  covalent geometry    : angle       0.51592 ( 9270)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 0.660 
Fit side-chains
REVERT: L   17 GLN cc_start: 0.7381 (mm-40) cc_final: 0.7076 (tt0)
REVERT: L   69 THR cc_start: 0.9140 (t) cc_final: 0.8653 (m)
REVERT: L   78 LEU cc_start: 0.7931 (tp) cc_final: 0.7672 (mt)
REVERT: A   56 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8226 (mt-10)
REVERT: A   58 SER cc_start: 0.8585 (t) cc_final: 0.8319 (m)
REVERT: A   82 ASN cc_start: 0.8402 (t0) cc_final: 0.8166 (m-40)
REVERT: C  501 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.8362 (m-10)
  outliers start: 26
  outliers final: 19
  residues processed: 121
  average time/residue: 0.2019
  time to fit residues: 31.7714
Evaluate side-chains
  124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   97 ASN
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   24 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  415 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  501 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.2980
   chunk 2 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.134641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.105239 restraints weight = 8147.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.98
r_work: 0.3016 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6830  Z= 0.204
  Angle     :  0.564   4.785   9300  Z= 0.304
  Chirality :  0.046   0.170   1022
  Planarity :  0.005   0.036   1192
  Dihedral  :  5.696  52.527    978
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 15.08 %
    Favored  : 81.39 %
  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: -0.82 (0.26), residues: 838
  helix: -3.87 (0.45), residues: 54
  sheet:  0.72 (0.33), residues: 248
  loop : -0.81 (0.23), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  47 
 HIS   0.002   0.001   HIS R 505 
 PHE   0.011   0.001   PHE C 486 
 TYR   0.022   0.002   TYR L  49 
 ARG   0.004   0.000   ARG C 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00085 (    2)
  link_NAG-ASN         : angle       1.21252 (    6)
  hydrogen bonds       : bond        0.02842 (  224)
  hydrogen bonds       : angle       6.01284 (  558)
  SS BOND              : bond        0.00311 (   12)
  SS BOND              : angle       1.06099 (   24)
  covalent geometry    : bond        0.00483 ( 6816)
  covalent geometry    : angle       0.56126 ( 9270)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.770 
Fit side-chains
REVERT: H   64 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7520 (tptm)
REVERT: L   17 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6993 (tt0)
REVERT: L   69 THR cc_start: 0.9141 (t) cc_final: 0.8677 (m)
REVERT: L   78 LEU cc_start: 0.7953 (tp) cc_final: 0.7665 (mt)
REVERT: A   56 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8150 (mt-10)
REVERT: A   58 SER cc_start: 0.8668 (t) cc_final: 0.8394 (m)
REVERT: A   82 ASN cc_start: 0.8399 (t0) cc_final: 0.8140 (m-40)
REVERT: C  501 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8380 (m-10)
  outliers start: 26
  outliers final: 19
  residues processed: 125
  average time/residue: 0.2094
  time to fit residues: 34.3055
Evaluate side-chains
  130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue   97 ASN
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  389 ASP
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   24 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  415 THR
Chi-restraints excluded: chain C residue  501 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 70 optimal weight:    0.3980
   chunk 32 optimal weight:    0.0980
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0270
   chunk 71 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0980
   overall best weight:    0.1638

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

Flipped N/Q/H residues before XYZ refinement:
C 450 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.139847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.108946 restraints weight = 8075.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.22
r_work: 0.3059 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6830  Z= 0.093
  Angle     :  0.492   5.196   9300  Z= 0.265
  Chirality :  0.043   0.167   1022
  Planarity :  0.004   0.033   1192
  Dihedral  :  5.468  53.172    978
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.58 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.27), residues: 838
  helix: -3.81 (0.46), residues: 54
  sheet:  0.78 (0.33), residues: 248
  loop : -0.63 (0.24), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.009   0.001   PHE C 486 
 TYR   0.013   0.001   TYR R 421 
 ARG   0.004   0.000   ARG H  71 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00170 (    2)
  link_NAG-ASN         : angle       1.00418 (    6)
  hydrogen bonds       : bond        0.02402 (  224)
  hydrogen bonds       : angle       5.84326 (  558)
  SS BOND              : bond        0.00280 (   12)
  SS BOND              : angle       0.79617 (   24)
  covalent geometry    : bond        0.00206 ( 6816)
  covalent geometry    : angle       0.49094 ( 9270)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.788 
Fit side-chains
REVERT: H   64 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7103 (tptm)
REVERT: L   17 GLN cc_start: 0.7151 (mm-40) cc_final: 0.6624 (tt0)
REVERT: L   69 THR cc_start: 0.8891 (t) cc_final: 0.8402 (m)
REVERT: L   86 TYR cc_start: 0.8644 (m-80) cc_final: 0.8382 (m-80)
REVERT: A   56 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7993 (mt-10)
REVERT: A   82 ASN cc_start: 0.8264 (t0) cc_final: 0.7965 (m-40)
REVERT: C  501 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7842 (m-10)
  outliers start: 19
  outliers final: 12
  residues processed: 122
  average time/residue: 0.2306
  time to fit residues: 36.4179
Evaluate side-chains
  119 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  501 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0980
   chunk 9 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 19 optimal weight:    3.9990
   chunk 45 optimal weight:    0.3980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.135107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.104224 restraints weight = 8242.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 2.17
r_work: 0.3075 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6830  Z= 0.154
  Angle     :  0.531   7.135   9300  Z= 0.285
  Chirality :  0.044   0.168   1022
  Planarity :  0.004   0.033   1192
  Dihedral  :  5.527  52.735    978
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.30 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.27), residues: 838
  helix: -3.39 (0.46), residues: 66
  sheet:  0.75 (0.33), residues: 248
  loop : -0.58 (0.24), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.008   0.001   PHE A  52 
 TYR   0.020   0.001   TYR L  49 
 ARG   0.004   0.000   ARG C 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00112 (    2)
  link_NAG-ASN         : angle       1.10137 (    6)
  hydrogen bonds       : bond        0.02633 (  224)
  hydrogen bonds       : angle       5.86680 (  558)
  SS BOND              : bond        0.00299 (   12)
  SS BOND              : angle       0.91095 (   24)
  covalent geometry    : bond        0.00363 ( 6816)
  covalent geometry    : angle       0.52874 ( 9270)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.754 
Fit side-chains
REVERT: H   64 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7348 (tptm)
REVERT: L   17 GLN cc_start: 0.7149 (mm-40) cc_final: 0.6710 (tt0)
REVERT: A   56 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8018 (mt-10)
REVERT: A   82 ASN cc_start: 0.8310 (t0) cc_final: 0.8018 (m-40)
REVERT: C  501 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.8256 (m-10)
  outliers start: 20
  outliers final: 15
  residues processed: 116
  average time/residue: 0.2074
  time to fit residues: 31.3640
Evaluate side-chains
  121 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue   97 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   97 ASN
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  417 ASN
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  501 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 79 optimal weight:    0.2980
   chunk 49 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 80 optimal weight:    0.0980
   chunk 52 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.136135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.105333 restraints weight = 8305.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.18
r_work: 0.3040 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.111   6830  Z= 0.185
  Angle     :  0.952  59.200   9300  Z= 0.560
  Chirality :  0.045   0.242   1022
  Planarity :  0.004   0.033   1192
  Dihedral  :  5.544  52.717    978
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.98 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.13 %
  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: -0.64 (0.27), residues: 838
  helix: -3.40 (0.47), residues: 66
  sheet:  0.74 (0.33), residues: 248
  loop : -0.59 (0.24), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.008   0.001   PHE A  52 
 TYR   0.020   0.002   TYR L  49 
 ARG   0.003   0.000   ARG C 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00115 (    2)
  link_NAG-ASN         : angle       1.11217 (    6)
  hydrogen bonds       : bond        0.02639 (  224)
  hydrogen bonds       : angle       5.86248 (  558)
  SS BOND              : bond        0.00325 (   12)
  SS BOND              : angle       0.97294 (   24)
  covalent geometry    : bond        0.00421 ( 6816)
  covalent geometry    : angle       0.95181 ( 9270)

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.692 
Fit side-chains
REVERT: H   64 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7308 (tptm)
REVERT: L   17 GLN cc_start: 0.7104 (mm-40) cc_final: 0.6683 (tt0)
REVERT: A   56 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7994 (mt-10)
REVERT: A   82 ASN cc_start: 0.8299 (t0) cc_final: 0.7999 (m-40)
REVERT: C  501 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8228 (m-10)
  outliers start: 17
  outliers final: 14
  residues processed: 112
  average time/residue: 0.2123
  time to fit residues: 30.8675
Evaluate side-chains
  119 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue   97 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  417 ASN
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  501 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 53 optimal weight:    0.1980
   chunk 80 optimal weight:    0.3980
   chunk 54 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.136979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.105805 restraints weight = 8162.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.24
r_work: 0.3017 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.111   6830  Z= 0.185
  Angle     :  0.952  59.200   9300  Z= 0.560
  Chirality :  0.045   0.242   1022
  Planarity :  0.004   0.033   1192
  Dihedral  :  5.544  52.717    978
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.98 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.13 %
  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: -0.64 (0.27), residues: 838
  helix: -3.40 (0.47), residues: 66
  sheet:  0.74 (0.33), residues: 248
  loop : -0.59 (0.24), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.008   0.001   PHE A  52 
 TYR   0.020   0.002   TYR L  49 
 ARG   0.003   0.000   ARG C 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00115 (    2)
  link_NAG-ASN         : angle       1.11217 (    6)
  hydrogen bonds       : bond        0.02639 (  224)
  hydrogen bonds       : angle       5.86248 (  558)
  SS BOND              : bond        0.00556 (   12)
  SS BOND              : angle       1.01112 (   24)
  covalent geometry    : bond        0.00421 ( 6816)
  covalent geometry    : angle       0.95181 ( 9270)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4327.46 seconds
wall clock time: 76 minutes 5.17 seconds (4565.17 seconds total)