Starting phenix.real_space_refine
on Thu Jun  5 11:06:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b3h_44139/06_2025/9b3h_44139.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b3h_44139/06_2025/9b3h_44139.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b3h_44139/06_2025/9b3h_44139.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b3h_44139/06_2025/9b3h_44139.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b3h_44139/06_2025/9b3h_44139.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b3h_44139/06_2025/9b3h_44139.cif"
  }
  resolution = 4.0
  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=  -0.002 sd=   0.014
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      51      5.16       5
     C    3757      2.51       5
     N    1021      2.21       5
     O    1150      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5979
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 531, 4129
          Classifications: {'peptide': 531}
          Link IDs: {'PTRANS': 22, 'TRANS': 508}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1780
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 8, 'TRANS': 207}
    Chain: "C"
      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: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 4.05, per 1000 atoms: 0.68
  Number of scatterers: 5979
  At special positions: 0
  Unit cell: (70.281, 97.407, 126.999, 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      51     16.00
     O    1150      8.00
     N    1021      7.00
     C    3757      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=19, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A 272 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  69 " - pdb=" SG  CYS A  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  82 " - pdb=" SG  CYS A 114 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  88 " - pdb=" SG  CYS A 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  96 " - pdb=" SG  CYS A 127 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 175 " - pdb=" SG  CYS A 231 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 204 " - pdb=" SG  CYS A 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 246 " - pdb=" SG  CYS A 264 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 258 " - pdb=" SG  CYS A 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 276 " - pdb=" SG  CYS A 288 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 283 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 295 " - pdb=" SG  CYS A 310 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 345 " - pdb=" SG  CYS A 470 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 383 " - pdb=" SG  CYS A 399 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 461 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 484 " - pdb=" SG  CYS A 548 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 512 " - pdb=" SG  CYS A 527 " 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=1, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG A 701 " - " ASN A 511 "
      " NAG A 702 " - " ASN A 553 "
      " NAG A 703 " - " ASN A  91 "
      " NAG C   1 " - " ASN A 439 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.75
  Conformation dependent library (CDL) restraints added in 880.1 milliseconds
  

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1374

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 13 sheets defined
      13.9% alpha, 30.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 51 through 56
      removed outlier: 3.835A  pdb=" N   THR A  56 " --> pdb=" O   LYS A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
    Processing helix  chain 'A' and resid 105 through 116
    Processing helix  chain 'A' and resid 167 through 178
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 239 through 241
      No H-bonds generated for 'chain 'A' and resid 239 through 241'
    Processing helix  chain 'A' and resid 255 through 257
      No H-bonds generated for 'chain 'A' and resid 255 through 257'
    Processing helix  chain 'A' and resid 267 through 271
      removed outlier: 4.072A  pdb=" N   LEU A 271 " --> pdb=" O   SER A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 294
    Processing helix  chain 'A' and resid 304 through 308
      removed outlier: 3.803A  pdb=" N   VAL A 308 " --> pdb=" O   GLU A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 338
      removed outlier: 3.502A  pdb=" N   SER A 338 " --> pdb=" O   LYS A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 400
    Processing helix  chain 'A' and resid 401 through 406
      removed outlier: 5.488A  pdb=" N   HIS A 406 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 496
    Processing helix  chain 'A' and resid 582 through 591
    Processing helix  chain 'A' and resid 591 through 596
      removed outlier: 4.121A  pdb=" N   ILE A 595 " --> pdb=" O   GLY A 591 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 76
    Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103
      removed outlier: 6.974A  pdb=" N   CYS A  96 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 138
    Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 138
      removed outlier: 3.512A  pdb=" N   VAL A 229 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   ALA A 227 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL A 230 " --> pdb=" O   ASP A 186 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 203
    Processing sheet with id=AA6, first strand: chain 'A' and resid 243 through 245
    Processing sheet with id=AA7, first strand: chain 'A' and resid 281 through 282
    Processing sheet with id=AA8, first strand: chain 'A' and resid 372 through 377
      removed outlier: 3.743A  pdb=" N   CYS A 383 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   GLU A 377 " --> pdb=" O   ILE A 381 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   ILE A 381 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   TRP A 392 " --> pdb=" O   ILE A 388 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL A 425 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR A 412 " --> pdb=" O   VAL A 425 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   VAL A 429 " --> pdb=" O   TYR A 408 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   TYR A 408 " --> pdb=" O   VAL A 429 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 483 through 488
      removed outlier: 6.317A  pdb=" N   THR A 577 " --> pdb=" O   VAL A 561 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL A 561 " --> pdb=" O   THR A 577 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   LEU A 546 " --> pdb=" O   TRP A 558 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   GLN A 549 " --> pdb=" O   LYS A 483 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LYS A 483 " --> pdb=" O   GLN A 549 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 109 through 116
      removed outlier: 3.523A  pdb=" N   ILE B 136 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER B 134 " --> pdb=" O   THR B 111 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 141 through 143
      removed outlier: 3.929A  pdb=" N   LEU B 157 " --> pdb=" O   VAL B 161 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   VAL B 161 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 228 through 235
      removed outlier: 7.299A  pdb=" N   THR B 199 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 243 through 248
      removed outlier: 3.703A  pdb=" N   PHE B 258 " --> pdb=" O   GLN B 244 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR B 246 " --> pdb=" O   GLU B 256 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   PHE B 248 " --> pdb=" O   LYS B 254 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   LYS B 254 " --> pdb=" O   PHE B 248 " (cutoff:3.500A)

    185 hydrogen bonds defined for protein.
    453 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: 1.93

  Time building geometry restraints manager: 1.93 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: 1951
        1.35 -     1.47: 1508
        1.47 -     1.59: 2596
        1.59 -     1.71: 0
        1.71 -     1.83: 62
  Bond restraints: 6117
  Sorted by residual:
  bond pdb=" C1  NAG A 702 "
       pdb=" O5  NAG A 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.34e+00
  bond pdb=" C1  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.61e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.54e+00
  bond pdb=" CB  ASP A 242 "
       pdb=" CG  ASP A 242 "
    ideal  model  delta    sigma   weight residual
    1.516  1.551 -0.035 2.50e-02 1.60e+03 1.97e+00
  bond pdb=" CB  ASP A  77 "
       pdb=" CG  ASP A  77 "
    ideal  model  delta    sigma   weight residual
    1.516  1.550 -0.034 2.50e-02 1.60e+03 1.83e+00
  ... (remaining 6112 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 8058
        1.97 -     3.95: 159
        3.95 -     5.92: 32
        5.92 -     7.89: 10
        7.89 -     9.86: 4
  Bond angle restraints: 8263
  Sorted by residual:
  angle pdb=" CB  MET A 373 "
        pdb=" CG  MET A 373 "
        pdb=" SD  MET A 373 "
      ideal   model   delta    sigma   weight residual
     112.70  122.56   -9.86 3.00e+00 1.11e-01 1.08e+01
  angle pdb=" CB  LYS B 195 "
        pdb=" CG  LYS B 195 "
        pdb=" CD  LYS B 195 "
      ideal   model   delta    sigma   weight residual
     111.30  118.75   -7.45 2.30e+00 1.89e-01 1.05e+01
  angle pdb=" CA  LYS B 137 "
        pdb=" CB  LYS B 137 "
        pdb=" CG  LYS B 137 "
      ideal   model   delta    sigma   weight residual
     114.10  120.57   -6.47 2.00e+00 2.50e-01 1.05e+01
  angle pdb=" CB  LEU A 594 "
        pdb=" CG  LEU A 594 "
        pdb=" CD2 LEU A 594 "
      ideal   model   delta    sigma   weight residual
     110.70  119.55   -8.85 3.00e+00 1.11e-01 8.69e+00
  angle pdb=" CA  MET A 373 "
        pdb=" CB  MET A 373 "
        pdb=" CG  MET A 373 "
      ideal   model   delta    sigma   weight residual
     114.10  119.62   -5.52 2.00e+00 2.50e-01 7.60e+00
  ... (remaining 8258 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.38: 3262
       16.38 -    32.76: 383
       32.76 -    49.15: 90
       49.15 -    65.53: 12
       65.53 -    81.91: 15
  Dihedral angle restraints: 3762
    sinusoidal: 1613
      harmonic: 2149
  Sorted by residual:
  dihedral pdb=" CB  CYS A  88 "
           pdb=" SG  CYS A  88 "
           pdb=" SG  CYS A 107 "
           pdb=" CB  CYS A 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  172.09  -79.09     1      1.00e+01 1.00e-02 7.78e+01
  dihedral pdb=" CB  CYS A  64 "
           pdb=" SG  CYS A  64 "
           pdb=" SG  CYS A  75 "
           pdb=" CB  CYS A  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.41   45.59     1      1.00e+01 1.00e-02 2.88e+01
  dihedral pdb=" CB  CYS A 276 "
           pdb=" SG  CYS A 276 "
           pdb=" SG  CYS A 288 "
           pdb=" CB  CYS A 288 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.72   40.72     1      1.00e+01 1.00e-02 2.32e+01
  ... (remaining 3759 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 666
       0.049 -    0.098: 160
       0.098 -    0.147: 51
       0.147 -    0.196: 2
       0.196 -    0.245: 1
  Chirality restraints: 880
  Sorted by residual:
  chirality pdb=" CG  LEU A 594 "
            pdb=" CB  LEU A 594 "
            pdb=" CD1 LEU A 594 "
            pdb=" CD2 LEU A 594 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CB  VAL A 590 "
            pdb=" CA  VAL A 590 "
            pdb=" CG1 VAL A 590 "
            pdb=" CG2 VAL A 590 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.39e-01
  chirality pdb=" CA  ILE B 257 "
            pdb=" N   ILE B 257 "
            pdb=" C   ILE B 257 "
            pdb=" CB  ILE B 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.48e-01
  ... (remaining 877 not shown)

  Planarity restraints: 1075
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 340 "   -0.045 5.00e-02 4.00e+02   6.78e-02 7.36e+00
        pdb=" N   PRO A 341 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 341 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 341 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A  77 "   -0.013 2.00e-02 2.50e+03   2.52e-02 6.37e+00
        pdb=" C   ASP A  77 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ASP A  77 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLY A  78 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 242 "    0.010 2.00e-02 2.50e+03   2.05e-02 4.19e+00
        pdb=" C   ASP A 242 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ASP A 242 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER A 243 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1072 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 168
        2.69 -     3.24: 6036
        3.24 -     3.79: 9878
        3.79 -     4.35: 12913
        4.35 -     4.90: 20819
  Nonbonded interactions: 49814
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 290 "
            pdb=" OD1 ASN B 292 "
     model   vdw
     2.133 3.040
  nonbonded pdb=" O   ARG A 592 "
            pdb=" OG  SER A 596 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" OG1 THR B 169 "
            pdb=" O   ARG B 174 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" OH  TYR B 179 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OG1 THR A 303 "
            pdb=" OE1 GLU A 305 "
     model   vdw
     2.202 3.040
  ... (remaining 49809 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 group one per residue
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:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.530
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6142  Z= 0.155
  Angle     :  0.729   9.864   8316  Z= 0.360
  Chirality :  0.047   0.245    880
  Planarity :  0.005   0.068   1071
  Dihedral  : 14.644  81.912   2331
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 22.58 %
    Favored  : 77.27 %
  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:  1.02 (0.31), residues: 739
  helix: -0.09 (0.71), residues: 45
  sheet:  1.13 (0.38), residues: 180
  loop :  0.71 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 503 
 HIS   0.003   0.001   HIS A 507 
 PHE   0.019   0.001   PHE B 287 
 TYR   0.010   0.001   TYR B 112 
 ARG   0.008   0.001   ARG B 228 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00261 (    4)
  link_NAG-ASN         : angle       2.03490 (   12)
  link_BETA1-4         : bond        0.00892 (    1)
  link_BETA1-4         : angle       1.65823 (    3)
  hydrogen bonds       : bond        0.26600 (  179)
  hydrogen bonds       : angle      10.37375 (  453)
  SS BOND              : bond        0.00387 (   19)
  SS BOND              : angle       1.17691 (   38)
  covalent geometry    : bond        0.00364 ( 6117)
  covalent geometry    : angle       0.72219 ( 8263)
  Misc. bond           : bond        0.00021 (    1)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  244 GLN cc_start: 0.7886 (mm110) cc_final: 0.7614 (mm110)
REVERT: B  283 MET cc_start: 0.7976 (mmm) cc_final: 0.7667 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 53
  average time/residue: 0.2183
  time to fit residues: 15.8456
Evaluate side-chains
  51 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  594 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 43 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A 382 HIS
B 148 ASN
B 170 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.060770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.045680 restraints weight = 21687.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.047823 restraints weight = 11506.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.049365 restraints weight = 7569.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.1178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6142  Z= 0.159
  Angle     :  0.611   7.337   8316  Z= 0.323
  Chirality :  0.045   0.142    880
  Planarity :  0.004   0.055   1071
  Dihedral  :  5.061  34.698    909
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.59 %
    Favored  : 81.57 %
  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:  0.94 (0.31), residues: 739
  helix: -0.18 (0.68), residues: 51
  sheet:  1.00 (0.37), residues: 180
  loop :  0.70 (0.29), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 392 
 HIS   0.004   0.001   HIS A 507 
 PHE   0.018   0.001   PHE B 221 
 TYR   0.010   0.001   TYR B 263 
 ARG   0.002   0.001   ARG A 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00175 (    4)
  link_NAG-ASN         : angle       1.82890 (   12)
  link_BETA1-4         : bond        0.00586 (    1)
  link_BETA1-4         : angle       1.19158 (    3)
  hydrogen bonds       : bond        0.04532 (  179)
  hydrogen bonds       : angle       7.17835 (  453)
  SS BOND              : bond        0.00286 (   19)
  SS BOND              : angle       1.00873 (   38)
  covalent geometry    : bond        0.00360 ( 6117)
  covalent geometry    : angle       0.60426 ( 8263)
  Misc. bond           : bond        0.00031 (    1)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 MET cc_start: 0.8613 (ppp) cc_final: 0.8344 (ppp)
REVERT: A  588 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.9000 (pp30)
REVERT: B  172 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7240 (tpt)
  outliers start: 12
  outliers final: 6
  residues processed: 64
  average time/residue: 0.1786
  time to fit residues: 15.9981
Evaluate side-chains
  56 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain A residue  510 ASN
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain B residue  172 MET
Chi-restraints excluded: chain B residue  193 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 41 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 382 HIS
B 302 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.058102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.042996 restraints weight = 22374.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.045072 restraints weight = 11769.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.046552 restraints weight = 7770.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6142  Z= 0.239
  Angle     :  0.628   8.105   8316  Z= 0.329
  Chirality :  0.045   0.140    880
  Planarity :  0.004   0.054   1071
  Dihedral  :  4.833  24.396    907
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 16.44 %
    Favored  : 80.49 %
  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:  0.98 (0.31), residues: 739
  helix: -0.35 (0.63), residues: 51
  sheet:  1.01 (0.37), residues: 180
  loop :  0.76 (0.30), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 238 
 HIS   0.005   0.001   HIS A 507 
 PHE   0.015   0.001   PHE B 258 
 TYR   0.010   0.001   TYR B 200 
 ARG   0.006   0.001   ARG A 455 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00222 (    4)
  link_NAG-ASN         : angle       1.90420 (   12)
  link_BETA1-4         : bond        0.00547 (    1)
  link_BETA1-4         : angle       1.59156 (    3)
  hydrogen bonds       : bond        0.04428 (  179)
  hydrogen bonds       : angle       6.83396 (  453)
  SS BOND              : bond        0.00377 (   19)
  SS BOND              : angle       1.01080 (   38)
  covalent geometry    : bond        0.00530 ( 6117)
  covalent geometry    : angle       0.62090 ( 8263)
  Misc. bond           : bond        0.00086 (    1)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 48
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8636 (t0) cc_final: 0.8284 (t0)
REVERT: A  159 MET cc_start: 0.8632 (ppp) cc_final: 0.8337 (ppp)
REVERT: A  329 MET cc_start: 0.9001 (mmm) cc_final: 0.8616 (mmm)
REVERT: B  170 GLN cc_start: 0.9038 (mm110) cc_final: 0.8833 (mm-40)
REVERT: B  172 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7554 (tpt)
REVERT: B  203 GLN cc_start: 0.8609 (mt0) cc_final: 0.8404 (mt0)
REVERT: B  222 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8780 (tp)
REVERT: B  244 GLN cc_start: 0.8185 (mm110) cc_final: 0.7788 (mm110)
  outliers start: 20
  outliers final: 12
  residues processed: 65
  average time/residue: 0.1756
  time to fit residues: 16.0574
Evaluate side-chains
  56 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain A residue  510 ASN
Chi-restraints excluded: chain B residue  172 MET
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  238 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 382 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.058216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.043215 restraints weight = 22454.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.045339 restraints weight = 11621.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.046853 restraints weight = 7580.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6142  Z= 0.177
  Angle     :  0.570   8.994   8316  Z= 0.300
  Chirality :  0.044   0.153    880
  Planarity :  0.004   0.046   1071
  Dihedral  :  4.597  22.383    907
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.51 %
    Favored  : 80.34 %
  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:  0.96 (0.32), residues: 739
  helix: -0.12 (0.65), residues: 51
  sheet:  0.80 (0.36), residues: 184
  loop :  0.81 (0.30), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 392 
 HIS   0.004   0.001   HIS A 507 
 PHE   0.013   0.001   PHE B 258 
 TYR   0.008   0.001   TYR B 122 
 ARG   0.003   0.000   ARG B 270 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00221 (    4)
  link_NAG-ASN         : angle       1.72972 (   12)
  link_BETA1-4         : bond        0.00552 (    1)
  link_BETA1-4         : angle       1.39623 (    3)
  hydrogen bonds       : bond        0.03864 (  179)
  hydrogen bonds       : angle       6.42495 (  453)
  SS BOND              : bond        0.00321 (   19)
  SS BOND              : angle       1.00339 (   38)
  covalent geometry    : bond        0.00398 ( 6117)
  covalent geometry    : angle       0.56316 ( 8263)
  Misc. bond           : bond        0.00070 (    1)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8625 (t0) cc_final: 0.8289 (t0)
REVERT: A  159 MET cc_start: 0.8732 (ppp) cc_final: 0.8373 (ppp)
REVERT: A  329 MET cc_start: 0.9036 (mmm) cc_final: 0.8798 (mmm)
REVERT: B  170 GLN cc_start: 0.9115 (mm110) cc_final: 0.8891 (mm-40)
REVERT: B  172 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7554 (tpt)
REVERT: B  203 GLN cc_start: 0.8475 (mt0) cc_final: 0.8141 (mt0)
REVERT: B  244 GLN cc_start: 0.8216 (mm110) cc_final: 0.7880 (mm110)
  outliers start: 14
  outliers final: 10
  residues processed: 59
  average time/residue: 0.1686
  time to fit residues: 14.0040
Evaluate side-chains
  55 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain A residue  510 ASN
Chi-restraints excluded: chain B residue  172 MET
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  238 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 37 optimal weight:    0.3980
   chunk 49 optimal weight:    8.9990
   chunk 68 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 73 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3044 r_free = 0.3044 target = 0.059023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.043970 restraints weight = 22083.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.046095 restraints weight = 11447.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.047613 restraints weight = 7480.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6142  Z= 0.129
  Angle     :  0.551   9.428   8316  Z= 0.287
  Chirality :  0.043   0.159    880
  Planarity :  0.004   0.043   1071
  Dihedral  :  4.388  20.538    907
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.43 %
    Favored  : 79.57 %
  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:  1.02 (0.32), residues: 739
  helix:  0.06 (0.67), residues: 51
  sheet:  0.84 (0.37), residues: 182
  loop :  0.84 (0.30), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 585 
 HIS   0.004   0.001   HIS A 507 
 PHE   0.012   0.001   PHE B 258 
 TYR   0.009   0.001   TYR B 224 
 ARG   0.003   0.000   ARG B 270 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00238 (    4)
  link_NAG-ASN         : angle       1.53489 (   12)
  link_BETA1-4         : bond        0.00638 (    1)
  link_BETA1-4         : angle       1.35259 (    3)
  hydrogen bonds       : bond        0.03576 (  179)
  hydrogen bonds       : angle       6.22060 (  453)
  SS BOND              : bond        0.00253 (   19)
  SS BOND              : angle       0.90497 (   38)
  covalent geometry    : bond        0.00294 ( 6117)
  covalent geometry    : angle       0.54520 ( 8263)
  Misc. bond           : bond        0.00040 (    1)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8598 (t0) cc_final: 0.8266 (t0)
REVERT: A  159 MET cc_start: 0.8801 (ppp) cc_final: 0.8419 (ppp)
REVERT: A  329 MET cc_start: 0.9092 (mmm) cc_final: 0.8640 (mmm)
REVERT: A  417 TRP cc_start: 0.8461 (p-90) cc_final: 0.8231 (p90)
REVERT: A  588 GLN cc_start: 0.9373 (OUTLIER) cc_final: 0.8962 (pp30)
REVERT: B  170 GLN cc_start: 0.9121 (mm110) cc_final: 0.8914 (mm-40)
REVERT: B  172 MET cc_start: 0.7949 (tpt) cc_final: 0.7701 (tpt)
REVERT: B  222 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8809 (tp)
REVERT: B  244 GLN cc_start: 0.8226 (mm110) cc_final: 0.7845 (mm110)
  outliers start: 13
  outliers final: 8
  residues processed: 63
  average time/residue: 0.1773
  time to fit residues: 15.5066
Evaluate side-chains
  55 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain A residue  510 ASN
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  238 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 51 optimal weight:    0.0870
   chunk 57 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 61 optimal weight:    8.9990
   chunk 1 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 55 optimal weight:    7.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    2.3764

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

Flipped N/Q/H residues before XYZ refinement:
A 382 HIS
** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.057647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.042789 restraints weight = 22054.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.044866 restraints weight = 11576.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.046358 restraints weight = 7604.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6142  Z= 0.205
  Angle     :  0.580   6.316   8316  Z= 0.308
  Chirality :  0.043   0.156    880
  Planarity :  0.004   0.041   1071
  Dihedral  :  4.496  21.874    907
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 20.43 %
    Favored  : 77.27 %
  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:  0.89 (0.32), residues: 739
  helix:  0.04 (0.65), residues: 51
  sheet:  0.64 (0.37), residues: 183
  loop :  0.78 (0.30), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 417 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.014   0.001   PHE B 258 
 TYR   0.008   0.001   TYR B 122 
 ARG   0.007   0.001   ARG B 228 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00204 (    4)
  link_NAG-ASN         : angle       1.68581 (   12)
  link_BETA1-4         : bond        0.00723 (    1)
  link_BETA1-4         : angle       1.62358 (    3)
  hydrogen bonds       : bond        0.03785 (  179)
  hydrogen bonds       : angle       6.24514 (  453)
  SS BOND              : bond        0.00349 (   19)
  SS BOND              : angle       0.90596 (   38)
  covalent geometry    : bond        0.00460 ( 6117)
  covalent geometry    : angle       0.57448 ( 8263)
  Misc. bond           : bond        0.00081 (    1)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8634 (t0) cc_final: 0.8327 (t0)
REVERT: A  113 GLU cc_start: 0.8603 (tp30) cc_final: 0.8313 (tp30)
REVERT: A  159 MET cc_start: 0.8789 (ppp) cc_final: 0.8321 (ppp)
REVERT: A  329 MET cc_start: 0.9117 (mmm) cc_final: 0.8824 (mmm)
REVERT: A  588 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.8960 (pp30)
REVERT: B  203 GLN cc_start: 0.8997 (mt0) cc_final: 0.8599 (mt0)
REVERT: B  222 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8832 (tp)
REVERT: B  244 GLN cc_start: 0.8122 (mm110) cc_final: 0.7866 (mm110)
  outliers start: 15
  outliers final: 12
  residues processed: 59
  average time/residue: 0.1623
  time to fit residues: 13.6614
Evaluate side-chains
  56 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain A residue  510 ASN
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  238 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 38 optimal weight:    0.0170
   chunk 31 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 17 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.9620

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

Flipped N/Q/H residues before XYZ refinement:
A 444 GLN
B 148 ASN
B 170 GLN
B 302 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.059129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.043985 restraints weight = 22213.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.046131 restraints weight = 11460.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.047657 restraints weight = 7468.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6142  Z= 0.118
  Angle     :  0.564  10.494   8316  Z= 0.294
  Chirality :  0.043   0.160    880
  Planarity :  0.003   0.040   1071
  Dihedral  :  4.314  20.472    907
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.97 %
    Favored  : 77.73 %
  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:  0.95 (0.32), residues: 739
  helix:  0.24 (0.67), residues: 51
  sheet:  0.65 (0.37), residues: 181
  loop :  0.82 (0.30), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 417 
 HIS   0.003   0.001   HIS A 507 
 PHE   0.011   0.001   PHE B 221 
 TYR   0.009   0.001   TYR B 224 
 ARG   0.005   0.001   ARG B 228 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00274 (    4)
  link_NAG-ASN         : angle       1.43182 (   12)
  link_BETA1-4         : bond        0.00645 (    1)
  link_BETA1-4         : angle       1.37517 (    3)
  hydrogen bonds       : bond        0.03432 (  179)
  hydrogen bonds       : angle       6.08308 (  453)
  SS BOND              : bond        0.00217 (   19)
  SS BOND              : angle       0.85513 (   38)
  covalent geometry    : bond        0.00272 ( 6117)
  covalent geometry    : angle       0.55966 ( 8263)
  Misc. bond           : bond        0.00034 (    1)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8658 (t0) cc_final: 0.8349 (t0)
REVERT: A  159 MET cc_start: 0.8843 (ppp) cc_final: 0.8325 (ppp)
REVERT: A  329 MET cc_start: 0.9121 (mmm) cc_final: 0.8811 (mmm)
REVERT: A  588 GLN cc_start: 0.9397 (OUTLIER) cc_final: 0.8965 (pp30)
REVERT: B  203 GLN cc_start: 0.8885 (mt0) cc_final: 0.8493 (mt0)
REVERT: B  222 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8825 (tp)
REVERT: B  244 GLN cc_start: 0.8240 (mm110) cc_final: 0.7935 (mm110)
  outliers start: 15
  outliers final: 8
  residues processed: 59
  average time/residue: 0.1684
  time to fit residues: 13.8553
Evaluate side-chains
  54 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  238 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.058215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.043259 restraints weight = 21943.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.045317 restraints weight = 11638.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.046793 restraints weight = 7682.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6142  Z= 0.178
  Angle     :  0.607  10.879   8316  Z= 0.313
  Chirality :  0.044   0.185    880
  Planarity :  0.003   0.038   1071
  Dihedral  :  4.389  23.291    907
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 20.12 %
    Favored  : 77.88 %
  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:  0.85 (0.31), residues: 739
  helix:  0.27 (0.65), residues: 51
  sheet:  0.56 (0.37), residues: 181
  loop :  0.75 (0.30), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 392 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.013   0.001   PHE B 258 
 TYR   0.007   0.001   TYR B 122 
 ARG   0.006   0.001   ARG B 228 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00199 (    4)
  link_NAG-ASN         : angle       1.53430 (   12)
  link_BETA1-4         : bond        0.00604 (    1)
  link_BETA1-4         : angle       1.51864 (    3)
  hydrogen bonds       : bond        0.03558 (  179)
  hydrogen bonds       : angle       6.18777 (  453)
  SS BOND              : bond        0.00277 (   19)
  SS BOND              : angle       1.04832 (   38)
  covalent geometry    : bond        0.00403 ( 6117)
  covalent geometry    : angle       0.60090 ( 8263)
  Misc. bond           : bond        0.00067 (    1)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8663 (t0) cc_final: 0.8349 (t0)
REVERT: A  159 MET cc_start: 0.8847 (ppp) cc_final: 0.8193 (ppp)
REVERT: A  329 MET cc_start: 0.9120 (mmm) cc_final: 0.8826 (mmm)
REVERT: A  588 GLN cc_start: 0.9388 (OUTLIER) cc_final: 0.8964 (pp30)
REVERT: B  203 GLN cc_start: 0.8880 (mt0) cc_final: 0.8299 (mt0)
REVERT: B  222 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8830 (tp)
REVERT: B  244 GLN cc_start: 0.8216 (mm110) cc_final: 0.7965 (mm110)
  outliers start: 13
  outliers final: 10
  residues processed: 54
  average time/residue: 0.1856
  time to fit residues: 14.3183
Evaluate side-chains
  54 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain A residue  510 ASN
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  238 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 13 optimal weight:    0.4980
   chunk 48 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 72 optimal weight:    8.9990
   chunk 7 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 9 optimal weight:    0.1980
   chunk 1 optimal weight:    5.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.059615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.044536 restraints weight = 21861.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.046623 restraints weight = 11491.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.048146 restraints weight = 7577.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6142  Z= 0.117
  Angle     :  0.597  11.399   8316  Z= 0.305
  Chirality :  0.044   0.180    880
  Planarity :  0.003   0.038   1071
  Dihedral  :  4.202  20.194    907
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 20.43 %
    Favored  : 78.03 %
  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:  0.97 (0.32), residues: 739
  helix:  0.36 (0.68), residues: 51
  sheet:  0.66 (0.38), residues: 181
  loop :  0.82 (0.30), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 166 
 HIS   0.007   0.001   HIS A 382 
 PHE   0.011   0.001   PHE B 221 
 TYR   0.008   0.001   TYR B 224 
 ARG   0.005   0.000   ARG B 270 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00269 (    4)
  link_NAG-ASN         : angle       1.31456 (   12)
  link_BETA1-4         : bond        0.00632 (    1)
  link_BETA1-4         : angle       1.36683 (    3)
  hydrogen bonds       : bond        0.03296 (  179)
  hydrogen bonds       : angle       6.08374 (  453)
  SS BOND              : bond        0.00231 (   19)
  SS BOND              : angle       1.03836 (   38)
  covalent geometry    : bond        0.00273 ( 6117)
  covalent geometry    : angle       0.59241 ( 8263)
  Misc. bond           : bond        0.00026 (    1)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8646 (t0) cc_final: 0.8337 (t0)
REVERT: A  113 GLU cc_start: 0.8698 (tp30) cc_final: 0.8461 (tp30)
REVERT: A  159 MET cc_start: 0.8948 (ppp) cc_final: 0.8324 (ppp)
REVERT: A  329 MET cc_start: 0.9073 (mmm) cc_final: 0.8752 (mmm)
REVERT: A  382 HIS cc_start: 0.8046 (t70) cc_final: 0.7835 (t-90)
REVERT: A  588 GLN cc_start: 0.9383 (OUTLIER) cc_final: 0.8965 (pp30)
REVERT: B  203 GLN cc_start: 0.8788 (mt0) cc_final: 0.8473 (mt0)
REVERT: B  222 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8815 (tp)
REVERT: B  244 GLN cc_start: 0.8224 (mm110) cc_final: 0.7974 (mm110)
  outliers start: 10
  outliers final: 7
  residues processed: 52
  average time/residue: 0.1592
  time to fit residues: 11.7741
Evaluate side-chains
  52 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  238 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 72 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.058959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.043941 restraints weight = 21887.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.046023 restraints weight = 11614.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.047513 restraints weight = 7655.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6142  Z= 0.148
  Angle     :  0.605  11.509   8316  Z= 0.309
  Chirality :  0.044   0.182    880
  Planarity :  0.003   0.038   1071
  Dihedral  :  4.207  21.115    907
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 20.43 %
    Favored  : 77.88 %
  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:  0.97 (0.32), residues: 739
  helix:  0.37 (0.67), residues: 51
  sheet:  0.68 (0.38), residues: 181
  loop :  0.82 (0.30), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 417 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.012   0.001   PHE B 258 
 TYR   0.010   0.001   TYR B 200 
 ARG   0.006   0.000   ARG B 228 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    4)
  link_NAG-ASN         : angle       1.36783 (   12)
  link_BETA1-4         : bond        0.00648 (    1)
  link_BETA1-4         : angle       1.45594 (    3)
  hydrogen bonds       : bond        0.03379 (  179)
  hydrogen bonds       : angle       6.04909 (  453)
  SS BOND              : bond        0.00262 (   19)
  SS BOND              : angle       1.00462 (   38)
  covalent geometry    : bond        0.00341 ( 6117)
  covalent geometry    : angle       0.60027 ( 8263)
  Misc. bond           : bond        0.00052 (    1)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 1.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8661 (t0) cc_final: 0.8343 (t0)
REVERT: A  113 GLU cc_start: 0.8650 (tp30) cc_final: 0.8360 (tp30)
REVERT: A  159 MET cc_start: 0.8936 (ppp) cc_final: 0.8322 (ppp)
REVERT: A  329 MET cc_start: 0.9065 (mmm) cc_final: 0.8732 (mmm)
REVERT: A  382 HIS cc_start: 0.8026 (t70) cc_final: 0.7809 (t-90)
REVERT: A  588 GLN cc_start: 0.9383 (OUTLIER) cc_final: 0.8967 (pp30)
REVERT: B  203 GLN cc_start: 0.8926 (mt0) cc_final: 0.8595 (mt0)
REVERT: B  222 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8814 (tp)
REVERT: B  244 GLN cc_start: 0.8200 (mm110) cc_final: 0.7938 (mm110)
  outliers start: 11
  outliers final: 9
  residues processed: 53
  average time/residue: 0.1917
  time to fit residues: 15.3861
Evaluate side-chains
  54 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 1.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 CYS
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  238 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0970
   chunk 20 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.059126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.044212 restraints weight = 22074.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.046289 restraints weight = 11549.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.047764 restraints weight = 7555.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6142  Z= 0.139
  Angle     :  0.597  11.410   8316  Z= 0.305
  Chirality :  0.044   0.184    880
  Planarity :  0.003   0.038   1071
  Dihedral  :  4.182  20.890    907
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 20.58 %
    Favored  : 77.73 %
  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:  0.98 (0.32), residues: 739
  helix:  0.37 (0.67), residues: 51
  sheet:  0.68 (0.38), residues: 183
  loop :  0.82 (0.30), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 417 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.012   0.001   PHE B 258 
 TYR   0.009   0.001   TYR B 200 
 ARG   0.006   0.000   ARG B 228 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00232 (    4)
  link_NAG-ASN         : angle       1.34881 (   12)
  link_BETA1-4         : bond        0.00635 (    1)
  link_BETA1-4         : angle       1.46650 (    3)
  hydrogen bonds       : bond        0.03316 (  179)
  hydrogen bonds       : angle       6.06283 (  453)
  SS BOND              : bond        0.00265 (   19)
  SS BOND              : angle       0.99301 (   38)
  covalent geometry    : bond        0.00319 ( 6117)
  covalent geometry    : angle       0.59241 ( 8263)
  Misc. bond           : bond        0.00049 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2077.17 seconds
wall clock time: 37 minutes 43.07 seconds (2263.07 seconds total)