Starting phenix.real_space_refine
on Sat May 10 10:50:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b3h_44139/05_2025/9b3h_44139.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b3h_44139/05_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_44139/05_2025/9b3h_44139.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b3h_44139/05_2025/9b3h_44139.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b3h_44139/05_2025/9b3h_44139.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b3h_44139/05_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 3.85, per 1000 atoms: 0.64
  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: 1.48
  Conformation dependent library (CDL) restraints added in 838.0 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: 1.84

  Time building geometry restraints manager: 1.74 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:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     17.410
  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:             0.010
  Load rotamer database and sin/cos tables:2.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.760
-------------------------------------------------------------------------------
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  : 0.782 
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: 0.1978
  time to fit residues: 14.2976
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  : 0.742 
-------------------------------------------------------------------------------
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 = 0.060769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.045672 restraints weight = 21704.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.047801 restraints weight = 11536.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.049351 restraints weight = 7593.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.2762
-------------------------------------------------------------------------------
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  : 0.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 MET cc_start: 0.8612 (ppp) cc_final: 0.8343 (ppp)
REVERT: A  588 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.9001 (pp30)
REVERT: B  172 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7238 (tpt)
  outliers start: 12
  outliers final: 6
  residues processed: 64
  average time/residue: 0.1632
  time to fit residues: 14.5030
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  : 0.677 
-------------------------------------------------------------------------------
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:    0.0470
   chunk 34 optimal weight:    0.4980
   chunk 7 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   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:    6.9990
   overall best weight:    2.1084

-------------------------------------------------------------------------------
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 = 0.3053 r_free = 0.3053 target = 0.059427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.044294 restraints weight = 22067.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.046410 restraints weight = 11522.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.047948 restraints weight = 7541.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6142  Z= 0.188
  Angle     :  0.598   7.745   8316  Z= 0.312
  Chirality :  0.044   0.143    880
  Planarity :  0.004   0.055   1071
  Dihedral  :  4.698  25.948    907
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.20 %
    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:  1.01 (0.31), residues: 739
  helix: -0.28 (0.65), residues: 51
  sheet:  0.96 (0.37), residues: 180
  loop :  0.80 (0.29), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 417 
 HIS   0.004   0.001   HIS A 507 
 PHE   0.014   0.001   PHE B 258 
 TYR   0.010   0.001   TYR B 263 
 ARG   0.008   0.001   ARG B 270 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00185 (    4)
  link_NAG-ASN         : angle       1.76443 (   12)
  link_BETA1-4         : bond        0.00527 (    1)
  link_BETA1-4         : angle       1.39296 (    3)
  hydrogen bonds       : bond        0.04249 (  179)
  hydrogen bonds       : angle       6.82892 (  453)
  SS BOND              : bond        0.00302 (   19)
  SS BOND              : angle       0.93696 (   38)
  covalent geometry    : bond        0.00421 ( 6117)
  covalent geometry    : angle       0.59184 ( 8263)
  Misc. bond           : bond        0.00061 (    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
  64 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 MET cc_start: 0.8682 (ppp) cc_final: 0.8389 (ppp)
REVERT: A  329 MET cc_start: 0.8975 (mmm) cc_final: 0.8622 (mmm)
REVERT: A  405 MET cc_start: 0.8641 (tpt) cc_final: 0.8133 (tpp)
REVERT: B  170 GLN cc_start: 0.8992 (mm110) cc_final: 0.8773 (mm-40)
REVERT: B  172 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7527 (tpt)
REVERT: B  203 GLN cc_start: 0.8566 (mt0) cc_final: 0.8224 (mt0)
REVERT: B  270 ARG cc_start: 0.8858 (ttm-80) cc_final: 0.8627 (tpp80)
  outliers start: 15
  outliers final: 10
  residues processed: 62
  average time/residue: 0.1822
  time to fit residues: 15.9738
Evaluate side-chains
  56 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
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  209 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 45 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 62 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
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 = 0.3014 r_free = 0.3014 target = 0.057966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2581 r_free = 0.2581 target = 0.042758 restraints weight = 22606.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.044848 restraints weight = 11808.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.046349 restraints weight = 7776.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6142  Z= 0.204
  Angle     :  0.591   9.047   8316  Z= 0.311
  Chirality :  0.044   0.153    880
  Planarity :  0.004   0.046   1071
  Dihedral  :  4.614  22.589    907
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.05 %
    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:  0.98 (0.32), residues: 739
  helix: -0.07 (0.65), residues: 51
  sheet:  0.87 (0.37), residues: 182
  loop :  0.80 (0.30), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 392 
 HIS   0.005   0.001   HIS A 507 
 PHE   0.013   0.001   PHE B 258 
 TYR   0.009   0.001   TYR B 263 
 ARG   0.004   0.001   ARG B 270 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00212 (    4)
  link_NAG-ASN         : angle       1.76007 (   12)
  link_BETA1-4         : bond        0.00543 (    1)
  link_BETA1-4         : angle       1.53566 (    3)
  hydrogen bonds       : bond        0.03954 (  179)
  hydrogen bonds       : angle       6.42555 (  453)
  SS BOND              : bond        0.00345 (   19)
  SS BOND              : angle       1.01346 (   38)
  covalent geometry    : bond        0.00455 ( 6117)
  covalent geometry    : angle       0.58392 ( 8263)
  Misc. bond           : bond        0.00085 (    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
  65 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8606 (t0) cc_final: 0.8311 (t0)
REVERT: A  159 MET cc_start: 0.8735 (ppp) cc_final: 0.8376 (ppp)
REVERT: A  329 MET cc_start: 0.9067 (mmm) cc_final: 0.8820 (mmm)
REVERT: B  170 GLN cc_start: 0.9111 (mm110) cc_final: 0.8909 (mm-40)
REVERT: B  172 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7604 (tpt)
REVERT: B  203 GLN cc_start: 0.8445 (mt0) cc_final: 0.8201 (mt0)
REVERT: B  222 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8782 (tp)
REVERT: B  244 GLN cc_start: 0.8195 (mm110) cc_final: 0.7853 (mm110)
REVERT: B  270 ARG cc_start: 0.8850 (ttm-80) cc_final: 0.8590 (tpp80)
  outliers start: 17
  outliers final: 11
  residues processed: 63
  average time/residue: 0.2060
  time to fit residues: 18.1479
Evaluate side-chains
  57 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
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  209 ILE
Chi-restraints excluded: chain B residue  222 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:    0.2980
   chunk 49 optimal weight:    6.9990
   chunk 68 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    2.2586

-------------------------------------------------------------------------------
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 = 0.3008 r_free = 0.3008 target = 0.057629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2581 r_free = 0.2581 target = 0.042647 restraints weight = 22276.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.044717 restraints weight = 11595.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.046231 restraints weight = 7601.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6142  Z= 0.197
  Angle     :  0.582   9.249   8316  Z= 0.306
  Chirality :  0.044   0.154    880
  Planarity :  0.004   0.044   1071
  Dihedral  :  4.558  22.776    907
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.43 %
    Favored  : 79.11 %
  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:  0.90 (0.32), residues: 739
  helix: -0.01 (0.66), residues: 51
  sheet:  0.69 (0.37), residues: 182
  loop :  0.78 (0.30), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 585 
 HIS   0.005   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 167 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00219 (    4)
  link_NAG-ASN         : angle       1.71590 (   12)
  link_BETA1-4         : bond        0.00603 (    1)
  link_BETA1-4         : angle       1.50019 (    3)
  hydrogen bonds       : bond        0.03794 (  179)
  hydrogen bonds       : angle       6.30011 (  453)
  SS BOND              : bond        0.00354 (   19)
  SS BOND              : angle       1.00906 (   38)
  covalent geometry    : bond        0.00442 ( 6117)
  covalent geometry    : angle       0.57560 ( 8263)
  Misc. bond           : bond        0.00083 (    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
  61 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 45
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8639 (t0) cc_final: 0.8344 (t0)
REVERT: A  159 MET cc_start: 0.8760 (ppp) cc_final: 0.8391 (ppp)
REVERT: A  329 MET cc_start: 0.9116 (mmm) cc_final: 0.8835 (mmm)
REVERT: A  417 TRP cc_start: 0.8492 (p-90) cc_final: 0.8275 (p90)
REVERT: A  588 GLN cc_start: 0.9384 (OUTLIER) cc_final: 0.8956 (pp30)
REVERT: B  222 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8797 (tp)
REVERT: B  244 GLN cc_start: 0.8086 (mm110) cc_final: 0.7827 (mm110)
REVERT: B  314 MET cc_start: 0.7497 (tpp) cc_final: 0.7274 (tpp)
  outliers start: 16
  outliers final: 12
  residues processed: 60
  average time/residue: 0.1729
  time to fit residues: 14.2975
Evaluate side-chains
  54 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 40
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 32 optimal weight:    0.4980
   chunk 69 optimal weight:    0.0370
   chunk 56 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    1.6862

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

Flipped N/Q/H residues before XYZ refinement:
B 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.058256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.043328 restraints weight = 21849.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.045399 restraints weight = 11611.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.046865 restraints weight = 7670.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
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      :  0.004   0.032   6142  Z= 0.159
  Angle     :  0.572  10.183   8316  Z= 0.299
  Chirality :  0.043   0.157    880
  Planarity :  0.004   0.042   1071
  Dihedral  :  4.426  21.749    907
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.20 %
    Favored  : 78.34 %
  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:  0.90 (0.32), residues: 739
  helix:  0.07 (0.66), residues: 51
  sheet:  0.67 (0.37), residues: 182
  loop :  0.77 (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   0.013   0.001   PHE B 258 
 TYR   0.007   0.001   TYR B 224 
 ARG   0.007   0.001   ARG B 228 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00219 (    4)
  link_NAG-ASN         : angle       1.59101 (   12)
  link_BETA1-4         : bond        0.00628 (    1)
  link_BETA1-4         : angle       1.47331 (    3)
  hydrogen bonds       : bond        0.03600 (  179)
  hydrogen bonds       : angle       6.20173 (  453)
  SS BOND              : bond        0.00288 (   19)
  SS BOND              : angle       0.90061 (   38)
  covalent geometry    : bond        0.00361 ( 6117)
  covalent geometry    : angle       0.56629 ( 8263)
  Misc. bond           : bond        0.00058 (    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: 16
    poor density    : 44
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8627 (t0) cc_final: 0.8324 (t0)
REVERT: A  113 GLU cc_start: 0.8686 (tp30) cc_final: 0.8336 (tp30)
REVERT: A  159 MET cc_start: 0.8802 (ppp) cc_final: 0.8330 (ppp)
REVERT: A  329 MET cc_start: 0.9109 (mmm) cc_final: 0.8802 (mmm)
REVERT: A  588 GLN cc_start: 0.9384 (OUTLIER) cc_final: 0.8958 (pp30)
REVERT: B  203 GLN cc_start: 0.8929 (mt0) cc_final: 0.8566 (mt0)
REVERT: B  222 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8822 (tp)
REVERT: B  244 GLN cc_start: 0.8184 (mm110) cc_final: 0.7881 (mm110)
  outliers start: 16
  outliers final: 11
  residues processed: 59
  average time/residue: 0.1704
  time to fit residues: 13.8064
Evaluate side-chains
  53 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
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  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  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:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0010
   chunk 48 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   overall best weight:    1.7590

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

Flipped N/Q/H residues before XYZ refinement:
B 148 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.058230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.043284 restraints weight = 22201.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.045332 restraints weight = 11713.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.046834 restraints weight = 7706.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2582

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= 0.164
  Angle     :  0.582   9.561   8316  Z= 0.303
  Chirality :  0.043   0.173    880
  Planarity :  0.003   0.040   1071
  Dihedral  :  4.392  21.355    907
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 20.12 %
    Favored  : 77.57 %
  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:  0.86 (0.32), residues: 739
  helix:  0.09 (0.66), residues: 51
  sheet:  0.56 (0.37), residues: 181
  loop :  0.78 (0.30), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 417 
 HIS   0.004   0.001   HIS A 507 
 PHE   0.013   0.001   PHE B 258 
 TYR   0.007   0.001   TYR B 122 
 ARG   0.005   0.000   ARG B 270 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00220 (    4)
  link_NAG-ASN         : angle       1.56346 (   12)
  link_BETA1-4         : bond        0.00653 (    1)
  link_BETA1-4         : angle       1.49345 (    3)
  hydrogen bonds       : bond        0.03601 (  179)
  hydrogen bonds       : angle       6.24813 (  453)
  SS BOND              : bond        0.00280 (   19)
  SS BOND              : angle       0.87628 (   38)
  covalent geometry    : bond        0.00371 ( 6117)
  covalent geometry    : angle       0.57732 ( 8263)
  Misc. bond           : bond        0.00059 (    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
  58 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8660 (t0) cc_final: 0.8367 (t0)
REVERT: A  159 MET cc_start: 0.8825 (ppp) cc_final: 0.8195 (ppp)
REVERT: A  329 MET cc_start: 0.9113 (mmm) cc_final: 0.8806 (mmm)
REVERT: A  588 GLN cc_start: 0.9389 (OUTLIER) cc_final: 0.8962 (pp30)
REVERT: B  203 GLN cc_start: 0.8854 (mt0) cc_final: 0.8565 (mt0)
REVERT: B  222 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8828 (tp)
REVERT: B  244 GLN cc_start: 0.8231 (mm110) cc_final: 0.7980 (mm110)
  outliers start: 15
  outliers final: 12
  residues processed: 57
  average time/residue: 0.1708
  time to fit residues: 13.9478
Evaluate side-chains
  52 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
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  226 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  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:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 54 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.7784

-------------------------------------------------------------------------------
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**
A 444 GLN
B 148 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.058167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.043227 restraints weight = 21998.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.045301 restraints weight = 11681.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.046760 restraints weight = 7729.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6142  Z= 0.166
  Angle     :  0.608  12.590   8316  Z= 0.313
  Chirality :  0.044   0.174    880
  Planarity :  0.003   0.039   1071
  Dihedral  :  4.404  23.592    907
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  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:  0.83 (0.32), residues: 739
  helix:  0.12 (0.67), residues: 51
  sheet:  0.53 (0.37), residues: 181
  loop :  0.76 (0.30), residues: 507

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   0.013   0.001   PHE B 258 
 TYR   0.008   0.001   TYR B 200 
 ARG   0.007   0.001   ARG B 228 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00212 (    4)
  link_NAG-ASN         : angle       1.53598 (   12)
  link_BETA1-4         : bond        0.00638 (    1)
  link_BETA1-4         : angle       1.51579 (    3)
  hydrogen bonds       : bond        0.03541 (  179)
  hydrogen bonds       : angle       6.27491 (  453)
  SS BOND              : bond        0.00291 (   19)
  SS BOND              : angle       1.09319 (   38)
  covalent geometry    : bond        0.00377 ( 6117)
  covalent geometry    : angle       0.60172 ( 8263)
  Misc. bond           : bond        0.00061 (    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
  56 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8661 (t0) cc_final: 0.8371 (t0)
REVERT: A  159 MET cc_start: 0.8847 (ppp) cc_final: 0.8196 (ppp)
REVERT: A  329 MET cc_start: 0.9117 (mmm) cc_final: 0.8810 (mmm)
REVERT: A  588 GLN cc_start: 0.9388 (OUTLIER) cc_final: 0.8960 (pp30)
REVERT: B  203 GLN cc_start: 0.8972 (mt0) cc_final: 0.8640 (mt0)
REVERT: B  222 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8833 (tp)
REVERT: B  244 GLN cc_start: 0.8226 (mm110) cc_final: 0.7956 (mm110)
  outliers start: 15
  outliers final: 12
  residues processed: 55
  average time/residue: 0.1786
  time to fit residues: 13.6068
Evaluate side-chains
  54 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 40
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
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  226 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  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:    7.9990
   chunk 48 optimal weight:    0.4980
   chunk 29 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.8386

-------------------------------------------------------------------------------
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 = 0.3048 r_free = 0.3048 target = 0.059368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.044292 restraints weight = 21899.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.046435 restraints weight = 11336.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.047972 restraints weight = 7379.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6142  Z= 0.116
  Angle     :  0.596  11.198   8316  Z= 0.306
  Chirality :  0.044   0.163    880
  Planarity :  0.003   0.039   1071
  Dihedral  :  4.217  22.435    907
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 21.04 %
    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:  0.93 (0.32), residues: 739
  helix:  0.21 (0.68), residues: 51
  sheet:  0.61 (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   0.009   0.001   TYR B 224 
 ARG   0.008   0.001   ARG B 228 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00280 (    4)
  link_NAG-ASN         : angle       1.32273 (   12)
  link_BETA1-4         : bond        0.00667 (    1)
  link_BETA1-4         : angle       1.39047 (    3)
  hydrogen bonds       : bond        0.03313 (  179)
  hydrogen bonds       : angle       6.19222 (  453)
  SS BOND              : bond        0.00232 (   19)
  SS BOND              : angle       1.04545 (   38)
  covalent geometry    : bond        0.00271 ( 6117)
  covalent geometry    : angle       0.59135 ( 8263)
  Misc. bond           : bond        0.00021 (    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
  55 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8633 (t0) cc_final: 0.8328 (t0)
REVERT: A  159 MET cc_start: 0.8943 (ppp) cc_final: 0.8319 (ppp)
REVERT: A  329 MET cc_start: 0.9064 (mmm) cc_final: 0.8717 (mmm)
REVERT: A  382 HIS cc_start: 0.8053 (t70) cc_final: 0.7842 (t-90)
REVERT: A  588 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.8965 (pp30)
REVERT: B  203 GLN cc_start: 0.8937 (mt0) cc_final: 0.8641 (mt0)
REVERT: B  244 GLN cc_start: 0.8146 (mm110) cc_final: 0.7862 (mm110)
  outliers start: 11
  outliers final: 6
  residues processed: 54
  average time/residue: 0.1657
  time to fit residues: 12.6591
Evaluate side-chains
  50 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
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  588 GLN
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:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 3 optimal weight:    0.3980
   chunk 23 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0020
   overall best weight:    0.5588

-------------------------------------------------------------------------------
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 = 0.3066 r_free = 0.3066 target = 0.060193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.045150 restraints weight = 21577.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.047271 restraints weight = 11414.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.048751 restraints weight = 7489.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6142  Z= 0.109
  Angle     :  0.596  11.596   8316  Z= 0.305
  Chirality :  0.044   0.163    880
  Planarity :  0.003   0.039   1071
  Dihedral  :  4.074  20.650    907
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 21.35 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.32), residues: 739
  helix:  0.30 (0.69), residues: 51
  sheet:  0.63 (0.38), residues: 179
  loop :  0.87 (0.30), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 166 
 HIS   0.007   0.001   HIS A 382 
 PHE   0.011   0.001   PHE B 258 
 TYR   0.008   0.001   TYR B 308 
 ARG   0.006   0.000   ARG B 228 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00289 (    4)
  link_NAG-ASN         : angle       1.21775 (   12)
  link_BETA1-4         : bond        0.00674 (    1)
  link_BETA1-4         : angle       1.36926 (    3)
  hydrogen bonds       : bond        0.03175 (  179)
  hydrogen bonds       : angle       6.10892 (  453)
  SS BOND              : bond        0.00188 (   19)
  SS BOND              : angle       0.97358 (   38)
  covalent geometry    : bond        0.00254 ( 6117)
  covalent geometry    : angle       0.59233 ( 8263)
  Misc. bond           : bond        0.00014 (    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
  53 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8611 (t0) cc_final: 0.8300 (t0)
REVERT: A  159 MET cc_start: 0.8973 (ppp) cc_final: 0.8329 (ppp)
REVERT: A  324 MET cc_start: 0.8487 (mmm) cc_final: 0.7803 (mmm)
REVERT: A  329 MET cc_start: 0.9050 (mmm) cc_final: 0.8535 (mmm)
REVERT: A  382 HIS cc_start: 0.8039 (t70) cc_final: 0.7821 (t-90)
REVERT: A  588 GLN cc_start: 0.9364 (OUTLIER) cc_final: 0.8960 (pp30)
REVERT: B  203 GLN cc_start: 0.8888 (mt0) cc_final: 0.8581 (mt0)
REVERT: B  244 GLN cc_start: 0.8134 (mm110) cc_final: 0.7850 (mm110)
  outliers start: 8
  outliers final: 7
  residues processed: 52
  average time/residue: 0.1656
  time to fit residues: 12.2726
Evaluate side-chains
  52 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
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  238 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 66 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
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 = 0.2997 r_free = 0.2997 target = 0.057407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.042550 restraints weight = 22513.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.044599 restraints weight = 11925.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.046020 restraints weight = 7855.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.2930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   6142  Z= 0.251
  Angle     :  0.645  11.352   8316  Z= 0.336
  Chirality :  0.044   0.156    880
  Planarity :  0.004   0.037   1071
  Dihedral  :  4.405  22.699    907
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 21.66 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.31), residues: 739
  helix:  0.09 (0.66), residues: 51
  sheet:  0.48 (0.37), residues: 181
  loop :  0.69 (0.29), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 417 
 HIS   0.005   0.001   HIS A 382 
 PHE   0.014   0.001   PHE B 258 
 TYR   0.010   0.001   TYR B 200 
 ARG   0.007   0.001   ARG B 228 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00204 (    4)
  link_NAG-ASN         : angle       1.54292 (   12)
  link_BETA1-4         : bond        0.00697 (    1)
  link_BETA1-4         : angle       1.70141 (    3)
  hydrogen bonds       : bond        0.03694 (  179)
  hydrogen bonds       : angle       6.21245 (  453)
  SS BOND              : bond        0.00417 (   19)
  SS BOND              : angle       1.09625 (   38)
  covalent geometry    : bond        0.00559 ( 6117)
  covalent geometry    : angle       0.63929 ( 8263)
  Misc. bond           : bond        0.00107 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1873.98 seconds
wall clock time: 33 minutes 52.77 seconds (2032.77 seconds total)