Starting phenix.real_space_refine
on Thu Jun  5 14:17:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rtt_24688/06_2025/7rtt_24688.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rtt_24688/06_2025/7rtt_24688.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rtt_24688/06_2025/7rtt_24688.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rtt_24688/06_2025/7rtt_24688.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rtt_24688/06_2025/7rtt_24688.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rtt_24688/06_2025/7rtt_24688.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     S      50      5.16       5
     C    4027      2.51       5
     N    1013      2.21       5
     O    1176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6268
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 3058
          Classifications: {'peptide': 396}
          Link IDs: {'PTRANS': 9, 'TRANS': 386}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 3053
          Classifications: {'peptide': 395}
          Link IDs: {'PTRANS': 9, 'TRANS': 385}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          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
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          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
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          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
    Chain: "F"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.35, per 1000 atoms: 0.69
  Number of scatterers: 6268
  At special positions: 0
  Unit cell: (84.138, 70.494, 134.166, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      2     19.99
     S      50     16.00
     O    1176      8.00
     N    1013      7.00
     C    4027      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 382 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 300 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 274 " - pdb=" SG  CYS B 382 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 300 " - pdb=" SG  CYS B 367 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
    NAG-ASN
      " NAG C   1 " - " ASN A 129 "
      " NAG D   1 " - " ASN A 352 "
      " NAG E   1 " - " ASN B 129 "
      " NAG F   1 " - " ASN B 352 "
  Time building additional restraints: 1.79
  Conformation dependent library (CDL) restraints added in 890.1 milliseconds
  

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1474

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      85.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 19
      removed outlier: 3.790A  pdb=" N   LEU A  17 " --> pdb=" O   TRP A  13 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER A  19 " --> pdb=" O   VAL A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 72
      removed outlier: 3.595A  pdb=" N   PHE A  47 " --> pdb=" O   GLU A  43 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   LEU A  48 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLY A  49 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 158
      removed outlier: 3.625A  pdb=" N   GLY A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   MET A 118 " --> pdb=" O   THR A 114 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   HIS A 119 " --> pdb=" O   ASN A 115 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   GLN A 120 " --> pdb=" O   ASP A 116 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE A 122 " --> pdb=" O   MET A 118 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   SER A 158 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 188
      removed outlier: 3.555A  pdb=" N   GLN A 169 " --> pdb=" O   GLY A 165 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU A 188 " --> pdb=" O   GLN A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 235
      removed outlier: 3.672A  pdb=" N   THR A 195 " --> pdb=" O   TRP A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 270
      removed outlier: 3.668A  pdb=" N   ALA A 243 " --> pdb=" O   LYS A 239 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   ILE A 250 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   LEU A 251 " --> pdb=" O   CYS A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 276
      removed outlier: 3.753A  pdb=" N   ALA A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 285
      removed outlier: 3.581A  pdb=" N   TYR A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 299
      removed outlier: 3.522A  pdb=" N   THR A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 330
      removed outlier: 3.869A  pdb=" N   THR A 314 " --> pdb=" O   GLN A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 339
      No H-bonds generated for 'chain 'A' and resid 337 through 339'
    Processing helix  chain 'A' and resid 340 through 365
      removed outlier: 4.006A  pdb=" N   LEU A 344 " --> pdb=" O   ALA A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 383
      removed outlier: 4.222A  pdb=" N   LEU A 370 " --> pdb=" O   ASP A 366 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LYS A 372 " --> pdb=" O   ARG A 368 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   ASP A 373 " --> pdb=" O   GLY A 369 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ILE A 381 " --> pdb=" O   ALA A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 410
    Processing helix  chain 'A' and resid 411 through 413
      No H-bonds generated for 'chain 'A' and resid 411 through 413'
    Processing helix  chain 'B' and resid 11 through 19
      removed outlier: 3.901A  pdb=" N   LEU B  17 " --> pdb=" O   TRP B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 73
      removed outlier: 3.832A  pdb=" N   GLY B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 160
      removed outlier: 3.615A  pdb=" N   MET B 118 " --> pdb=" O   THR B 114 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLU B 151 " --> pdb=" O   LYS B 147 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   GLU B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE B 160 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 188
      removed outlier: 3.801A  pdb=" N   LEU B 188 " --> pdb=" O   GLN B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 234
      removed outlier: 3.840A  pdb=" N   LYS B 200 " --> pdb=" O   THR B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 237
      No H-bonds generated for 'chain 'B' and resid 235 through 237'
    Processing helix  chain 'B' and resid 240 through 276
      removed outlier: 4.112A  pdb=" N   SER B 244 " --> pdb=" O   CYS B 240 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE B 250 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU B 251 " --> pdb=" O   CYS B 247 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU B 253 " --> pdb=" O   GLY B 249 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ALA B 276 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 285
      removed outlier: 3.827A  pdb=" N   TYR B 280 " --> pdb=" O   ALA B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 299
    Processing helix  chain 'B' and resid 308 through 332
    Processing helix  chain 'B' and resid 340 through 365
      removed outlier: 4.163A  pdb=" N   GLY B 346 " --> pdb=" O   LYS B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 383
      removed outlier: 4.748A  pdb=" N   LEU B 370 " --> pdb=" O   ASP B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 410

    523 hydrogen bonds defined for protein.
    1569 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: 1.63

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1959
        1.34 -     1.46: 1527
        1.46 -     1.58: 2836
        1.58 -     1.70: 0
        1.70 -     1.82: 68
  Bond restraints: 6390
  Sorted by residual:
  bond pdb=" C1  BMA F   3 "
       pdb=" C2  BMA F   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.550 -0.031 2.00e-02 2.50e+03 2.42e+00
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.550 -0.031 2.00e-02 2.50e+03 2.36e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.35e+00
  bond pdb=" C1  BMA E   3 "
       pdb=" C2  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.548 -0.029 2.00e-02 2.50e+03 2.14e+00
  bond pdb=" C1  BMA C   3 "
       pdb=" C2  BMA C   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.548 -0.029 2.00e-02 2.50e+03 2.04e+00
  ... (remaining 6385 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 8453
        1.63 -     3.26: 193
        3.26 -     4.89: 43
        4.89 -     6.53: 15
        6.53 -     8.16: 2
  Bond angle restraints: 8706
  Sorted by residual:
  angle pdb=" C   VAL A  30 "
        pdb=" N   ASP A  31 "
        pdb=" CA  ASP A  31 "
      ideal   model   delta    sigma   weight residual
     121.54  126.85   -5.31 1.91e+00 2.74e-01 7.74e+00
  angle pdb=" CB  MET A 118 "
        pdb=" CG  MET A 118 "
        pdb=" SD  MET A 118 "
      ideal   model   delta    sigma   weight residual
     112.70  120.86   -8.16 3.00e+00 1.11e-01 7.39e+00
  angle pdb=" N   GLN A 302 "
        pdb=" CA  GLN A 302 "
        pdb=" C   GLN A 302 "
      ideal   model   delta    sigma   weight residual
     110.80  115.75   -4.95 2.13e+00 2.20e-01 5.40e+00
  angle pdb=" CA  TYR B 207 "
        pdb=" CB  TYR B 207 "
        pdb=" CG  TYR B 207 "
      ideal   model   delta    sigma   weight residual
     113.90  117.70   -3.80 1.80e+00 3.09e-01 4.45e+00
  angle pdb=" CA  GLN A 302 "
        pdb=" C   GLN A 302 "
        pdb=" N   SER A 303 "
      ideal   model   delta    sigma   weight residual
     116.84  120.40   -3.56 1.71e+00 3.42e-01 4.33e+00
  ... (remaining 8701 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.69: 3483
       21.69 -    43.38: 315
       43.38 -    65.07: 39
       65.07 -    86.76: 29
       86.76 -   108.45: 33
  Dihedral angle restraints: 3899
    sinusoidal: 1608
      harmonic: 2291
  Sorted by residual:
  dihedral pdb=" CB  CYS B 300 "
           pdb=" SG  CYS B 300 "
           pdb=" SG  CYS B 367 "
           pdb=" CB  CYS B 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.16   81.16     1      1.00e+01 1.00e-02 8.13e+01
  dihedral pdb=" CA  PHE B 273 "
           pdb=" C   PHE B 273 "
           pdb=" N   CYS B 274 "
           pdb=" CA  CYS B 274 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.59   21.41     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  ARG B 237 "
           pdb=" C   ARG B 237 "
           pdb=" N   SER B 238 "
           pdb=" CA  SER B 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.37   19.63     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 3896 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1016
       0.077 -    0.153: 61
       0.153 -    0.230: 0
       0.230 -    0.306: 5
       0.306 -    0.383: 1
  Chirality restraints: 1083
  Sorted by residual:
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 129 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.02   -0.38 2.00e-01 2.50e+01 3.67e+00
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" C5  BMA F   3 "
            pdb=" C4  BMA F   3 "
            pdb=" C6  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.83e+00
  ... (remaining 1080 not shown)

  Planarity restraints: 1063
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  20 "    0.050 5.00e-02 4.00e+02   7.59e-02 9.21e+00
        pdb=" N   PRO A  21 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A  21 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A  21 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 211 "   -0.017 2.00e-02 2.50e+03   1.39e-02 3.84e+00
        pdb=" CG  TYR B 211 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 211 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 211 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 211 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 211 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 211 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 211 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 315 "    0.009 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" C   PHE A 315 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   PHE A 315 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLN A 316 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1060 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1185
        2.77 -     3.30: 6518
        3.30 -     3.84: 10400
        3.84 -     4.37: 10633
        4.37 -     4.90: 19086
  Nonbonded interactions: 47822
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  41 "
            pdb=" OD2 ASP B 272 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OG1 THR B 170 "
            pdb=" OE1 GLN B 325 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   ILE A 226 "
            pdb=" OG1 THR A 230 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" NH1 ARG A 156 "
            pdb=" OD1 ASP A 343 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" OG  SER B 291 "
            pdb=" NH2 ARG B 295 "
     model   vdw
     2.319 3.120
  ... (remaining 47817 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 5 through 414 or resid 601))
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ 
 or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ 
))
  selection = (chain 'D' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ 
 or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ 
))
  selection = (chain 'E' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ 
 or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ 
))
  selection = chain 'F'
}

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:             0.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.220
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6406  Z= 0.166
  Angle     :  0.643   8.157   8750  Z= 0.308
  Chirality :  0.044   0.383   1083
  Planarity :  0.005   0.076   1059
  Dihedral  : 20.568 108.445   2413
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  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:  2.65 (0.32), residues: 783
  helix:  2.38 (0.21), residues: 649
  sheet:  None (None), residues: 0
  loop : -1.55 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  12 
 HIS   0.005   0.001   HIS A  18 
 PHE   0.011   0.001   PHE B 395 
 TYR   0.034   0.002   TYR B 211 
 ARG   0.003   0.000   ARG A 156 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00465 (    4)
  link_NAG-ASN         : angle       2.09446 (   12)
  link_BETA1-4         : bond        0.00542 (    8)
  link_BETA1-4         : angle       1.60143 (   24)
  hydrogen bonds       : bond        0.11051 (  523)
  hydrogen bonds       : angle       5.26886 ( 1569)
  SS BOND              : bond        0.00280 (    4)
  SS BOND              : angle       1.75512 (    8)
  covalent geometry    : bond        0.00335 ( 6390)
  covalent geometry    : angle       0.63207 ( 8706)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.709 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1678
  time to fit residues: 14.3911
Evaluate side-chains
  50 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 61 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0370
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.210913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.181159 restraints weight = 7010.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.183500 restraints weight = 7238.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.183213 restraints weight = 6177.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.4266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.0754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6406  Z= 0.135
  Angle     :  0.605   8.508   8750  Z= 0.283
  Chirality :  0.039   0.237   1083
  Planarity :  0.004   0.053   1059
  Dihedral  : 15.290  87.856   1087
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  6.27 %
    Favored  : 92.99 %
  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:  3.45 (0.32), residues: 783
  helix:  2.95 (0.20), residues: 650
  sheet:  None (None), residues: 0
  loop : -1.42 (0.62), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  13 
 HIS   0.005   0.001   HIS A  18 
 PHE   0.012   0.001   PHE B 273 
 TYR   0.014   0.001   TYR B 211 
 ARG   0.004   0.000   ARG B 156 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00517 (    4)
  link_NAG-ASN         : angle       1.90009 (   12)
  link_BETA1-4         : bond        0.00475 (    8)
  link_BETA1-4         : angle       2.73239 (   24)
  hydrogen bonds       : bond        0.04889 (  523)
  hydrogen bonds       : angle       3.57963 ( 1569)
  SS BOND              : bond        0.00251 (    4)
  SS BOND              : angle       0.77772 (    8)
  covalent geometry    : bond        0.00278 ( 6390)
  covalent geometry    : angle       0.58442 ( 8706)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.546 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 61
  average time/residue: 0.1944
  time to fit residues: 17.3738
Evaluate side-chains
  61 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 CYS
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue  364 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:    0.3980
   chunk 64 optimal weight:    0.0870
   chunk 37 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 63 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 46 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0020
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.4166

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.210886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.180480 restraints weight = 7051.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.182262 restraints weight = 6134.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.182977 restraints weight = 5652.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.4266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.1091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6406  Z= 0.117
  Angle     :  0.550   7.278   8750  Z= 0.258
  Chirality :  0.038   0.253   1083
  Planarity :  0.003   0.041   1059
  Dihedral  : 11.187  79.209   1087
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 10.75 %
    Favored  : 87.91 %
  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:  3.75 (0.32), residues: 783
  helix:  3.17 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.65 (0.63), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  13 
 HIS   0.004   0.001   HIS A  18 
 PHE   0.014   0.001   PHE A 220 
 TYR   0.009   0.001   TYR A 211 
 ARG   0.006   0.000   ARG B 156 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00358 (    4)
  link_NAG-ASN         : angle       1.96520 (   12)
  link_BETA1-4         : bond        0.00621 (    8)
  link_BETA1-4         : angle       2.64784 (   24)
  hydrogen bonds       : bond        0.04336 (  523)
  hydrogen bonds       : angle       3.28056 ( 1569)
  SS BOND              : bond        0.00220 (    4)
  SS BOND              : angle       0.55917 (    8)
  covalent geometry    : bond        0.00229 ( 6390)
  covalent geometry    : angle       0.52835 ( 8706)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.763 
Fit side-chains
  outliers start: 9
  outliers final: 7
  residues processed: 63
  average time/residue: 0.2278
  time to fit residues: 21.8213
Evaluate side-chains
  59 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  247 CYS
Chi-restraints excluded: chain A residue  248 CYS
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 76 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 4 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0370
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.209175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.179054 restraints weight = 7146.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.181201 restraints weight = 6882.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.181728 restraints weight = 5710.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.4261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6406  Z= 0.122
  Angle     :  0.544   7.749   8750  Z= 0.258
  Chirality :  0.038   0.265   1083
  Planarity :  0.003   0.033   1059
  Dihedral  :  9.449  71.740   1087
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.69 %
    Favored  : 85.82 %
  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:  3.86 (0.32), residues: 783
  helix:  3.25 (0.20), residues: 650
  sheet:  None (None), residues: 0
  loop : -1.43 (0.63), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  13 
 HIS   0.004   0.001   HIS A  18 
 PHE   0.011   0.001   PHE A 173 
 TYR   0.009   0.001   TYR B 374 
 ARG   0.002   0.000   ARG A 368 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00376 (    4)
  link_NAG-ASN         : angle       1.97720 (   12)
  link_BETA1-4         : bond        0.00567 (    8)
  link_BETA1-4         : angle       2.33261 (   24)
  hydrogen bonds       : bond        0.04381 (  523)
  hydrogen bonds       : angle       3.23449 ( 1569)
  SS BOND              : bond        0.00261 (    4)
  SS BOND              : angle       0.60543 (    8)
  covalent geometry    : bond        0.00256 ( 6390)
  covalent geometry    : angle       0.52636 ( 8706)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.625 
Fit side-chains
  outliers start: 10
  outliers final: 7
  residues processed: 64
  average time/residue: 0.1416
  time to fit residues: 13.4587
Evaluate side-chains
  63 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  247 CYS
Chi-restraints excluded: chain A residue  248 CYS
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 41 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 61 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
B  28 GLN
B 153 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.198904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.168396 restraints weight = 7255.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.169660 restraints weight = 7425.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.169824 restraints weight = 6675.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   6406  Z= 0.237
  Angle     :  0.711   8.099   8750  Z= 0.345
  Chirality :  0.044   0.240   1083
  Planarity :  0.004   0.036   1059
  Dihedral  :  8.435  62.028   1087
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 15.82 %
    Favored  : 82.09 %
  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:  3.05 (0.32), residues: 783
  helix:  2.69 (0.20), residues: 649
  sheet:  None (None), residues: 0
  loop : -1.61 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  12 
 HIS   0.008   0.002   HIS B 359 
 PHE   0.020   0.002   PHE B 273 
 TYR   0.024   0.002   TYR B 216 
 ARG   0.002   0.000   ARG A 368 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00560 (    4)
  link_NAG-ASN         : angle       2.27262 (   12)
  link_BETA1-4         : bond        0.00758 (    8)
  link_BETA1-4         : angle       2.37500 (   24)
  hydrogen bonds       : bond        0.06244 (  523)
  hydrogen bonds       : angle       3.69575 ( 1569)
  SS BOND              : bond        0.00627 (    4)
  SS BOND              : angle       1.28724 (    8)
  covalent geometry    : bond        0.00569 ( 6390)
  covalent geometry    : angle       0.69585 ( 8706)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.645 
Fit side-chains
REVERT: B    8 TYR cc_start: 0.7149 (t80) cc_final: 0.6599 (t80)
REVERT: B  378 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7293 (tp)
  outliers start: 14
  outliers final: 10
  residues processed: 70
  average time/residue: 0.1352
  time to fit residues: 14.0269
Evaluate side-chains
  65 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  247 CYS
Chi-restraints excluded: chain A residue  248 CYS
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  378 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0270
   chunk 23 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
B  28 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.203886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.173450 restraints weight = 7096.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.175256 restraints weight = 7304.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.175467 restraints weight = 6339.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6406  Z= 0.135
  Angle     :  0.584   8.111   8750  Z= 0.277
  Chirality :  0.038   0.218   1083
  Planarity :  0.003   0.030   1059
  Dihedral  :  7.740  55.231   1087
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 17.16 %
    Favored  : 80.90 %
  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:  3.42 (0.32), residues: 783
  helix:  2.97 (0.20), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.76 (0.61), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  13 
 HIS   0.007   0.001   HIS A 153 
 PHE   0.010   0.001   PHE B 273 
 TYR   0.010   0.001   TYR B 374 
 ARG   0.002   0.000   ARG A 368 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00330 (    4)
  link_NAG-ASN         : angle       2.10760 (   12)
  link_BETA1-4         : bond        0.00620 (    8)
  link_BETA1-4         : angle       2.14204 (   24)
  hydrogen bonds       : bond        0.05070 (  523)
  hydrogen bonds       : angle       3.39077 ( 1569)
  SS BOND              : bond        0.00333 (    4)
  SS BOND              : angle       0.67414 (    8)
  covalent geometry    : bond        0.00286 ( 6390)
  covalent geometry    : angle       0.56900 ( 8706)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A  151 GLU cc_start: 0.8134 (pp20) cc_final: 0.7833 (tm-30)
REVERT: B    8 TYR cc_start: 0.7088 (t80) cc_final: 0.6461 (t80)
  outliers start: 13
  outliers final: 11
  residues processed: 72
  average time/residue: 0.1689
  time to fit residues: 18.0911
Evaluate side-chains
  72 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 1.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  247 CYS
Chi-restraints excluded: chain A residue  248 CYS
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  364 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 69 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    0.4980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.203449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.172341 restraints weight = 7164.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.172943 restraints weight = 8236.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.173755 restraints weight = 6608.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.4180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6406  Z= 0.140
  Angle     :  0.586   7.973   8750  Z= 0.277
  Chirality :  0.038   0.224   1083
  Planarity :  0.003   0.029   1059
  Dihedral  :  6.858  54.457   1087
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.46 %
    Favored  : 80.00 %
  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:  3.37 (0.32), residues: 783
  helix:  2.96 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.09 (0.59), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  13 
 HIS   0.010   0.001   HIS A 153 
 PHE   0.016   0.001   PHE A 332 
 TYR   0.011   0.001   TYR B 216 
 ARG   0.002   0.000   ARG A 368 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00372 (    4)
  link_NAG-ASN         : angle       2.08079 (   12)
  link_BETA1-4         : bond        0.00629 (    8)
  link_BETA1-4         : angle       2.07594 (   24)
  hydrogen bonds       : bond        0.04927 (  523)
  hydrogen bonds       : angle       3.37501 ( 1569)
  SS BOND              : bond        0.00370 (    4)
  SS BOND              : angle       0.75392 (    8)
  covalent geometry    : bond        0.00305 ( 6390)
  covalent geometry    : angle       0.57187 ( 8706)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 1.275 
Fit side-chains
REVERT: B    8 TYR cc_start: 0.7081 (t80) cc_final: 0.6506 (t80)
REVERT: B  350 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7524 (tp)
REVERT: B  378 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7223 (tp)
  outliers start: 17
  outliers final: 11
  residues processed: 73
  average time/residue: 0.1791
  time to fit residues: 19.3187
Evaluate side-chains
  72 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  247 CYS
Chi-restraints excluded: chain A residue  248 CYS
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  378 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    0.0770
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0000
   chunk 28 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 60 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.5342

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

Flipped N/Q/H residues before XYZ refinement:
B  28 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.205407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.175663 restraints weight = 7092.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.176205 restraints weight = 6802.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.176866 restraints weight = 6341.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.4209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6406  Z= 0.123
  Angle     :  0.561   7.505   8750  Z= 0.266
  Chirality :  0.036   0.214   1083
  Planarity :  0.003   0.035   1059
  Dihedral  :  6.373  59.496   1087
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.61 %
    Favored  : 80.30 %
  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:  3.58 (0.32), residues: 783
  helix:  3.11 (0.20), residues: 655
  sheet:  None (None), residues: 0
  loop : -2.07 (0.59), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  13 
 HIS   0.010   0.001   HIS A 153 
 PHE   0.014   0.001   PHE B 220 
 TYR   0.009   0.001   TYR B 374 
 ARG   0.002   0.000   ARG B 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00318 (    4)
  link_NAG-ASN         : angle       2.04145 (   12)
  link_BETA1-4         : bond        0.00543 (    8)
  link_BETA1-4         : angle       1.97443 (   24)
  hydrogen bonds       : bond        0.04599 (  523)
  hydrogen bonds       : angle       3.29547 ( 1569)
  SS BOND              : bond        0.00284 (    4)
  SS BOND              : angle       0.54274 (    8)
  covalent geometry    : bond        0.00256 ( 6390)
  covalent geometry    : angle       0.54680 ( 8706)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.604 
Fit side-chains
REVERT: B  245 MET cc_start: 0.6795 (tpp) cc_final: 0.6592 (tmm)
REVERT: B  350 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7438 (tp)
  outliers start: 14
  outliers final: 10
  residues processed: 71
  average time/residue: 0.1293
  time to fit residues: 13.5714
Evaluate side-chains
  70 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 CYS
Chi-restraints excluded: chain A residue  248 CYS
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  364 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  28 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.204227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.173067 restraints weight = 7150.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.176673 restraints weight = 6426.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.176542 restraints weight = 5214.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6406  Z= 0.140
  Angle     :  0.572   7.847   8750  Z= 0.274
  Chirality :  0.037   0.224   1083
  Planarity :  0.003   0.033   1059
  Dihedral  :  5.989  57.751   1087
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 17.01 %
    Favored  : 81.04 %
  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:  3.49 (0.32), residues: 783
  helix:  3.06 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.14 (0.59), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  12 
 HIS   0.011   0.001   HIS A 153 
 PHE   0.014   0.002   PHE A 220 
 TYR   0.011   0.001   TYR B 216 
 ARG   0.002   0.000   ARG B 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00368 (    4)
  link_NAG-ASN         : angle       2.03017 (   12)
  link_BETA1-4         : bond        0.00575 (    8)
  link_BETA1-4         : angle       1.91586 (   24)
  hydrogen bonds       : bond        0.04841 (  523)
  hydrogen bonds       : angle       3.34368 ( 1569)
  SS BOND              : bond        0.00384 (    4)
  SS BOND              : angle       0.91632 (    8)
  covalent geometry    : bond        0.00310 ( 6390)
  covalent geometry    : angle       0.55886 ( 8706)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.908 
Fit side-chains
REVERT: B    8 TYR cc_start: 0.7105 (t80) cc_final: 0.6521 (t80)
REVERT: B  350 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7506 (tp)
  outliers start: 13
  outliers final: 10
  residues processed: 73
  average time/residue: 0.1249
  time to fit residues: 14.0636
Evaluate side-chains
  73 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 CYS
Chi-restraints excluded: chain A residue  248 CYS
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  364 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    0.0270
   chunk 48 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0070
   chunk 22 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 3 optimal weight:    0.3980
   chunk 40 optimal weight:    0.1980
   overall best weight:    0.3056

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

Flipped N/Q/H residues before XYZ refinement:
B 316 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.207464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.177031 restraints weight = 7161.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.177009 restraints weight = 7006.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.179473 restraints weight = 6043.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.4228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6406  Z= 0.114
  Angle     :  0.533   8.165   8750  Z= 0.256
  Chirality :  0.035   0.204   1083
  Planarity :  0.003   0.039   1059
  Dihedral  :  5.553  57.620   1087
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 17.76 %
    Favored  : 80.90 %
  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:  3.75 (0.32), residues: 783
  helix:  3.24 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.12 (0.59), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  13 
 HIS   0.011   0.001   HIS A 153 
 PHE   0.016   0.001   PHE A 332 
 TYR   0.012   0.001   TYR B 210 
 ARG   0.002   0.000   ARG A 156 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00257 (    4)
  link_NAG-ASN         : angle       1.97671 (   12)
  link_BETA1-4         : bond        0.00519 (    8)
  link_BETA1-4         : angle       1.75105 (   24)
  hydrogen bonds       : bond        0.04226 (  523)
  hydrogen bonds       : angle       3.21428 ( 1569)
  SS BOND              : bond        0.00183 (    4)
  SS BOND              : angle       0.52389 (    8)
  covalent geometry    : bond        0.00224 ( 6390)
  covalent geometry    : angle       0.52069 ( 8706)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.670 
Fit side-chains
REVERT: B    8 TYR cc_start: 0.7097 (t80) cc_final: 0.6544 (t80)
REVERT: B  350 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7286 (tp)
  outliers start: 9
  outliers final: 8
  residues processed: 66
  average time/residue: 0.1413
  time to fit residues: 13.9627
Evaluate side-chains
  67 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 CYS
Chi-restraints excluded: chain A residue  248 CYS
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  364 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 3 optimal weight:    0.0000
   chunk 77 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.204966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.174565 restraints weight = 7178.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.176817 restraints weight = 7442.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.177160 restraints weight = 5829.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.4217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6406  Z= 0.129
  Angle     :  0.541   8.102   8750  Z= 0.260
  Chirality :  0.037   0.220   1083
  Planarity :  0.003   0.037   1059
  Dihedral  :  5.469  59.019   1087
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 17.91 %
    Favored  : 80.75 %
  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:  3.65 (0.32), residues: 783
  helix:  3.17 (0.20), residues: 657
  sheet:  None (None), residues: 0
  loop : -2.19 (0.59), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  12 
 HIS   0.004   0.001   HIS A  18 
 PHE   0.023   0.002   PHE A 173 
 TYR   0.013   0.001   TYR B 210 
 ARG   0.002   0.000   ARG B 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00360 (    4)
  link_NAG-ASN         : angle       1.95070 (   12)
  link_BETA1-4         : bond        0.00556 (    8)
  link_BETA1-4         : angle       1.70731 (   24)
  hydrogen bonds       : bond        0.04519 (  523)
  hydrogen bonds       : angle       3.25458 ( 1569)
  SS BOND              : bond        0.00361 (    4)
  SS BOND              : angle       0.74642 (    8)
  covalent geometry    : bond        0.00280 ( 6390)
  covalent geometry    : angle       0.52907 ( 8706)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2128.02 seconds
wall clock time: 39 minutes 9.98 seconds (2349.98 seconds total)