Starting phenix.real_space_refine
on Tue Mar  3 14:52:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rtt_24688/03_2026/7rtt_24688.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rtt_24688/03_2026/7rtt_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rtt_24688/03_2026/7rtt_24688.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rtt_24688/03_2026/7rtt_24688.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rtt_24688/03_2026/7rtt_24688.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rtt_24688/03_2026/7rtt_24688.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.55, per 1000 atoms: 0.25
  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: 0.72
  Conformation dependent library (CDL) restraints added in 233.5 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: 0.16
  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: 0.93

  Time building geometry restraints manager: 0.88 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 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:             1.640
  Set stop_for_unknowns flag:              0.010
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.430
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.660
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.003   0.000   ARG A 156 
 TYR   0.034   0.002   TYR B 211 
 PHE   0.011   0.001   PHE B 395 
 TRP   0.006   0.001   TRP A  12 
 HIS   0.005   0.001   HIS A  18 

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

*********************** 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  : 0.230 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0688
  time to fit residues: 6.0356
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  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.208190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.178467 restraints weight = 7067.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.180724 restraints weight = 7164.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.180494 restraints weight = 6207.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.180963 restraints weight = 4725.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.181301 restraints weight = 4244.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.4248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
moved from start:          0.0876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6406  Z= 0.153
  Angle     :  0.639   8.807   8750  Z= 0.298
  Chirality :  0.041   0.259   1083
  Planarity :  0.004   0.053   1059
  Dihedral  : 14.495  85.344   1087
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  7.61 %
    Favored  : 91.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.30 (0.32), residues: 783
  helix:  2.84 (0.20), residues: 650
  sheet:  None (None), residues: 0
  loop : -1.45 (0.62), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 156 
 TYR   0.013   0.001   TYR B 211 
 PHE   0.013   0.001   PHE B 273 
 TRP   0.007   0.001   TRP A  12 
 HIS   0.004   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6390)
  covalent geometry    : angle       0.61698 ( 8706)
  SS BOND              : bond        0.00339 (    4)
  SS BOND              : angle       0.90919 (    8)
  hydrogen bonds       : bond        0.05054 (  523)
  hydrogen bonds       : angle       3.60126 ( 1569)
  link_BETA1-4         : bond        0.00674 (    8)
  link_BETA1-4         : angle       2.93925 (   24)
  link_NAG-ASN         : bond        0.00605 (    4)
  link_NAG-ASN         : angle       1.89670 (   12)

*********************** 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
  67 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.224 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 64
  average time/residue: 0.0680
  time to fit residues: 6.2241
Evaluate side-chains
  64 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
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  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 70 optimal weight:    0.0870
   chunk 2 optimal weight:    0.0870
   chunk 6 optimal weight:    0.9980
   chunk 52 optimal weight:    0.2980
   chunk 38 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0570
   chunk 3 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.2654

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.211485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.181191 restraints weight = 6974.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.183048 restraints weight = 6673.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.183585 restraints weight = 5727.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.184095 restraints weight = 4550.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.184435 restraints weight = 4070.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.4283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6406  Z= 0.114
  Angle     :  0.548   7.236   8750  Z= 0.256
  Chirality :  0.038   0.250   1083
  Planarity :  0.003   0.041   1059
  Dihedral  : 11.330  79.978   1087
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 11.79 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.85 (0.32), residues: 783
  helix:  3.23 (0.20), residues: 650
  sheet:  None (None), residues: 0
  loop : -1.35 (0.63), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 156 
 TYR   0.007   0.001   TYR B 374 
 PHE   0.008   0.001   PHE B 395 
 TRP   0.006   0.001   TRP B  13 
 HIS   0.005   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 6390)
  covalent geometry    : angle       0.52677 ( 8706)
  SS BOND              : bond        0.00211 (    4)
  SS BOND              : angle       0.48210 (    8)
  hydrogen bonds       : bond        0.04280 (  523)
  hydrogen bonds       : angle       3.28794 ( 1569)
  link_BETA1-4         : bond        0.00548 (    8)
  link_BETA1-4         : angle       2.64344 (   24)
  link_NAG-ASN         : bond        0.00314 (    4)
  link_NAG-ASN         : angle       1.95496 (   12)

*********************** 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
  62 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.226 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 60
  average time/residue: 0.0801
  time to fit residues: 6.7421
Evaluate side-chains
  59 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 CYS
Chi-restraints excluded: chain A residue  408 CYS
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 50 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4510 r_free = 0.4510 target = 0.208909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.178959 restraints weight = 7134.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.180366 restraints weight = 7262.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.180831 restraints weight = 6517.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.181514 restraints weight = 5045.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.182098 restraints weight = 4461.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.4252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.1279

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= 0.131
  Angle     :  0.558   7.827   8750  Z= 0.265
  Chirality :  0.038   0.264   1083
  Planarity :  0.003   0.035   1059
  Dihedral  :  9.594  72.270   1087
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 14.03 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.79 (0.32), residues: 783
  helix:  3.21 (0.20), residues: 650
  sheet:  None (None), residues: 0
  loop : -1.46 (0.63), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 212 
 TYR   0.010   0.001   TYR B 374 
 PHE   0.011   0.001   PHE B 273 
 TRP   0.007   0.001   TRP A  12 
 HIS   0.005   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6390)
  covalent geometry    : angle       0.54021 ( 8706)
  SS BOND              : bond        0.00301 (    4)
  SS BOND              : angle       0.66930 (    8)
  hydrogen bonds       : bond        0.04550 (  523)
  hydrogen bonds       : angle       3.28462 ( 1569)
  link_BETA1-4         : bond        0.00594 (    8)
  link_BETA1-4         : angle       2.38975 (   24)
  link_NAG-ASN         : bond        0.00421 (    4)
  link_NAG-ASN         : angle       1.98134 (   12)

*********************** 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
  64 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.216 
Fit side-chains
  outliers start: 9
  outliers final: 6
  residues processed: 62
  average time/residue: 0.0553
  time to fit residues: 5.1887
Evaluate side-chains
  60 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
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  408 CYS
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  364 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 70 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0370
   chunk 1 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.6258

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.207670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.176197 restraints weight = 7229.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.176268 restraints weight = 7848.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.177082 restraints weight = 7252.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.178692 restraints weight = 5411.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.179067 restraints weight = 4492.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.4226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6406  Z= 0.126
  Angle     :  0.534   8.093   8750  Z= 0.256
  Chirality :  0.037   0.244   1083
  Planarity :  0.003   0.031   1059
  Dihedral  :  8.375  63.681   1087
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.82 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.79 (0.32), residues: 783
  helix:  3.21 (0.20), residues: 651
  sheet:  None (None), residues: 0
  loop : -1.53 (0.62), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 156 
 TYR   0.011   0.001   TYR B 210 
 PHE   0.010   0.001   PHE B 273 
 TRP   0.007   0.001   TRP B  13 
 HIS   0.004   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6390)
  covalent geometry    : angle       0.51716 ( 8706)
  SS BOND              : bond        0.00297 (    4)
  SS BOND              : angle       0.59529 (    8)
  hydrogen bonds       : bond        0.04479 (  523)
  hydrogen bonds       : angle       3.21952 ( 1569)
  link_BETA1-4         : bond        0.00660 (    8)
  link_BETA1-4         : angle       2.14144 (   24)
  link_NAG-ASN         : bond        0.00336 (    4)
  link_NAG-ASN         : angle       2.03504 (   12)

*********************** 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
  66 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.216 
Fit side-chains
  outliers start: 12
  outliers final: 8
  residues processed: 62
  average time/residue: 0.0476
  time to fit residues: 4.6992
Evaluate side-chains
  61 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
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  326 VAL
Chi-restraints excluded: chain B residue  364 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.2786

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.201750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.171309 restraints weight = 7221.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.172243 restraints weight = 7336.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.172491 restraints weight = 6949.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.173134 restraints weight = 5573.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.174844 restraints weight = 4855.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.4188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7092
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6406  Z= 0.187
  Angle     :  0.639   8.091   8750  Z= 0.305
  Chirality :  0.040   0.233   1083
  Planarity :  0.004   0.070   1059
  Dihedral  :  7.663  54.926   1087
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.57 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.33 (0.32), residues: 783
  helix:  2.89 (0.20), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.66 (0.63), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 156 
 TYR   0.015   0.002   TYR B 216 
 PHE   0.015   0.002   PHE B 273 
 TRP   0.007   0.001   TRP A  12 
 HIS   0.005   0.002   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 6390)
  covalent geometry    : angle       0.62422 ( 8706)
  SS BOND              : bond        0.00523 (    4)
  SS BOND              : angle       1.01862 (    8)
  hydrogen bonds       : bond        0.05390 (  523)
  hydrogen bonds       : angle       3.43292 ( 1569)
  link_BETA1-4         : bond        0.00673 (    8)
  link_BETA1-4         : angle       2.21629 (   24)
  link_NAG-ASN         : bond        0.00480 (    4)
  link_NAG-ASN         : angle       2.12406 (   12)

*********************** 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
  73 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.217 
Fit side-chains
REVERT: B  378 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7302 (tp)
  outliers start: 13
  outliers final: 10
  residues processed: 69
  average time/residue: 0.0490
  time to fit residues: 5.3840
Evaluate side-chains
  68 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
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  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  364 MET
Chi-restraints excluded: chain B residue  378 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4471 r_free = 0.4471 target = 0.204245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.172903 restraints weight = 7159.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.173473 restraints weight = 8388.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.174356 restraints weight = 6834.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.174809 restraints weight = 5651.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.177799 restraints weight = 4999.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.4217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7032
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6406  Z= 0.138
  Angle     :  0.574   7.840   8750  Z= 0.273
  Chirality :  0.037   0.219   1083
  Planarity :  0.004   0.065   1059
  Dihedral  :  7.131  56.115   1087
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 17.91 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.53 (0.32), residues: 783
  helix:  3.06 (0.20), residues: 649
  sheet:  None (None), residues: 0
  loop : -1.68 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 156 
 TYR   0.010   0.001   TYR B 374 
 PHE   0.013   0.001   PHE A 220 
 TRP   0.007   0.001   TRP A  12 
 HIS   0.003   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6390)
  covalent geometry    : angle       0.55879 ( 8706)
  SS BOND              : bond        0.00379 (    4)
  SS BOND              : angle       0.69656 (    8)
  hydrogen bonds       : bond        0.04909 (  523)
  hydrogen bonds       : angle       3.31606 ( 1569)
  link_BETA1-4         : bond        0.00620 (    8)
  link_BETA1-4         : angle       2.09983 (   24)
  link_NAG-ASN         : bond        0.00360 (    4)
  link_NAG-ASN         : angle       2.10944 (   12)

*********************** 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
  71 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.213 
Fit side-chains
REVERT: B  378 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7233 (tp)
  outliers start: 11
  outliers final: 8
  residues processed: 68
  average time/residue: 0.0588
  time to fit residues: 5.8788
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  : 0.204 
-------------------------------------------------------------------------------
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  285 THR
Chi-restraints excluded: chain A residue  364 MET
Chi-restraints excluded: chain A residue  408 CYS
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 30 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 66 optimal weight:    0.6980
   chunk 7 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 28 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4475 r_free = 0.4475 target = 0.204330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.173953 restraints weight = 7253.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.176178 restraints weight = 7543.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.176995 restraints weight = 5884.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.177320 restraints weight = 4741.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.177449 restraints weight = 4228.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6406  Z= 0.137
  Angle     :  0.573   7.531   8750  Z= 0.272
  Chirality :  0.037   0.222   1083
  Planarity :  0.004   0.065   1059
  Dihedral  :  6.534  57.245   1087
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 18.36 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.62 (0.32), residues: 783
  helix:  3.13 (0.20), residues: 649
  sheet:  None (None), residues: 0
  loop : -1.69 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 156 
 TYR   0.010   0.001   TYR B 374 
 PHE   0.013   0.001   PHE A 220 
 TRP   0.007   0.001   TRP B  13 
 HIS   0.004   0.001   HIS B 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6390)
  covalent geometry    : angle       0.55904 ( 8706)
  SS BOND              : bond        0.00369 (    4)
  SS BOND              : angle       0.70605 (    8)
  hydrogen bonds       : bond        0.04825 (  523)
  hydrogen bonds       : angle       3.30450 ( 1569)
  link_BETA1-4         : bond        0.00586 (    8)
  link_BETA1-4         : angle       2.03318 (   24)
  link_NAG-ASN         : bond        0.00360 (    4)
  link_NAG-ASN         : angle       2.06973 (   12)

*********************** 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
  69 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.222 
Fit side-chains
REVERT: B  350 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7487 (tp)
  outliers start: 10
  outliers final: 8
  residues processed: 66
  average time/residue: 0.0571
  time to fit residues: 5.6314
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  : 0.220 
-------------------------------------------------------------------------------
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  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 46 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 48 optimal weight:    0.1980
   chunk 70 optimal weight:    0.0020
   chunk 69 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0970
   chunk 6 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.3586

-------------------------------------------------------------------------------
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 = 0.4509 r_free = 0.4509 target = 0.208050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.178265 restraints weight = 7195.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.179856 restraints weight = 6945.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.180168 restraints weight = 5959.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.180718 restraints weight = 4873.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.183251 restraints weight = 4404.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.4272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6942
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6406  Z= 0.113
  Angle     :  0.529   6.747   8750  Z= 0.252
  Chirality :  0.035   0.205   1083
  Planarity :  0.004   0.059   1059
  Dihedral  :  5.851  57.571   1087
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 18.21 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.87 (0.32), residues: 783
  helix:  3.31 (0.20), residues: 650
  sheet:  None (None), residues: 0
  loop : -1.72 (0.61), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 156 
 TYR   0.009   0.001   TYR B 374 
 PHE   0.021   0.001   PHE A 173 
 TRP   0.007   0.001   TRP B  13 
 HIS   0.003   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 6390)
  covalent geometry    : angle       0.51575 ( 8706)
  SS BOND              : bond        0.00188 (    4)
  SS BOND              : angle       0.39607 (    8)
  hydrogen bonds       : bond        0.04214 (  523)
  hydrogen bonds       : angle       3.17316 ( 1569)
  link_BETA1-4         : bond        0.00530 (    8)
  link_BETA1-4         : angle       1.85770 (   24)
  link_NAG-ASN         : bond        0.00251 (    4)
  link_NAG-ASN         : angle       1.98147 (   12)

*********************** 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
  67 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  316 GLN cc_start: 0.6908 (tp40) cc_final: 0.6699 (tm-30)
REVERT: B    8 TYR cc_start: 0.7124 (t80) cc_final: 0.6614 (t80)
REVERT: B  350 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7322 (tp)
  outliers start: 11
  outliers final: 6
  residues processed: 65
  average time/residue: 0.0617
  time to fit residues: 5.7629
Evaluate side-chains
  61 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
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 B residue  148 VAL
Chi-restraints excluded: chain B residue  350 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 68 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 14 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4463 r_free = 0.4463 target = 0.203060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.171722 restraints weight = 7190.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.172642 restraints weight = 8084.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.173765 restraints weight = 6420.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.174220 restraints weight = 5135.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.175771 restraints weight = 4640.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.1972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6406  Z= 0.159
  Angle     :  0.595   8.132   8750  Z= 0.285
  Chirality :  0.038   0.228   1083
  Planarity :  0.004   0.056   1059
  Dihedral  :  5.731  57.894   1087
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 18.66 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.63 (0.32), residues: 783
  helix:  3.14 (0.20), residues: 651
  sheet:  None (None), residues: 0
  loop : -1.82 (0.61), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 156 
 TYR   0.016   0.001   TYR B 210 
 PHE   0.023   0.002   PHE A 173 
 TRP   0.007   0.001   TRP A  12 
 HIS   0.004   0.001   HIS B 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6390)
  covalent geometry    : angle       0.58267 ( 8706)
  SS BOND              : bond        0.00455 (    4)
  SS BOND              : angle       0.80535 (    8)
  hydrogen bonds       : bond        0.04888 (  523)
  hydrogen bonds       : angle       3.31938 ( 1569)
  link_BETA1-4         : bond        0.00587 (    8)
  link_BETA1-4         : angle       1.84953 (   24)
  link_NAG-ASN         : bond        0.00400 (    4)
  link_NAG-ASN         : angle       2.03049 (   12)

********************** 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
  67 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.211 
Fit side-chains
REVERT: B    8 TYR cc_start: 0.7118 (t80) cc_final: 0.6816 (t80)
REVERT: B  350 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7531 (tp)
  outliers start: 8
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0472
  time to fit residues: 4.9390
Evaluate side-chains
  64 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
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  350 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 32 optimal weight:    0.3980
   chunk 9 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 72 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4475 r_free = 0.4475 target = 0.204179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.173090 restraints weight = 7136.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.174184 restraints weight = 8044.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.174911 restraints weight = 6513.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.175592 restraints weight = 5223.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.177436 restraints weight = 4594.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6406  Z= 0.137
  Angle     :  0.564   8.172   8750  Z= 0.270
  Chirality :  0.037   0.217   1083
  Planarity :  0.004   0.054   1059
  Dihedral  :  5.546  59.059   1087
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 18.96 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.66 (0.32), residues: 783
  helix:  3.17 (0.20), residues: 651
  sheet:  None (None), residues: 0
  loop : -1.85 (0.61), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 156 
 TYR   0.013   0.001   TYR B 210 
 PHE   0.021   0.001   PHE A 173 
 TRP   0.008   0.001   TRP B  13 
 HIS   0.003   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6390)
  covalent geometry    : angle       0.55209 ( 8706)
  SS BOND              : bond        0.00403 (    4)
  SS BOND              : angle       0.87045 (    8)
  hydrogen bonds       : bond        0.04749 (  523)
  hydrogen bonds       : angle       3.28591 ( 1569)
  link_BETA1-4         : bond        0.00561 (    8)
  link_BETA1-4         : angle       1.73540 (   24)
  link_NAG-ASN         : bond        0.00329 (    4)
  link_NAG-ASN         : angle       2.03681 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 958.33 seconds
wall clock time: 17 minutes 15.23 seconds (1035.23 seconds total)