Starting phenix.real_space_refine
on Thu Jul  2 10:19:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k0e_36762/07_2026/8k0e_36762.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k0e_36762/07_2026/8k0e_36762.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k0e_36762/07_2026/8k0e_36762.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k0e_36762/07_2026/8k0e_36762.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k0e_36762/07_2026/8k0e_36762.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k0e_36762/07_2026/8k0e_36762.map"
  }
  resolution = 3.65
  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=   0.005 sd=   0.077
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
     Fe      1      7.16       5
     S      47      5.16       5
     C    5273      2.51       5
     N    1403      2.21       5
     O    1576      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8300
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 646, 5193
          Classifications: {'peptide': 646}
          Link IDs: {'PTRANS': 33, 'TRANS': 612}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2994
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2994
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 18, 'TRANS': 343}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 0
          Ad-hoc single atom residues: {' FE': 1}
          Chain breaks: 1
  Time building chain proxies: 1.49, per 1000 atoms: 0.18
  Number of scatterers: 8300
  At special positions: 0
  Unit cell: (81.4, 105.6, 125.4, 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)
     Fe      1     26.01
     S      47     16.00
     O    1576      8.00
     N    1403      7.00
     C    5273      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  75 " - pdb=" SG  CYS A 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 242 " - pdb=" SG  CYS A 282 " 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 D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 540 "
      " NAG D   1 " - " ASN A 316 "
      " NAG E   1 " - " ASN B 363 "
      " NAG F   1 " - " ASN B  87 "
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 378.6 milliseconds
  

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1922

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 3 sheets defined
      65.2% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 49
      removed outlier: 3.746A  pdb=" N   LEU A  38 " --> pdb=" O   THR A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 83
      removed outlier: 3.814A  pdb=" N   ALA A  80 " --> pdb=" O   ARG A  76 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ALA A  81 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 125
      removed outlier: 3.692A  pdb=" N   GLY A 125 " --> pdb=" O   ARG A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 142
      removed outlier: 3.923A  pdb=" N   GLU A 137 " --> pdb=" O   SER A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 156
    Processing helix  chain 'A' and resid 158 through 173
    Processing helix  chain 'A' and resid 176 through 189
      removed outlier: 3.521A  pdb=" N   GLN A 180 " --> pdb=" O   HIS A 176 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   MET A 189 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 197
    Processing helix  chain 'A' and resid 203 through 217
      removed outlier: 3.549A  pdb=" N   GLN A 207 " --> pdb=" O   GLN A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 4.038A  pdb=" N   HIS A 227 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU A 228 " --> pdb=" O   ALA A 224 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   TYR A 235 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 281
      removed outlier: 3.644A  pdb=" N   THR A 269 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 285
    Processing helix  chain 'A' and resid 298 through 315
    Processing helix  chain 'A' and resid 316 through 329
    Processing helix  chain 'A' and resid 334 through 348
    Processing helix  chain 'A' and resid 349 through 356
      removed outlier: 3.541A  pdb=" N   ILE A 356 " --> pdb=" O   HIS A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 384
    Processing helix  chain 'A' and resid 400 through 428
    Processing helix  chain 'A' and resid 441 through 447
    Processing helix  chain 'A' and resid 479 through 493
      removed outlier: 3.578A  pdb=" N   CYS A 483 " --> pdb=" O   SER A 479 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA A 493 " --> pdb=" O   LEU A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 528
    Processing helix  chain 'A' and resid 531 through 553
      removed outlier: 3.862A  pdb=" N   ALA A 535 " --> pdb=" O   PRO A 531 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   PHE A 553 " --> pdb=" O   MET A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 576
      removed outlier: 3.863A  pdb=" N   GLN A 576 " --> pdb=" O   GLU A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 598
    Processing helix  chain 'A' and resid 686 through 699
    Processing helix  chain 'B' and resid 37 through 41
      removed outlier: 3.864A  pdb=" N   GLU B  40 " --> pdb=" O   PRO B  37 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU B  41 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 37 through 41'
    Processing helix  chain 'B' and resid 43 through 57
    Processing helix  chain 'B' and resid 60 through 90
      removed outlier: 3.776A  pdb=" N   CYS B  88 " --> pdb=" O   CYS B  84 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   SER B  89 " --> pdb=" O   HIS B  85 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ALA B  90 " --> pdb=" O   ARG B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 102
    Processing helix  chain 'B' and resid 103 through 123
    Processing helix  chain 'B' and resid 124 through 125
      No H-bonds generated for 'chain 'B' and resid 124 through 125'
    Processing helix  chain 'B' and resid 126 through 131
      removed outlier: 4.205A  pdb=" N   GLN B 131 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 144
    Processing helix  chain 'B' and resid 146 through 157
      removed outlier: 4.200A  pdb=" N   PHE B 150 " --> pdb=" O   GLU B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 175
      removed outlier: 3.820A  pdb=" N   LYS B 174 " --> pdb=" O   THR B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 191
    Processing helix  chain 'B' and resid 204 through 219
      removed outlier: 3.729A  pdb=" N   SER B 208 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 246
      Proline residue:  B 234  - end of helix
    Processing helix  chain 'B' and resid 258 through 276
      removed outlier: 4.427A  pdb=" N   HIS B 266 " --> pdb=" O   SER B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 308
    Processing helix  chain 'B' and resid 310 through 325
      Proline residue:  B 316  - end of helix
    Processing helix  chain 'B' and resid 328 through 341
      removed outlier: 3.722A  pdb=" N   HIS B 341 " --> pdb=" O   TYR B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 352
      removed outlier: 3.827A  pdb=" N   PHE B 352 " --> pdb=" O   ASP B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 376
    Processing sheet with id=AA1, first strand: chain 'A' and resid 458 through 461
      removed outlier: 6.194A  pdb=" N   LEU A 459 " --> pdb=" O   ASP A 475 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   ASP A 475 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ARG A 647 " --> pdb=" O   TYR A 617 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA A 673 " --> pdb=" O   HIS A 565 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   HIS A 565 " --> pdb=" O   ALA A 673 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   TYR A 563 " --> pdb=" O   TRP A 675 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   THR A 677 " --> pdb=" O   PHE A 561 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   PHE A 561 " --> pdb=" O   THR A 677 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   VAL A 516 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 584 through 587
      removed outlier: 6.223A  pdb=" N   VAL A 661 " --> pdb=" O   PRO A 585 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   HIS A 587 " --> pdb=" O   HIS A 659 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   PHE A 627 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLU A 640 " --> pdb=" O   PHE A 627 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   PHE A 629 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 284 through 285
      removed outlier: 4.194A  pdb=" N   ILE B 285 " --> pdb=" O   TYR B 288 " (cutoff:3.500A)

    482 hydrogen bonds defined for protein.
    1407 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: 1.08

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1735
        1.33 -     1.45: 2087
        1.45 -     1.58: 4613
        1.58 -     1.70: 0
        1.70 -     1.82: 70
  Bond restraints: 8505
  Sorted by residual:
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.480 -0.074 2.00e-02 2.50e+03 1.38e+01
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.479 -0.073 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.62e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.27e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.26e+00
  ... (remaining 8500 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.30: 11437
        3.30 -     6.60: 64
        6.60 -     9.90: 9
        9.90 -    13.20: 3
       13.20 -    16.50: 2
  Bond angle restraints: 11515
  Sorted by residual:
  angle pdb=" CA  LEU A 183 "
        pdb=" CB  LEU A 183 "
        pdb=" CG  LEU A 183 "
      ideal   model   delta    sigma   weight residual
     116.30  132.80  -16.50 3.50e+00 8.16e-02 2.22e+01
  angle pdb=" CB  MET A 177 "
        pdb=" CG  MET A 177 "
        pdb=" SD  MET A 177 "
      ideal   model   delta    sigma   weight residual
     112.70  126.80  -14.10 3.00e+00 1.11e-01 2.21e+01
  angle pdb=" CA  LEU A 445 "
        pdb=" CB  LEU A 445 "
        pdb=" CG  LEU A 445 "
      ideal   model   delta    sigma   weight residual
     116.30  129.47  -13.17 3.50e+00 8.16e-02 1.41e+01
  angle pdb=" CA  LEU A 215 "
        pdb=" CB  LEU A 215 "
        pdb=" CG  LEU A 215 "
      ideal   model   delta    sigma   weight residual
     116.30  128.23  -11.93 3.50e+00 8.16e-02 1.16e+01
  angle pdb=" N   GLY B 125 "
        pdb=" CA  GLY B 125 "
        pdb=" C   GLY B 125 "
      ideal   model   delta    sigma   weight residual
     110.21  113.23   -3.02 9.10e-01 1.21e+00 1.10e+01
  ... (remaining 11510 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.71: 4638
       24.71 -    49.42: 474
       49.42 -    74.12: 69
       74.12 -    98.83: 26
       98.83 -   123.54: 18
  Dihedral angle restraints: 5225
    sinusoidal: 2237
      harmonic: 2988
  Sorted by residual:
  dihedral pdb=" CB  CYS A  75 "
           pdb=" SG  CYS A  75 "
           pdb=" SG  CYS A 123 "
           pdb=" CB  CYS A 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.25  -88.75     1      1.00e+01 1.00e-02 9.39e+01
  dihedral pdb=" CB  CYS A 242 "
           pdb=" SG  CYS A 242 "
           pdb=" SG  CYS A 282 "
           pdb=" CB  CYS A 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.78  -43.78     1      1.00e+01 1.00e-02 2.67e+01
  dihedral pdb=" C2  NAG C   1 "
           pdb=" C1  NAG C   1 "
           pdb=" O5  NAG C   1 "
           pdb=" C5  NAG C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   60.58 -123.54     1      3.00e+01 1.11e-03 1.66e+01
  ... (remaining 5222 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 904
       0.041 -    0.081: 243
       0.081 -    0.122: 70
       0.122 -    0.162: 6
       0.162 -    0.203: 3
  Chirality restraints: 1226
  Sorted by residual:
  chirality pdb=" CG  LEU A 138 "
            pdb=" CB  LEU A 138 "
            pdb=" CD1 LEU A 138 "
            pdb=" CD2 LEU A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  MET B 331 "
            pdb=" N   MET B 331 "
            pdb=" C   MET B 331 "
            pdb=" CB  MET B 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.45e-01
  chirality pdb=" CB  THR A  34 "
            pdb=" CA  THR A  34 "
            pdb=" OG1 THR A  34 "
            pdb=" CG2 THR A  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 6.95e-01
  ... (remaining 1223 not shown)

  Planarity restraints: 1512
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  94 "   -0.061 5.00e-02 4.00e+02   8.98e-02 1.29e+01
        pdb=" N   PRO A  95 "    0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 604 "   -0.042 5.00e-02 4.00e+02   6.33e-02 6.41e+00
        pdb=" N   PRO A 605 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 605 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 605 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 657 "   -0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO A 658 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 658 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 658 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1509 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 125
        2.66 -     3.22: 7857
        3.22 -     3.78: 12732
        3.78 -     4.34: 15006
        4.34 -     4.90: 24964
  Nonbonded interactions: 60684
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 312 "
            pdb=" OH  TYR A 343 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" O   TYR A 185 "
            pdb=" OG1 THR A 188 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" OG  SER A 133 "
            pdb=" OE1 GLU A 135 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" O4  NAG D   2 "
            pdb=" O7  NAG D   2 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OD2 ASP A 199 "
            pdb=" OG1 THR A 202 "
     model   vdw
     2.256 3.040
  ... (remaining 60679 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 'C'
  selection = chain 'D'
  selection = chain 'E'
  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:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.300
  Find NCS groups from input model:        0.030
  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:0.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   8515  Z= 0.172
  Angle     :  0.745  16.502  11543  Z= 0.362
  Chirality :  0.041   0.203   1226
  Planarity :  0.005   0.090   1508
  Dihedral  : 21.029 123.539   3297
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  : 28.88 %
    Favored  : 71.00 %
  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:  1.22 (0.27), residues: 1000
  helix:  2.07 (0.21), residues: 605
  sheet: -0.25 (0.86), residues: 38
  loop : -1.35 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 471 
 TYR   0.019   0.001   TYR B 338 
 PHE   0.018   0.001   PHE A 110 
 TRP   0.010   0.001   TRP B 345 
 HIS   0.003   0.001   HIS B 351 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.17 ( 8505)
  covalent geometry    : angle       0.73798 /  0.36 (11515)
  SS BOND              : bond        0.00253 /  0.14 (    2)
  SS BOND              : angle       0.38200 /  0.17 (    4)
  hydrogen bonds       : bond        0.14031 /  9.59 (  482)
  hydrogen bonds       : angle       5.13183 /  3.76 ( 1407)
  link_BETA1-4         : bond        0.00571 /  0.36 (    4)
  link_BETA1-4         : angle       2.36309 /  1.27 (   12)
  link_NAG-ASN         : bond        0.00301 /  0.17 (    4)
  link_NAG-ASN         : angle       2.29855 /  1.32 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A  471 ARG cc_start: 0.8378 (mtt90) cc_final: 0.7828 (mtt90)
REVERT: A  696 MET cc_start: 0.8437 (ttm) cc_final: 0.8191 (ttm)
REVERT: B  308 LEU cc_start: 0.8808 (tp) cc_final: 0.8494 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 108
  average time/residue: 0.0585
  time to fit residues: 9.6267
Evaluate side-chains
  102 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  377 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0170
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    8.9990
   overall best weight:    0.7018

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 180 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.145429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.101745 restraints weight = 15783.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.105941 restraints weight = 9264.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.108697 restraints weight = 6808.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.110379 restraints weight = 5654.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.110990 restraints weight = 5057.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.0821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8515  Z= 0.129
  Angle     :  0.642  10.377  11543  Z= 0.311
  Chirality :  0.041   0.208   1226
  Planarity :  0.005   0.061   1508
  Dihedral  : 14.751 109.385   1301
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 25.89 %
    Favored  : 71.92 %
  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:  1.54 (0.27), residues: 1000
  helix:  2.27 (0.21), residues: 613
  sheet:  0.17 (0.82), residues: 38
  loop : -1.26 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 354 
 TYR   0.020   0.001   TYR B 338 
 PHE   0.015   0.001   PHE A 622 
 TRP   0.009   0.001   TRP B 345 
 HIS   0.004   0.001   HIS A 481 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.13 ( 8505)
  covalent geometry    : angle       0.63104 /  0.31 (11515)
  SS BOND              : bond        0.00235 /  0.13 (    2)
  SS BOND              : angle       0.82665 /  0.51 (    4)
  hydrogen bonds       : bond        0.05090 /  3.46 (  482)
  hydrogen bonds       : angle       4.01664 /  2.94 ( 1407)
  link_BETA1-4         : bond        0.00326 /  0.20 (    4)
  link_BETA1-4         : angle       2.97107 /  1.67 (   12)
  link_NAG-ASN         : bond        0.00421 /  0.25 (    4)
  link_NAG-ASN         : angle       2.38202 /  1.45 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 TYR cc_start: 0.9302 (t80) cc_final: 0.8943 (t80)
REVERT: A  234 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8124 (mp0)
REVERT: A  444 ARG cc_start: 0.8957 (ttm170) cc_final: 0.8410 (mtt-85)
REVERT: B  338 TYR cc_start: 0.8668 (m-10) cc_final: 0.8445 (m-10)
  outliers start: 19
  outliers final: 8
  residues processed: 122
  average time/residue: 0.0527
  time to fit residues: 9.8785
Evaluate side-chains
  111 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  674 LEU
Chi-restraints excluded: chain B residue  139 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0870
   chunk 83 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    1.1562

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 481 HIS
** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 657 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.145479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.103240 restraints weight = 15973.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.107377 restraints weight = 10346.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.108209 restraints weight = 7246.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.108640 restraints weight = 6993.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.108850 restraints weight = 6756.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.1104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8515  Z= 0.132
  Angle     :  0.610   9.575  11543  Z= 0.292
  Chirality :  0.040   0.242   1226
  Planarity :  0.004   0.059   1508
  Dihedral  : 13.225 107.930   1301
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 24.74 %
    Favored  : 71.81 %
  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:  1.71 (0.27), residues: 1000
  helix:  2.30 (0.21), residues: 624
  sheet:  0.51 (0.74), residues: 48
  loop : -1.14 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 471 
 TYR   0.012   0.001   TYR B 267 
 PHE   0.012   0.001   PHE A 331 
 TRP   0.014   0.001   TRP B 345 
 HIS   0.004   0.001   HIS A 205 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 8505)
  covalent geometry    : angle       0.59786 /  0.29 (11515)
  SS BOND              : bond        0.00084 /  0.05 (    2)
  SS BOND              : angle       0.98382 /  0.59 (    4)
  hydrogen bonds       : bond        0.04805 /  3.29 (  482)
  hydrogen bonds       : angle       3.86191 /  2.82 ( 1407)
  link_BETA1-4         : bond        0.00592 /  0.34 (    4)
  link_BETA1-4         : angle       2.82501 /  1.61 (   12)
  link_NAG-ASN         : bond        0.00344 /  0.22 (    4)
  link_NAG-ASN         : angle       2.50582 /  1.49 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7971 (pt0)
REVERT: A  234 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8051 (mp0)
REVERT: A  444 ARG cc_start: 0.8957 (ttm170) cc_final: 0.8560 (mtt-85)
REVERT: B  345 TRP cc_start: 0.8736 (m-90) cc_final: 0.8445 (m-90)
  outliers start: 30
  outliers final: 15
  residues processed: 124
  average time/residue: 0.0556
  time to fit residues: 10.6232
Evaluate side-chains
  117 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  674 LEU
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  347 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 86 optimal weight:    0.5980
   chunk 87 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 71 optimal weight:    0.2980
   chunk 97 optimal weight:    0.7980
   chunk 58 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.145609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.101934 restraints weight = 16032.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.106161 restraints weight = 9398.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.108898 restraints weight = 6882.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.110611 restraints weight = 5712.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.111444 restraints weight = 5091.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8515  Z= 0.120
  Angle     :  0.610   9.410  11543  Z= 0.288
  Chirality :  0.040   0.263   1226
  Planarity :  0.004   0.057   1508
  Dihedral  : 12.521 107.609   1301
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 26.12 %
    Favored  : 71.00 %
  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:  1.76 (0.27), residues: 1000
  helix:  2.33 (0.21), residues: 624
  sheet:  0.68 (0.75), residues: 48
  loop : -1.12 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 471 
 TYR   0.021   0.001   TYR A 343 
 PHE   0.010   0.001   PHE A 331 
 TRP   0.010   0.001   TRP B 345 
 HIS   0.004   0.001   HIS A 205 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 ( 8505)
  covalent geometry    : angle       0.59827 /  0.28 (11515)
  SS BOND              : bond        0.00149 /  0.08 (    2)
  SS BOND              : angle       0.80323 /  0.48 (    4)
  hydrogen bonds       : bond        0.04484 /  3.06 (  482)
  hydrogen bonds       : angle       3.75735 /  2.74 ( 1407)
  link_BETA1-4         : bond        0.00565 /  0.34 (    4)
  link_BETA1-4         : angle       2.99263 /  1.72 (   12)
  link_NAG-ASN         : bond        0.00314 /  0.19 (    4)
  link_NAG-ASN         : angle       2.41114 /  1.45 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 TYR cc_start: 0.9353 (t80) cc_final: 0.9152 (t80)
REVERT: A  234 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8058 (mp0)
REVERT: A  444 ARG cc_start: 0.9019 (ttm170) cc_final: 0.8474 (mtt-85)
REVERT: A  485 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8142 (mt-10)
REVERT: B  244 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8545 (tt)
REVERT: B  345 TRP cc_start: 0.8558 (m-90) cc_final: 0.8354 (m-90)
  outliers start: 25
  outliers final: 14
  residues processed: 118
  average time/residue: 0.0625
  time to fit residues: 11.3662
Evaluate side-chains
  118 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  244 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   chunk 98 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 70 optimal weight:    8.9990
   chunk 24 optimal weight:    0.6980
   chunk 94 optimal weight:    8.9990
   chunk 74 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 54 optimal weight:    0.4980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 180 GLN
A 481 HIS
** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 657 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.149139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.105733 restraints weight = 15494.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.110045 restraints weight = 8825.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.112890 restraints weight = 6380.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.114689 restraints weight = 5237.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.115700 restraints weight = 4644.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8515  Z= 0.111
  Angle     :  0.607  12.269  11543  Z= 0.284
  Chirality :  0.039   0.278   1226
  Planarity :  0.004   0.055   1508
  Dihedral  : 11.746 107.105   1301
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 26.47 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.84 (0.27), residues: 1000
  helix:  2.35 (0.21), residues: 626
  sheet:  0.86 (0.76), residues: 48
  loop : -1.05 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 471 
 TYR   0.024   0.001   TYR A 343 
 PHE   0.009   0.001   PHE B 256 
 TRP   0.007   0.001   TRP B 345 
 HIS   0.004   0.001   HIS A 205 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 ( 8505)
  covalent geometry    : angle       0.59445 /  0.28 (11515)
  SS BOND              : bond        0.00172 /  0.10 (    2)
  SS BOND              : angle       0.73174 /  0.41 (    4)
  hydrogen bonds       : bond        0.04075 /  2.79 (  482)
  hydrogen bonds       : angle       3.61009 /  2.64 ( 1407)
  link_BETA1-4         : bond        0.00568 /  0.34 (    4)
  link_BETA1-4         : angle       3.13577 /  1.83 (   12)
  link_NAG-ASN         : bond        0.00276 /  0.16 (    4)
  link_NAG-ASN         : angle       2.31641 /  1.39 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7899 (pt0)
REVERT: A  180 GLN cc_start: 0.9133 (tp40) cc_final: 0.8700 (tp-100)
REVERT: A  234 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7963 (mp0)
REVERT: A  444 ARG cc_start: 0.8982 (ttm170) cc_final: 0.8467 (mtt-85)
REVERT: A  471 ARG cc_start: 0.8330 (mtt90) cc_final: 0.7674 (mtt90)
REVERT: A  485 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8141 (mt-10)
REVERT: B  181 MET cc_start: 0.9429 (mmm) cc_final: 0.9009 (mmp)
REVERT: B  244 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8481 (tt)
REVERT: B  345 TRP cc_start: 0.8564 (m-90) cc_final: 0.8358 (m-90)
  outliers start: 29
  outliers final: 18
  residues processed: 126
  average time/residue: 0.0621
  time to fit residues: 11.8643
Evaluate side-chains
  119 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0270
   chunk 83 optimal weight:    8.9990
   chunk 77 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.6238

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 657 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.149445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.106170 restraints weight = 15388.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.110500 restraints weight = 8803.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.113371 restraints weight = 6373.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.115165 restraints weight = 5237.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.116158 restraints weight = 4648.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8515  Z= 0.110
  Angle     :  0.612  11.486  11543  Z= 0.284
  Chirality :  0.040   0.287   1226
  Planarity :  0.004   0.055   1508
  Dihedral  : 11.232 106.980   1301
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 27.04 %
    Favored  : 69.85 %
  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:  1.94 (0.27), residues: 1000
  helix:  2.39 (0.21), residues: 626
  sheet:  1.03 (0.76), residues: 48
  loop : -0.96 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 471 
 TYR   0.022   0.001   TYR A 343 
 PHE   0.009   0.001   PHE A 676 
 TRP   0.006   0.001   TRP B 345 
 HIS   0.003   0.000   HIS A 205 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 ( 8505)
  covalent geometry    : angle       0.59967 /  0.28 (11515)
  SS BOND              : bond        0.00126 /  0.07 (    2)
  SS BOND              : angle       0.65593 /  0.36 (    4)
  hydrogen bonds       : bond        0.03898 /  2.66 (  482)
  hydrogen bonds       : angle       3.58652 /  2.62 ( 1407)
  link_BETA1-4         : bond        0.00667 /  0.40 (    4)
  link_BETA1-4         : angle       3.19455 /  1.90 (   12)
  link_NAG-ASN         : bond        0.00257 /  0.14 (    4)
  link_NAG-ASN         : angle       2.24912 /  1.36 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   37 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8267 (mm)
REVERT: A   86 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7992 (pt0)
REVERT: A  180 GLN cc_start: 0.9121 (tp40) cc_final: 0.8604 (tp-100)
REVERT: A  234 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7972 (mp0)
REVERT: A  444 ARG cc_start: 0.8961 (ttm170) cc_final: 0.8654 (mtt-85)
REVERT: A  471 ARG cc_start: 0.8356 (mtt90) cc_final: 0.7762 (mtt90)
REVERT: A  485 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8069 (mt-10)
REVERT: B  113 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7392 (tt)
REVERT: B  181 MET cc_start: 0.9442 (mmm) cc_final: 0.9043 (mmp)
  outliers start: 27
  outliers final: 14
  residues processed: 120
  average time/residue: 0.0566
  time to fit residues: 10.4632
Evaluate side-chains
  118 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0570
   chunk 36 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7498

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 536 HIS
** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.150077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.104490 restraints weight = 15514.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.108975 restraints weight = 9060.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.111858 restraints weight = 6631.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.113698 restraints weight = 5499.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.114441 restraints weight = 4906.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8515  Z= 0.115
  Angle     :  0.633  13.113  11543  Z= 0.291
  Chirality :  0.040   0.296   1226
  Planarity :  0.004   0.055   1508
  Dihedral  : 10.823 107.196   1301
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 27.73 %
    Favored  : 69.28 %
  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:  2.02 (0.27), residues: 1000
  helix:  2.45 (0.21), residues: 623
  sheet:  1.17 (0.77), residues: 48
  loop : -0.91 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 471 
 TYR   0.017   0.001   TYR A 343 
 PHE   0.012   0.001   PHE B 256 
 TRP   0.020   0.001   TRP B 345 
 HIS   0.004   0.000   HIS A 205 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 8505)
  covalent geometry    : angle       0.62057 /  0.29 (11515)
  SS BOND              : bond        0.00156 /  0.09 (    2)
  SS BOND              : angle       0.71075 /  0.37 (    4)
  hydrogen bonds       : bond        0.03879 /  2.66 (  482)
  hydrogen bonds       : angle       3.55014 /  2.60 ( 1407)
  link_BETA1-4         : bond        0.00602 /  0.36 (    4)
  link_BETA1-4         : angle       3.23608 /  1.92 (   12)
  link_NAG-ASN         : bond        0.00271 /  0.16 (    4)
  link_NAG-ASN         : angle       2.18700 /  1.31 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8257 (mm)
REVERT: A   86 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7898 (pt0)
REVERT: A  234 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7894 (mp0)
REVERT: A  444 ARG cc_start: 0.8983 (ttm170) cc_final: 0.8564 (mtt-85)
REVERT: A  471 ARG cc_start: 0.8355 (mtt90) cc_final: 0.7714 (mtt90)
REVERT: A  485 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8056 (mt-10)
REVERT: B  113 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7426 (tt)
REVERT: B  181 MET cc_start: 0.9429 (mmm) cc_final: 0.9046 (mmp)
  outliers start: 26
  outliers final: 14
  residues processed: 117
  average time/residue: 0.0564
  time to fit residues: 10.1733
Evaluate side-chains
  116 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0070
   chunk 16 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 92 optimal weight:    7.9990
   chunk 83 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.5998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 481 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.148176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.103862 restraints weight = 16161.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.108117 restraints weight = 9587.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.110954 restraints weight = 7087.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.112700 restraints weight = 5888.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.113361 restraints weight = 5263.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8515  Z= 0.110
  Angle     :  0.633  15.627  11543  Z= 0.289
  Chirality :  0.040   0.300   1226
  Planarity :  0.004   0.055   1508
  Dihedral  : 10.485 106.000   1301
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 27.85 %
    Favored  : 69.62 %
  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:  2.06 (0.27), residues: 1000
  helix:  2.47 (0.21), residues: 625
  sheet:  1.26 (0.77), residues: 48
  loop : -0.90 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 471 
 TYR   0.022   0.001   TYR A 343 
 PHE   0.009   0.001   PHE A 154 
 TRP   0.022   0.001   TRP B 345 
 HIS   0.006   0.001   HIS B 169 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.11 ( 8505)
  covalent geometry    : angle       0.62042 /  0.29 (11515)
  SS BOND              : bond        0.00125 /  0.07 (    2)
  SS BOND              : angle       0.74920 /  0.39 (    4)
  hydrogen bonds       : bond        0.03733 /  2.56 (  482)
  hydrogen bonds       : angle       3.51273 /  2.57 ( 1407)
  link_BETA1-4         : bond        0.00609 /  0.36 (    4)
  link_BETA1-4         : angle       3.27815 /  1.95 (   12)
  link_NAG-ASN         : bond        0.00248 /  0.14 (    4)
  link_NAG-ASN         : angle       2.14431 /  1.30 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7974 (pt0)
REVERT: A  234 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7823 (mp0)
REVERT: A  444 ARG cc_start: 0.8925 (ttm170) cc_final: 0.8554 (mtt-85)
REVERT: A  471 ARG cc_start: 0.8369 (mtt90) cc_final: 0.7732 (mtt90)
REVERT: A  485 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8056 (mt-10)
REVERT: B  113 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7563 (tt)
REVERT: B  181 MET cc_start: 0.9428 (mmm) cc_final: 0.9048 (mmp)
  outliers start: 22
  outliers final: 15
  residues processed: 110
  average time/residue: 0.0546
  time to fit residues: 9.3209
Evaluate side-chains
  112 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 83 optimal weight:    8.9990
   chunk 5 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 50 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 96 optimal weight:   10.0000
   chunk 49 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 167 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.145121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.102091 restraints weight = 16818.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.106240 restraints weight = 9990.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.109004 restraints weight = 7370.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.110709 restraints weight = 6121.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.111817 restraints weight = 5466.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8515  Z= 0.136
  Angle     :  0.666  15.518  11543  Z= 0.306
  Chirality :  0.041   0.325   1226
  Planarity :  0.004   0.057   1508
  Dihedral  : 10.118 106.327   1301
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 27.73 %
    Favored  : 69.51 %
  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:  2.05 (0.27), residues: 1000
  helix:  2.45 (0.21), residues: 627
  sheet:  1.27 (0.77), residues: 49
  loop : -0.89 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 471 
 TYR   0.024   0.001   TYR A 257 
 PHE   0.013   0.001   PHE A 676 
 TRP   0.022   0.001   TRP B 345 
 HIS   0.005   0.001   HIS A 303 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.14 ( 8505)
  covalent geometry    : angle       0.65397 /  0.30 (11515)
  SS BOND              : bond        0.00157 /  0.09 (    2)
  SS BOND              : angle       0.62350 /  0.32 (    4)
  hydrogen bonds       : bond        0.04299 /  2.97 (  482)
  hydrogen bonds       : angle       3.57824 /  2.62 ( 1407)
  link_BETA1-4         : bond        0.00585 /  0.34 (    4)
  link_BETA1-4         : angle       3.28558 /  1.96 (   12)
  link_NAG-ASN         : bond        0.00197 /  0.12 (    4)
  link_NAG-ASN         : angle       2.21431 /  1.34 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7742 (pt0)
REVERT: A  104 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7625 (mm)
REVERT: A  234 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7815 (mp0)
REVERT: A  444 ARG cc_start: 0.8900 (ttm170) cc_final: 0.8551 (mtt-85)
REVERT: A  471 ARG cc_start: 0.8411 (mtt90) cc_final: 0.7729 (mtt90)
REVERT: A  485 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8017 (mt-10)
REVERT: B  113 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7647 (tt)
REVERT: B  181 MET cc_start: 0.9441 (mmm) cc_final: 0.9055 (mmp)
  outliers start: 24
  outliers final: 15
  residues processed: 111
  average time/residue: 0.0605
  time to fit residues: 10.3268
Evaluate side-chains
  113 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0770
   chunk 95 optimal weight:    0.4980
   chunk 97 optimal weight:    0.7980
   chunk 60 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0270
   chunk 59 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.4396

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.147599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.104687 restraints weight = 16821.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.108963 restraints weight = 9956.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.111796 restraints weight = 7327.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.113542 restraints weight = 6069.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.114696 restraints weight = 5411.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8515  Z= 0.111
  Angle     :  0.661  16.375  11543  Z= 0.300
  Chirality :  0.040   0.304   1226
  Planarity :  0.004   0.054   1508
  Dihedral  :  9.993 106.626   1301
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 29.23 %
    Favored  : 68.81 %
  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:  2.04 (0.28), residues: 1000
  helix:  2.40 (0.21), residues: 632
  sheet:  1.43 (0.78), residues: 49
  loop : -0.86 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 471 
 TYR   0.024   0.001   TYR A 343 
 PHE   0.009   0.001   PHE A 154 
 TRP   0.023   0.001   TRP B 345 
 HIS   0.004   0.001   HIS B 169 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.11 ( 8505)
  covalent geometry    : angle       0.64968 /  0.30 (11515)
  SS BOND              : bond        0.00179 /  0.10 (    2)
  SS BOND              : angle       0.58290 /  0.30 (    4)
  hydrogen bonds       : bond        0.03683 /  2.53 (  482)
  hydrogen bonds       : angle       3.42597 /  2.51 ( 1407)
  link_BETA1-4         : bond        0.00605 /  0.35 (    4)
  link_BETA1-4         : angle       3.34081 /  1.98 (   12)
  link_NAG-ASN         : bond        0.00285 /  0.16 (    4)
  link_NAG-ASN         : angle       2.04514 /  1.26 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7926 (pt0)
REVERT: A  234 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7819 (mp0)
REVERT: A  444 ARG cc_start: 0.8888 (ttm170) cc_final: 0.8575 (mtt-85)
REVERT: A  471 ARG cc_start: 0.8361 (mtt90) cc_final: 0.7699 (mtt90)
REVERT: A  485 GLU cc_start: 0.8622 (mt-10) cc_final: 0.7983 (mt-10)
REVERT: B  143 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8227 (tm-30)
REVERT: B  181 MET cc_start: 0.9437 (mmm) cc_final: 0.9028 (mmp)
REVERT: B  351 HIS cc_start: 0.8708 (m90) cc_final: 0.8306 (m90)
  outliers start: 17
  outliers final: 12
  residues processed: 113
  average time/residue: 0.0636
  time to fit residues: 11.1029
Evaluate side-chains
  111 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    0.0570
   chunk 19 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 69 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.7298

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.145845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.103778 restraints weight = 15758.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.107443 restraints weight = 10090.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.109881 restraints weight = 7684.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.111476 restraints weight = 6512.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.112327 restraints weight = 5866.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8515  Z= 0.116
  Angle     :  0.653  16.100  11543  Z= 0.298
  Chirality :  0.040   0.322   1226
  Planarity :  0.004   0.056   1508
  Dihedral  :  9.726 107.010   1301
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 28.77 %
    Favored  : 69.51 %
  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:  2.06 (0.28), residues: 1000
  helix:  2.45 (0.21), residues: 628
  sheet:  1.44 (0.77), residues: 49
  loop : -0.92 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 471 
 TYR   0.026   0.001   TYR A 343 
 PHE   0.015   0.001   PHE B 256 
 TRP   0.031   0.001   TRP B 345 
 HIS   0.004   0.001   HIS A 303 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 ( 8505)
  covalent geometry    : angle       0.64102 /  0.30 (11515)
  SS BOND              : bond        0.00121 /  0.07 (    2)
  SS BOND              : angle       0.69093 /  0.36 (    4)
  hydrogen bonds       : bond        0.03755 /  2.58 (  482)
  hydrogen bonds       : angle       3.45831 /  2.53 ( 1407)
  link_BETA1-4         : bond        0.00540 /  0.31 (    4)
  link_BETA1-4         : angle       3.33648 /  1.98 (   12)
  link_NAG-ASN         : bond        0.00233 /  0.13 (    4)
  link_NAG-ASN         : angle       2.10599 /  1.29 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1312.50 seconds
wall clock time: 23 minutes 14.88 seconds (1394.88 seconds total)