Starting phenix.real_space_refine
on Thu Jul  2 05:13:19 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8t2u_40988/07_2026/8t2u_40988.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t2u_40988/07_2026/8t2u_40988.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8t2u_40988/07_2026/8t2u_40988.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8t2u_40988/07_2026/8t2u_40988.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t2u_40988/07_2026/8t2u_40988.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t2u_40988/07_2026/8t2u_40988.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t2u_40988/07_2026/8t2u_40988.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t2u_40988/07_2026/8t2u_40988.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.016
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: 6
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     Mg      1      5.21       5
     S      28      5.16       5
     C    4128      2.51       5
     N    1099      2.21       5
     O    1290      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 6552
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 448, 3435
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 26, 'TRANS': 421}
    Chain: "B"
      Number of atoms: 2895
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 368, 2886
          Classifications: {'peptide': 368}
          Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 349}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 368, 2886
          Classifications: {'peptide': 368}
          Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 349}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2927
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 56
          Unusual residues: {'MPT': 1}
          Classifications: {'peptide': 6, 'undetermined': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1}
            Not linked:
              pdbres="MPT C   1 "
              pdbres="HRG C   2 "
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'MPT:plan-1': 1, 'HRG:plan-2': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 2, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen chiralities: 4
    Chain: "E"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 2, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen chiralities: 4
    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 chiralities: 2
    Chain: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 18
          Unusual residues: {' CA': 4, 'NAG': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 19
          Unusual residues: {' CA': 2, ' MG': 1, 'NAG': 1}
          Classifications: {'undetermined': 4, 'water': 2}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AGLN B 272 " occ=0.48
      ... (16 atoms not shown)
      pdb=" NE2BGLN B 272 " occ=0.52
  Time building chain proxies: 2.18, per 1000 atoms: 0.33
  Number of scatterers: 6552
  At special positions: 0
  Unit cell: (81, 82.08, 127.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      6     19.99
     S      28     16.00
     Mg      1     11.99
     O    1290      8.00
     N    1099      7.00
     C    4128      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  56 " - pdb=" SG  CYS A  65 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 130 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 146 " - pdb=" SG  CYS A 167 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 177 " - pdb=" SG  CYS B 184 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 232 " - pdb=" SG  CYS B 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 374 " - pdb=" SG  CYS B 386 " distance=2.04

  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 additional links: simple=1, symmetry=0
    Simple link:   pdb=" SG  MPT C   1 " - pdb=" SG  CYS C   7 "
  Number of custom bonds: simple=2, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " BMA D   3 " - " BMA D   4 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
    BETA1-6
      " BMA E   3 " - " BMA E   4 "
    NAG-ASN
      " NAG A1101 " - " ASN A 249 "
      " NAG B2004 " - " ASN B  99 "
      " NAG D   1 " - " ASN A  15 "
      " NAG E   1 " - " ASN B 320 "
      " NAG F   1 " - " ASN B 371 "
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 562.4 milliseconds
  

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1496

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 13 sheets defined
      16.4% alpha, 25.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 151 through 158
      removed outlier: 3.560A  pdb=" N   ASN A 158 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 192
    Processing helix  chain 'A' and resid 200 through 207
    Processing helix  chain 'A' and resid 227 through 231
    Processing helix  chain 'A' and resid 318 through 320
      No H-bonds generated for 'chain 'A' and resid 318 through 320'
    Processing helix  chain 'B' and resid 123 through 126
    Processing helix  chain 'B' and resid 127 through 146
      removed outlier: 3.743A  pdb=" N   LEU B 138 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 174
    Processing helix  chain 'B' and resid 199 through 210
      removed outlier: 3.681A  pdb=" N   GLN B 210 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 231
      removed outlier: 3.813A  pdb=" N   ALA B 225 " --> pdb=" O   GLY B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 264
      removed outlier: 3.759A  pdb=" N   ARG B 261 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 287
      removed outlier: 4.434A  pdb=" N   THR B 285 " --> pdb=" O   SER B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 302
    Processing helix  chain 'B' and resid 314 through 325
      removed outlier: 3.674A  pdb=" N   TYR B 318 " --> pdb=" O   VAL B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 350
      removed outlier: 3.941A  pdb=" N   LEU B 343 " --> pdb=" O   ASN B 339 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LYS B 350 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12
    Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 27
      removed outlier: 3.734A  pdb=" N   SER A  22 " --> pdb=" O   GLY A  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 79
    Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 100
      removed outlier: 3.547A  pdb=" N   SER A  96 " --> pdb=" O   CYS A 107 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 175
    Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 242
      removed outlier: 6.789A  pdb=" N   VAL A 267 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   ARG A 279 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ILE A 269 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296
    Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 317
    Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 362
    Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 65
      removed outlier: 6.013A  pdb=" N   ARG B  87 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 83 through 84
    Processing sheet with id=AB3, first strand: chain 'B' and resid 190 through 197
      removed outlier: 4.951A  pdb=" N   HIS B 192 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ALA B 155 " --> pdb=" O   HIS B 192 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   LEU B 196 " --> pdb=" O   ILE B 151 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   ILE B 151 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ASP B 113 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   VAL B 247 " --> pdb=" O   ASP B 113 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   TYR B 115 " --> pdb=" O   VAL B 247 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   THR B 249 " --> pdb=" O   TYR B 115 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   LEU B 117 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   HIS B 244 " --> pdb=" O   ASN B 305 " (cutoff:3.500A)
      removed outlier: 8.132A  pdb=" N   ILE B 307 " --> pdb=" O   HIS B 244 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   LEU B 246 " --> pdb=" O   ILE B 307 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   ALA B 309 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   PHE B 248 " --> pdb=" O   ALA B 309 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 353 through 354

    224 hydrogen bonds defined for protein.
    564 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: 1.01

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.16 -     1.30: 1097
        1.30 -     1.44: 1832
        1.44 -     1.58: 3720
        1.58 -     1.72: 1
        1.72 -     1.86: 41
  Bond restraints: 6691
  Sorted by residual:
  bond pdb=" C   MET B 287 "
       pdb=" N   ASP B 288 "
    ideal  model  delta    sigma   weight residual
    1.331  1.243  0.088 1.26e-02 6.30e+03 4.87e+01
  bond pdb=" C   PRO A 362 "
       pdb=" O   PRO A 362 "
    ideal  model  delta    sigma   weight residual
    1.235  1.158  0.077 1.30e-02 5.92e+03 3.55e+01
  bond pdb=" C   GLN A  18 "
       pdb=" O   GLN A  18 "
    ideal  model  delta    sigma   weight residual
    1.233  1.166  0.067 1.29e-02 6.01e+03 2.69e+01
  bond pdb=" C   VAL A 239 "
       pdb=" O   VAL A 239 "
    ideal  model  delta    sigma   weight residual
    1.236  1.282 -0.046 9.90e-03 1.02e+04 2.19e+01
  bond pdb=" CA  ALA A 185 "
       pdb=" CB  ALA A 185 "
    ideal  model  delta    sigma   weight residual
    1.532  1.476  0.056 1.26e-02 6.30e+03 1.95e+01
  ... (remaining 6686 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 7463
        2.18 -     4.37: 1511
        4.37 -     6.55: 96
        6.55 -     8.73: 16
        8.73 -    10.91: 3
  Bond angle restraints: 9089
  Sorted by residual:
  angle pdb=" N   MET B 124 "
        pdb=" CA  MET B 124 "
        pdb=" C   MET B 124 "
      ideal   model   delta    sigma   weight residual
     112.34  104.96    7.38 1.30e+00 5.92e-01 3.22e+01
  angle pdb=" N   LYS B 253 "
        pdb=" CA  LYS B 253 "
        pdb=" C   LYS B 253 "
      ideal   model   delta    sigma   weight residual
     110.43  103.18    7.25 1.31e+00 5.83e-01 3.07e+01
  angle pdb=" C   GLN B 267 "
        pdb=" N   PRO B 268 "
        pdb=" CA  PRO B 268 "
      ideal   model   delta    sigma   weight residual
     119.84  126.70   -6.86 1.25e+00 6.40e-01 3.01e+01
  angle pdb=" CA  GLY A 193 "
        pdb=" C   GLY A 193 "
        pdb=" O   GLY A 193 "
      ideal   model   delta    sigma   weight residual
     122.22  118.73    3.49 6.50e-01 2.37e+00 2.88e+01
  angle pdb=" C   PHE A 417 "
        pdb=" CA  PHE A 417 "
        pdb=" CB  PHE A 417 "
      ideal   model   delta    sigma   weight residual
     109.90  102.04    7.86 1.56e+00 4.11e-01 2.54e+01
  ... (remaining 9084 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.55: 3756
       34.55 -    69.10: 126
       69.10 -   103.66: 12
      103.66 -   138.21: 0
      138.21 -   172.76: 1
  Dihedral angle restraints: 3895
    sinusoidal: 1544
      harmonic: 2351
  Sorted by residual:
  dihedral pdb=" CB  CYS B 232 "
           pdb=" SG  CYS B 232 "
           pdb=" SG  CYS B 273 "
           pdb=" CB  CYS B 273 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.81   47.19     1      1.00e+01 1.00e-02 3.08e+01
  dihedral pdb=" CA  PHE B 370 "
           pdb=" C   PHE B 370 "
           pdb=" N   ASN B 371 "
           pdb=" CA  ASN B 371 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.44   24.56     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CB  HRG C   2 "
           pdb=" CG  HRG C   2 "
           pdb=" CG' HRG C   2 "
           pdb=" CD  HRG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     261.95   89.19  172.76     1      3.00e+01 1.11e-03 2.12e+01
  ... (remaining 3892 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 890
       0.118 -    0.236: 134
       0.236 -    0.354: 2
       0.354 -    0.472: 0
       0.472 -    0.590: 1
  Chirality restraints: 1027
  Sorted by residual:
  chirality pdb=" C1  BMA E   3 "
            pdb=" O4  NAG E   2 "
            pdb=" C2  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-02 2.50e+03 8.02e+01
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.31   -0.09 2.00e-02 2.50e+03 2.07e+01
  chirality pdb=" C1  BMA D   3 "
            pdb=" O4  NAG D   2 "
            pdb=" C2  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.32   -0.08 2.00e-02 2.50e+03 1.71e+01
  ... (remaining 1024 not shown)

  Planarity restraints: 1180
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B2004 "    0.242 2.00e-02 2.50e+03   2.06e-01 5.30e+02
        pdb=" C7  NAG B2004 "   -0.116 2.00e-02 2.50e+03
        pdb=" C8  NAG B2004 "    0.185 2.00e-02 2.50e+03
        pdb=" N2  NAG B2004 "   -0.325 2.00e-02 2.50e+03
        pdb=" O7  NAG B2004 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   2 "   -0.176 2.00e-02 2.50e+03   1.50e-01 2.83e+02
        pdb=" C7  NAG F   2 "    0.084 2.00e-02 2.50e+03
        pdb=" C8  NAG F   2 "   -0.143 2.00e-02 2.50e+03
        pdb=" N2  NAG F   2 "    0.234 2.00e-02 2.50e+03
        pdb=" O7  NAG F   2 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   1 "   -0.182 2.00e-02 2.50e+03   1.49e-01 2.76e+02
        pdb=" C7  NAG F   1 "    0.066 2.00e-02 2.50e+03
        pdb=" C8  NAG F   1 "   -0.139 2.00e-02 2.50e+03
        pdb=" N2  NAG F   1 "    0.230 2.00e-02 2.50e+03
        pdb=" O7  NAG F   1 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1177 not shown)

  Histogram of nonbonded interaction distances:
        1.81 -     2.43: 101
        2.43 -     3.04: 4311
        3.04 -     3.66: 10616
        3.66 -     4.28: 15609
        4.28 -     4.90: 25335
  Nonbonded interactions: 55972
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 303 "
            pdb="CA    CA A1105 "
     model   vdw
     1.807 2.510
  nonbonded pdb=" OD1 ASN A 299 "
            pdb="CA    CA A1105 "
     model   vdw
     1.856 2.510
  nonbonded pdb=" OG  SER B 121 "
            pdb="MG    MG B2001 "
     model   vdw
     1.889 2.170
  nonbonded pdb=" OG  SER B 123 "
            pdb="MG    MG B2001 "
     model   vdw
     2.107 2.170
  nonbonded pdb="MG    MG B2001 "
            pdb=" O   HOH B3101 "
     model   vdw
     2.166 2.170
  ... (remaining 55967 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 'D'
  selection = chain 'E'
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.580
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
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      :  0.014   0.162   6712  Z= 1.020
  Angle     :  1.697  23.738   9139  Z= 1.138
  Chirality :  0.081   0.590   1027
  Planarity :  0.011   0.206   1175
  Dihedral  : 17.120 172.759   2378
  Min Nonbonded Distance : 1.807

Molprobity Statistics.
  All-atom Clashscore : 30.06
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.12 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 20.81 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.18 (0.28), residues: 816
  helix: -1.68 (0.46), residues: 102
  sheet: -0.96 (0.33), residues: 228
  loop : -1.65 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARG A 165 
 TYR   0.047   0.009   TYR A 288 
 PHE   0.074   0.010   PHE A  21 
 TRP   0.036   0.007   TRP A 110 
 HIS   0.018   0.005   HIS B 255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01390 /  0.99 ( 6691)
  covalent geometry    : angle       1.65557 /  1.13 ( 9089)
  SS BOND              : bond        0.01426 /  0.91 (    6)
  SS BOND              : angle       1.87863 /  1.07 (   12)
  hydrogen bonds       : bond        0.14342 /  9.69 (  224)
  hydrogen bonds       : angle       7.94152 /  5.78 (  564)
  Misc. bond           : bond        0.15493 / 10.74 (    2)
  link_BETA1-4         : bond        0.00787 /  0.53 (    6)
  link_BETA1-4         : angle       3.77616 /  2.30 (   18)
  link_BETA1-6         : bond        0.01530 /  1.02 (    1)
  link_BETA1-6         : angle       7.01020 /  5.19 (    3)
  link_NAG-ASN         : bond        0.00611 /  0.38 (    5)
  link_NAG-ASN         : angle       5.00578 /  3.04 (   15)
  link_SS              : bond        0.00987 /  0.66 (    1)
  link_SS              : angle      16.90657 / 12.04 (    2)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 66
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 ARG cc_start: 0.8167 (ptm160) cc_final: 0.7317 (mmm160)
REVERT: A  285 MET cc_start: 0.7220 (ttt) cc_final: 0.6886 (ttt)
REVERT: A  369 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8786 (p0)
REVERT: B  109 ASP cc_start: 0.8069 (m-30) cc_final: 0.7857 (p0)
REVERT: B  123 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8173 (p)
REVERT: B  261 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6856 (tpt-90)
  outliers start: 32
  outliers final: 10
  residues processed: 94
  average time/residue: 0.0844
  time to fit residues: 10.3795
Evaluate side-chains
  67 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  373 ASP
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   95 ASP
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  261 ARG
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  336 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 333 GLN
A 443 ASN
B 210 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.103118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.078136 restraints weight = 52862.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 7.82
r_work: 0.3501 rms_B_bonded: 7.41 restraints_weight: 2.0000
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3499
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3499 r_free = 0.3499    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3498
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.125   6712  Z= 0.189
  Angle     :  0.814  13.697   9139  Z= 0.391
  Chirality :  0.050   0.294   1027
  Planarity :  0.005   0.039   1175
  Dihedral  :  9.161 174.773    927
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.41 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 21.68 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.69 (0.29), residues: 816
  helix: -0.61 (0.53), residues: 103
  sheet: -0.74 (0.33), residues: 241
  loop : -1.45 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  87 
 TYR   0.028   0.003   TYR A 371 
 PHE   0.015   0.002   PHE A 191 
 TRP   0.016   0.002   TRP A 110 
 HIS   0.005   0.001   HIS B 255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00456 /  0.19 ( 6691)
  covalent geometry    : angle       0.78191 /  0.38 ( 9089)
  SS BOND              : bond        0.00434 /  0.24 (    6)
  SS BOND              : angle       0.95619 /  0.57 (   12)
  hydrogen bonds       : bond        0.04229 /  2.69 (  224)
  hydrogen bonds       : angle       6.63676 /  4.75 (  564)
  Misc. bond           : bond        0.00083 /  0.06 (    2)
  link_BETA1-4         : bond        0.01094 /  0.59 (    6)
  link_BETA1-4         : angle       3.28922 /  2.10 (   18)
  link_BETA1-6         : bond        0.01240 /  0.83 (    1)
  link_BETA1-6         : angle       3.38745 /  2.25 (    3)
  link_NAG-ASN         : bond        0.00793 /  0.42 (    5)
  link_NAG-ASN         : angle       4.09434 /  1.99 (   15)
  link_SS              : bond        0.00041 /  0.03 (    1)
  link_SS              : angle       0.53692 /  0.29 (    2)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8959 (mtpp) cc_final: 0.8409 (pptt)
REVERT: A   90 ARG cc_start: 0.8116 (ptm160) cc_final: 0.7277 (mmm160)
REVERT: B  277 SER cc_start: 0.8737 (t) cc_final: 0.8499 (p)
  outliers start: 19
  outliers final: 13
  residues processed: 74
  average time/residue: 0.0687
  time to fit residues: 7.0147
Evaluate side-chains
  68 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   95 ASP
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  351 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 78 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  79 GLN
B 133 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.102465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.079964 restraints weight = 23460.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 5.21
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3742 r_free = 0.3742    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7096
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.098   6712  Z= 0.170
  Angle     :  0.745  12.543   9139  Z= 0.359
  Chirality :  0.048   0.272   1027
  Planarity :  0.004   0.042   1175
  Dihedral  :  8.674 176.872    914
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 16.00
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.54 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 21.24 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.60 (0.29), residues: 816
  helix: -0.42 (0.53), residues: 102
  sheet: -0.71 (0.33), residues: 233
  loop : -1.39 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  87 
 TYR   0.028   0.002   TYR A 371 
 PHE   0.013   0.002   PHE A 191 
 TRP   0.014   0.002   TRP B 238 
 HIS   0.004   0.001   HIS B 255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.17 ( 6691)
  covalent geometry    : angle       0.71482 /  0.35 ( 9089)
  SS BOND              : bond        0.00190 /  0.10 (    6)
  SS BOND              : angle       1.07632 /  0.65 (   12)
  hydrogen bonds       : bond        0.03784 /  2.43 (  224)
  hydrogen bonds       : angle       6.29478 /  4.49 (  564)
  Misc. bond           : bond        0.00002 /  0.00 (    2)
  link_BETA1-4         : bond        0.01010 /  0.56 (    6)
  link_BETA1-4         : angle       2.94825 /  1.89 (   18)
  link_BETA1-6         : bond        0.01075 /  0.72 (    1)
  link_BETA1-6         : angle       2.63203 /  1.71 (    3)
  link_NAG-ASN         : bond        0.00697 /  0.38 (    5)
  link_NAG-ASN         : angle       3.93955 /  1.91 (   15)
  link_SS              : bond        0.00185 /  0.12 (    1)
  link_SS              : angle       0.50479 /  0.28 (    2)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 58
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6971 (pp)
REVERT: A   27 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8222 (pptt)
REVERT: A   88 LYS cc_start: 0.8199 (mttt) cc_final: 0.7719 (mtpt)
REVERT: A   90 ARG cc_start: 0.7816 (ptm160) cc_final: 0.7271 (mmm160)
REVERT: A  363 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6101 (tt)
  outliers start: 27
  outliers final: 14
  residues processed: 84
  average time/residue: 0.0636
  time to fit residues: 7.5237
Evaluate side-chains
  67 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 51
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  286 THR
Chi-restraints excluded: chain B residue  351 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 68 optimal weight:    0.0570
   chunk 65 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 69 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 78 optimal weight:    6.9990
   chunk 51 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    1.0100

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 228 GLN
B 269 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.101805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.080006 restraints weight = 19363.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 4.69
r_work: 0.3607 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3606
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3606
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.099   6712  Z= 0.179
  Angle     :  0.751  11.958   9139  Z= 0.362
  Chirality :  0.048   0.266   1027
  Planarity :  0.004   0.046   1175
  Dihedral  :  8.479 176.227    910
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 16.39
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.52 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 21.82 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 (0.29), residues: 816
  helix: -0.41 (0.53), residues: 103
  sheet: -0.61 (0.34), residues: 216
  loop : -1.37 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 303 
 TYR   0.028   0.002   TYR A 371 
 PHE   0.017   0.002   PHE B 248 
 TRP   0.017   0.002   TRP B 238 
 HIS   0.003   0.001   HIS B 255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00428 /  0.18 ( 6691)
  covalent geometry    : angle       0.72450 /  0.36 ( 9089)
  SS BOND              : bond        0.00199 /  0.11 (    6)
  SS BOND              : angle       1.05489 /  0.63 (   12)
  hydrogen bonds       : bond        0.03717 /  2.38 (  224)
  hydrogen bonds       : angle       6.17795 /  4.42 (  564)
  Misc. bond           : bond        0.00005 /  0.00 (    2)
  link_BETA1-4         : bond        0.00853 /  0.47 (    6)
  link_BETA1-4         : angle       2.80574 /  1.79 (   18)
  link_BETA1-6         : bond        0.00911 /  0.61 (    1)
  link_BETA1-6         : angle       2.33390 /  1.48 (    3)
  link_NAG-ASN         : bond        0.00669 /  0.37 (    5)
  link_NAG-ASN         : angle       3.80743 /  1.83 (   15)
  link_SS              : bond        0.00197 /  0.13 (    1)
  link_SS              : angle       0.48368 /  0.27 (    2)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 57
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7291 (pp)
REVERT: A   27 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8316 (pptt)
REVERT: A   90 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7349 (mmm160)
REVERT: A  363 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.5953 (tt)
REVERT: B  238 TRP cc_start: 0.6573 (m100) cc_final: 0.6059 (m100)
REVERT: B  387 MET cc_start: 0.7942 (mmm) cc_final: 0.7258 (tpp)
  outliers start: 29
  outliers final: 13
  residues processed: 82
  average time/residue: 0.0767
  time to fit residues: 8.8132
Evaluate side-chains
  66 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  406 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 46 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 33 optimal weight:    0.4980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  91 GLN ** 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 = 0.4177 r_free = 0.4177 target = 0.100767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.076473 restraints weight = 40606.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 6.88
r_work: 0.3492 rms_B_bonded: 6.78 restraints_weight: 2.0000
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3493
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3493 r_free = 0.3493    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3493 r_free = 0.3493    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3493
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.094   6712  Z= 0.189
  Angle     :  0.746  11.879   9139  Z= 0.360
  Chirality :  0.048   0.259   1027
  Planarity :  0.004   0.049   1175
  Dihedral  :  8.231 172.270    909
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 17.17
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.27 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 22.83 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.51 (0.29), residues: 816
  helix: -0.34 (0.54), residues: 103
  sheet: -0.63 (0.34), residues: 216
  loop : -1.34 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 239 
 TYR   0.023   0.002   TYR A 166 
 PHE   0.027   0.002   PHE B 248 
 TRP   0.014   0.001   TRP B 238 
 HIS   0.003   0.001   HIS B 255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.19 ( 6691)
  covalent geometry    : angle       0.72112 /  0.35 ( 9089)
  SS BOND              : bond        0.00162 /  0.10 (    6)
  SS BOND              : angle       1.15666 /  0.67 (   12)
  hydrogen bonds       : bond        0.03723 /  2.37 (  224)
  hydrogen bonds       : angle       6.09441 /  4.36 (  564)
  Misc. bond           : bond        0.00004 /  0.00 (    2)
  link_BETA1-4         : bond        0.00834 /  0.47 (    6)
  link_BETA1-4         : angle       2.70221 /  1.72 (   18)
  link_BETA1-6         : bond        0.00810 /  0.54 (    1)
  link_BETA1-6         : angle       2.11585 /  1.32 (    3)
  link_NAG-ASN         : bond        0.00658 /  0.37 (    5)
  link_NAG-ASN         : angle       3.63437 /  1.74 (   15)
  link_SS              : bond        0.00214 /  0.14 (    1)
  link_SS              : angle       0.47657 /  0.26 (    2)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 52
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7420 (pp)
REVERT: A   27 LYS cc_start: 0.8957 (mtpp) cc_final: 0.8367 (pptt)
REVERT: A   90 ARG cc_start: 0.8074 (ptm160) cc_final: 0.7303 (mmm160)
REVERT: A  197 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7089 (tm-30)
REVERT: A  363 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.5789 (tt)
REVERT: B  387 MET cc_start: 0.8099 (mmm) cc_final: 0.7622 (tpp)
REVERT: B  417 LYS cc_start: 0.9213 (ttmm) cc_final: 0.8993 (tptm)
  outliers start: 28
  outliers final: 19
  residues processed: 76
  average time/residue: 0.0644
  time to fit residues: 7.0288
Evaluate side-chains
  73 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 51
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  197 GLN
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  406 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.2586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  91 GLN ** 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 = 0.4164 r_free = 0.4164 target = 0.099835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.075714 restraints weight = 40786.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 6.86
r_work: 0.3481 rms_B_bonded: 6.74 restraints_weight: 2.0000
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3482
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3482
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.093   6712  Z= 0.195
  Angle     :  0.748  11.908   9139  Z= 0.362
  Chirality :  0.048   0.274   1027
  Planarity :  0.004   0.050   1175
  Dihedral  :  8.109 169.036    908
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 16.62
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.40 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 23.55 %
    Favored  : 72.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.52 (0.29), residues: 816
  helix: -0.32 (0.55), residues: 103
  sheet: -0.67 (0.34), residues: 217
  loop : -1.34 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 303 
 TYR   0.023   0.002   TYR A 166 
 PHE   0.024   0.002   PHE B 248 
 TRP   0.012   0.001   TRP B 238 
 HIS   0.003   0.001   HIS B 255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00463 /  0.19 ( 6691)
  covalent geometry    : angle       0.72526 /  0.36 ( 9089)
  SS BOND              : bond        0.00209 /  0.12 (    6)
  SS BOND              : angle       1.09407 /  0.66 (   12)
  hydrogen bonds       : bond        0.03692 /  2.36 (  224)
  hydrogen bonds       : angle       6.10611 /  4.37 (  564)
  Misc. bond           : bond        0.00008 /  0.01 (    2)
  link_BETA1-4         : bond        0.00856 /  0.48 (    6)
  link_BETA1-4         : angle       2.63679 /  1.69 (   18)
  link_BETA1-6         : bond        0.00740 /  0.49 (    1)
  link_BETA1-6         : angle       1.97944 /  1.23 (    3)
  link_NAG-ASN         : bond        0.00657 /  0.37 (    5)
  link_NAG-ASN         : angle       3.53620 /  1.69 (   15)
  link_SS              : bond        0.00213 /  0.14 (    1)
  link_SS              : angle       0.45948 /  0.25 (    2)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 55
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7464 (pp)
REVERT: A   27 LYS cc_start: 0.8958 (mtpp) cc_final: 0.8361 (pptt)
REVERT: A   90 ARG cc_start: 0.8210 (ptm160) cc_final: 0.7401 (mmm160)
REVERT: A  197 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7021 (tm-30)
REVERT: B  387 MET cc_start: 0.8169 (mmm) cc_final: 0.7781 (tpp)
  outliers start: 26
  outliers final: 17
  residues processed: 77
  average time/residue: 0.0765
  time to fit residues: 8.1245
Evaluate side-chains
  70 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 51
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  197 GLN
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  406 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 57 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    0.2980
   chunk 67 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0970
   chunk 75 optimal weight:    6.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  91 GLN ** 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 = 0.4173 r_free = 0.4173 target = 0.100368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.076363 restraints weight = 42926.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 6.98
r_work: 0.3487 rms_B_bonded: 6.87 restraints_weight: 2.0000
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3488
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3488 r_free = 0.3488    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3488 r_free = 0.3488    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3488
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   6712  Z= 0.177
  Angle     :  0.737  11.928   9139  Z= 0.355
  Chirality :  0.047   0.257   1027
  Planarity :  0.004   0.049   1175
  Dihedral  :  8.133 170.798    908
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.64 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 24.28 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.50 (0.29), residues: 816
  helix: -0.33 (0.55), residues: 104
  sheet: -0.67 (0.35), residues: 217
  loop : -1.30 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 327 
 TYR   0.018   0.002   TYR A 380 
 PHE   0.023   0.002   PHE B 248 
 TRP   0.011   0.001   TRP A 113 
 HIS   0.003   0.001   HIS B 255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.18 ( 6691)
  covalent geometry    : angle       0.71524 /  0.35 ( 9089)
  SS BOND              : bond        0.00181 /  0.11 (    6)
  SS BOND              : angle       1.06487 /  0.63 (   12)
  hydrogen bonds       : bond        0.03588 /  2.29 (  224)
  hydrogen bonds       : angle       6.13415 /  4.38 (  564)
  Misc. bond           : bond        0.00003 /  0.00 (    2)
  link_BETA1-4         : bond        0.00809 /  0.45 (    6)
  link_BETA1-4         : angle       2.57786 /  1.66 (   18)
  link_BETA1-6         : bond        0.00736 /  0.49 (    1)
  link_BETA1-6         : angle       1.87083 /  1.16 (    3)
  link_NAG-ASN         : bond        0.00636 /  0.35 (    5)
  link_NAG-ASN         : angle       3.37504 /  1.61 (   15)
  link_SS              : bond        0.00163 /  0.11 (    1)
  link_SS              : angle       0.32157 /  0.17 (    2)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 53
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7403 (pp)
REVERT: A   27 LYS cc_start: 0.8967 (mtpp) cc_final: 0.8383 (pptt)
REVERT: A   90 ARG cc_start: 0.8211 (ptm160) cc_final: 0.7376 (mmm160)
REVERT: A  197 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7117 (tm-30)
REVERT: B  387 MET cc_start: 0.8205 (mmm) cc_final: 0.7750 (tpp)
  outliers start: 28
  outliers final: 18
  residues processed: 76
  average time/residue: 0.0702
  time to fit residues: 7.4796
Evaluate side-chains
  72 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 52
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  197 GLN
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  406 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 79 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  91 GLN ** 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 = 0.4195 r_free = 0.4195 target = 0.101497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.077353 restraints weight = 42037.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 6.99
r_work: 0.3516 rms_B_bonded: 6.88 restraints_weight: 2.0000
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3513
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3513
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   6712  Z= 0.152
  Angle     :  0.727  11.561   9139  Z= 0.349
  Chirality :  0.047   0.253   1027
  Planarity :  0.004   0.047   1175
  Dihedral  :  8.057 175.188    906
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.03 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 25.00 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.40 (0.29), residues: 816
  helix: -0.32 (0.54), residues: 104
  sheet: -0.67 (0.33), residues: 240
  loop : -1.20 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 327 
 TYR   0.016   0.002   TYR A 380 
 PHE   0.023   0.001   PHE B 248 
 TRP   0.014   0.001   TRP A 113 
 HIS   0.003   0.001   HIS A 112 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.15 ( 6691)
  covalent geometry    : angle       0.70618 /  0.34 ( 9089)
  SS BOND              : bond        0.00158 /  0.09 (    6)
  SS BOND              : angle       1.00511 /  0.59 (   12)
  hydrogen bonds       : bond        0.03380 /  2.17 (  224)
  hydrogen bonds       : angle       6.04999 /  4.33 (  564)
  Misc. bond           : bond        0.00004 /  0.00 (    2)
  link_BETA1-4         : bond        0.00786 /  0.44 (    6)
  link_BETA1-4         : angle       2.48488 /  1.60 (   18)
  link_BETA1-6         : bond        0.00734 /  0.49 (    1)
  link_BETA1-6         : angle       1.72979 /  1.08 (    3)
  link_NAG-ASN         : bond        0.00611 /  0.34 (    5)
  link_NAG-ASN         : angle       3.33376 /  1.59 (   15)
  link_SS              : bond        0.00088 /  0.06 (    1)
  link_SS              : angle       0.16403 /  0.09 (    2)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8346 (pptt)
REVERT: A   90 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7410 (mmm160)
REVERT: A  197 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7125 (tm-30)
REVERT: A  285 MET cc_start: 0.5525 (ttt) cc_final: 0.5267 (ttt)
REVERT: B  387 MET cc_start: 0.8175 (mmm) cc_final: 0.7757 (tpp)
  outliers start: 23
  outliers final: 17
  residues processed: 74
  average time/residue: 0.0640
  time to fit residues: 6.6384
Evaluate side-chains
  70 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 52
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  197 GLN
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  406 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 44 optimal weight:    6.9990
   chunk 67 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0000
   chunk 48 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.8988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 141 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.101089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.078101 restraints weight = 29221.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 5.82
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3708 r_free = 0.3708    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3708 r_free = 0.3708    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.2916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   6712  Z= 0.164
  Angle     :  0.730  11.460   9139  Z= 0.353
  Chirality :  0.047   0.250   1027
  Planarity :  0.004   0.048   1175
  Dihedral  :  8.071 175.133    906
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.52 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 25.58 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.39 (0.29), residues: 816
  helix: -0.27 (0.54), residues: 104
  sheet: -0.67 (0.33), residues: 241
  loop : -1.19 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 327 
 TYR   0.021   0.002   TYR A 166 
 PHE   0.031   0.002   PHE B 248 
 TRP   0.060   0.002   TRP A 113 
 HIS   0.003   0.001   HIS A 112 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00392 /  0.16 ( 6691)
  covalent geometry    : angle       0.70998 /  0.35 ( 9089)
  SS BOND              : bond        0.00172 /  0.10 (    6)
  SS BOND              : angle       1.04266 /  0.62 (   12)
  hydrogen bonds       : bond        0.03427 /  2.19 (  224)
  hydrogen bonds       : angle       6.02553 /  4.31 (  564)
  Misc. bond           : bond        0.00002 /  0.00 (    2)
  link_BETA1-4         : bond        0.00781 /  0.44 (    6)
  link_BETA1-4         : angle       2.44943 /  1.58 (   18)
  link_BETA1-6         : bond        0.00711 /  0.47 (    1)
  link_BETA1-6         : angle       1.70277 /  1.07 (    3)
  link_NAG-ASN         : bond        0.00602 /  0.34 (    5)
  link_NAG-ASN         : angle       3.27341 /  1.56 (   15)
  link_SS              : bond        0.00123 /  0.08 (    1)
  link_SS              : angle       0.20718 /  0.11 (    2)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 54
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8722 (mtpp) cc_final: 0.8205 (pptt)
REVERT: A   90 ARG cc_start: 0.8061 (ptm160) cc_final: 0.7337 (mmm160)
REVERT: A  197 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7037 (tm-30)
REVERT: B  387 MET cc_start: 0.8114 (mmm) cc_final: 0.7694 (tpp)
  outliers start: 22
  outliers final: 17
  residues processed: 72
  average time/residue: 0.0664
  time to fit residues: 6.7249
Evaluate side-chains
  72 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 54
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  197 GLN
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  406 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    1.7388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 228 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.098524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.074090 restraints weight = 46355.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 7.22
r_work: 0.3442 rms_B_bonded: 7.01 restraints_weight: 2.0000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.104   6712  Z= 0.235
  Angle     :  0.772  12.193   9139  Z= 0.377
  Chirality :  0.048   0.255   1027
  Planarity :  0.005   0.051   1175
  Dihedral  :  8.007 165.438    906
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 18.56
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.89 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 26.16 %
    Favored  : 70.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.51 (0.29), residues: 816
  helix: -0.35 (0.53), residues: 104
  sheet: -0.69 (0.34), residues: 217
  loop : -1.31 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 281 
 TYR   0.029   0.003   TYR A 166 
 PHE   0.028   0.002   PHE B 248 
 TRP   0.042   0.002   TRP A 113 
 HIS   0.004   0.001   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00555 /  0.23 ( 6691)
  covalent geometry    : angle       0.75246 /  0.37 ( 9089)
  SS BOND              : bond        0.00270 /  0.16 (    6)
  SS BOND              : angle       1.29561 /  0.77 (   12)
  hydrogen bonds       : bond        0.03822 /  2.45 (  224)
  hydrogen bonds       : angle       6.12657 /  4.38 (  564)
  Misc. bond           : bond        0.00016 /  0.01 (    2)
  link_BETA1-4         : bond        0.00742 /  0.42 (    6)
  link_BETA1-4         : angle       2.45507 /  1.58 (   18)
  link_BETA1-6         : bond        0.00690 /  0.46 (    1)
  link_BETA1-6         : angle       1.78100 /  1.11 (    3)
  link_NAG-ASN         : bond        0.00574 /  0.33 (    5)
  link_NAG-ASN         : angle       3.22976 /  1.55 (   15)
  link_SS              : bond        0.00286 /  0.19 (    1)
  link_SS              : angle       0.49384 /  0.27 (    2)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 52
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8983 (mtpp) cc_final: 0.8406 (pptt)
REVERT: A  197 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6922 (tm-30)
REVERT: A  285 MET cc_start: 0.5791 (ttt) cc_final: 0.5566 (ttt)
REVERT: B  238 TRP cc_start: 0.6673 (m100) cc_final: 0.6059 (m100)
REVERT: B  266 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7816 (p)
REVERT: B  387 MET cc_start: 0.8284 (mmm) cc_final: 0.7662 (tpp)
  outliers start: 20
  outliers final: 16
  residues processed: 70
  average time/residue: 0.0715
  time to fit residues: 7.0969
Evaluate side-chains
  69 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  197 GLN
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  406 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0570
   chunk 75 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0970
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.5296

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  91 GLN ** 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 = 0.4194 r_free = 0.4194 target = 0.101601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.078540 restraints weight = 32858.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 6.12
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3714
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3714 r_free = 0.3714    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3714 r_free = 0.3714    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3714
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   6712  Z= 0.144
  Angle     :  0.729  11.613   9139  Z= 0.351
  Chirality :  0.047   0.257   1027
  Planarity :  0.004   0.047   1175
  Dihedral  :  8.135 176.150    906
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.03 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 26.16 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.36 (0.29), residues: 816
  helix: -0.27 (0.53), residues: 104
  sheet: -0.63 (0.33), residues: 241
  loop : -1.17 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  90 
 TYR   0.023   0.002   TYR A 166 
 PHE   0.030   0.002   PHE B 248 
 TRP   0.047   0.002   TRP A 113 
 HIS   0.003   0.001   HIS A 112 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.14 ( 6691)
  covalent geometry    : angle       0.70982 /  0.35 ( 9089)
  SS BOND              : bond        0.00170 /  0.10 (    6)
  SS BOND              : angle       0.93914 /  0.57 (   12)
  hydrogen bonds       : bond        0.03286 /  2.10 (  224)
  hydrogen bonds       : angle       6.06846 /  4.34 (  564)
  Misc. bond           : bond        0.00012 /  0.01 (    2)
  link_BETA1-4         : bond        0.00802 /  0.45 (    6)
  link_BETA1-4         : angle       2.40668 /  1.56 (   18)
  link_BETA1-6         : bond        0.00693 /  0.46 (    1)
  link_BETA1-6         : angle       1.53810 /  0.99 (    3)
  link_NAG-ASN         : bond        0.00588 /  0.32 (    5)
  link_NAG-ASN         : angle       3.18484 /  1.53 (   15)
  link_SS              : bond        0.00042 /  0.03 (    1)
  link_SS              : angle       0.10242 /  0.05 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2065.74 seconds
wall clock time: 36 minutes 1.92 seconds (2161.92 seconds total)