Starting phenix.real_space_refine
on Sat May  2 15:20:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t2u_40988/05_2026/8t2u_40988.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t2u_40988/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t2u_40988/05_2026/8t2u_40988.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t2u_40988/05_2026/8t2u_40988.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t2u_40988/05_2026/8t2u_40988.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t2u_40988/05_2026/8t2u_40988.cif"
  }
  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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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 dihedrals: 12
          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 dihedrals: 12
          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 dihedrals: 6
          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 dihedrals: 3
          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 dihedrals: 3
          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: 1.98, per 1000 atoms: 0.30
  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: 0.56
  Conformation dependent library (CDL) restraints added in 461.4 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: 0.24
  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: 0.97

  Time building geometry restraints manager: 0.69 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: 3942
       34.55 -    69.10: 142
       69.10 -   103.66: 42
      103.66 -   138.21: 12
      138.21 -   172.76: 1
  Dihedral angle restraints: 4139
    sinusoidal: 1788
      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 4136 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:             1.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.880
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
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  : 20.684 172.759   2622
  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
  covalent geometry    : bond        0.01390 ( 6691)
  covalent geometry    : angle       1.65557 ( 9089)
  SS BOND              : bond        0.01426 (    6)
  SS BOND              : angle       1.87863 (   12)
  hydrogen bonds       : bond        0.14342 (  224)
  hydrogen bonds       : angle       7.94152 (  564)
  Misc. bond           : bond        0.15493 (    2)
  link_BETA1-4         : bond        0.00787 (    6)
  link_BETA1-4         : angle       3.77616 (   18)
  link_BETA1-6         : bond        0.01530 (    1)
  link_BETA1-6         : angle       7.01020 (    3)
  link_NAG-ASN         : bond        0.00611 (    5)
  link_NAG-ASN         : angle       5.00578 (   15)
  link_SS              : bond        0.00987 (    1)
  link_SS              : angle      16.90657 (    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  : 0.185 
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: 0.0901
  time to fit residues: 11.0816
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  : 0.230 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4211 r_free = 0.4211 target = 0.102981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.077936 restraints weight = 52757.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 7.79
r_work: 0.3500 rms_B_bonded: 7.41 restraints_weight: 2.0000
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3498
|-occupancy refinement: start-------------------------------------------------|
| 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 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3497
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.119   6712  Z= 0.189
  Angle     :  0.834  13.783   9139  Z= 0.396
  Chirality :  0.051   0.333   1027
  Planarity :  0.005   0.039   1175
  Dihedral  : 16.400 174.843   1171
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.29 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 21.53 %
    Favored  : 75.43 %
  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: -1.70 (0.29), residues: 816
  helix: -0.65 (0.52), 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   0.008   0.001   ARG B  87 
 TYR   0.028   0.003   TYR A 371 
 PHE   0.014   0.002   PHE A 191 
 TRP   0.015   0.002   TRP A 113 
 HIS   0.005   0.001   HIS B 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 6691)
  covalent geometry    : angle       0.79487 ( 9089)
  SS BOND              : bond        0.00668 (    6)
  SS BOND              : angle       0.93659 (   12)
  hydrogen bonds       : bond        0.04317 (  224)
  hydrogen bonds       : angle       6.65056 (  564)
  Misc. bond           : bond        0.00116 (    2)
  link_BETA1-4         : bond        0.01464 (    6)
  link_BETA1-4         : angle       3.89408 (   18)
  link_BETA1-6         : bond        0.01403 (    1)
  link_BETA1-6         : angle       3.58985 (    3)
  link_NAG-ASN         : bond        0.00773 (    5)
  link_NAG-ASN         : angle       4.35999 (   15)
  link_SS              : bond        0.00136 (    1)
  link_SS              : angle       0.65353 (    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
  78 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8414 (pptt)
REVERT: A   90 ARG cc_start: 0.8143 (ptm160) cc_final: 0.7300 (mmm160)
REVERT: B  277 SER cc_start: 0.8718 (t) cc_final: 0.8480 (p)
  outliers start: 21
  outliers final: 13
  residues processed: 73
  average time/residue: 0.0764
  time to fit residues: 7.7770
Evaluate side-chains
  66 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 78 optimal weight:   30.0000
   chunk 36 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4154 r_free = 0.4154 target = 0.099796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.077235 restraints weight = 23749.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 5.22
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3684
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3684 r_free = 0.3684    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3684 r_free = 0.3684    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3684
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.122   6712  Z= 0.229
  Angle     :  0.812  12.775   9139  Z= 0.389
  Chirality :  0.051   0.309   1027
  Planarity :  0.005   0.048   1175
  Dihedral  : 13.890 173.199   1158
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 18.02
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.90 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 21.39 %
    Favored  : 73.84 %
  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: -1.76 (0.28), residues: 816
  helix: -0.50 (0.53), residues: 103
  sheet: -0.79 (0.33), residues: 231
  loop : -1.54 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 335 
 TYR   0.031   0.003   TYR A 371 
 PHE   0.016   0.002   PHE A 331 
 TRP   0.012   0.002   TRP A 110 
 HIS   0.004   0.001   HIS B 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 ( 6691)
  covalent geometry    : angle       0.77652 ( 9089)
  SS BOND              : bond        0.00287 (    6)
  SS BOND              : angle       1.31610 (   12)
  hydrogen bonds       : bond        0.04084 (  224)
  hydrogen bonds       : angle       6.31312 (  564)
  Misc. bond           : bond        0.00004 (    2)
  link_BETA1-4         : bond        0.01069 (    6)
  link_BETA1-4         : angle       3.75380 (   18)
  link_BETA1-6         : bond        0.00835 (    1)
  link_BETA1-6         : angle       2.63811 (    3)
  link_NAG-ASN         : bond        0.00683 (    5)
  link_NAG-ASN         : angle       4.04078 (   15)
  link_SS              : bond        0.00280 (    1)
  link_SS              : angle       0.76057 (    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
  93 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 60
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7102 (pp)
REVERT: A   27 LYS cc_start: 0.8791 (mtpp) cc_final: 0.8293 (pptt)
REVERT: A   90 ARG cc_start: 0.7939 (ptm160) cc_final: 0.7221 (mmm160)
REVERT: A  197 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7128 (tm-30)
REVERT: A  363 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.5993 (tt)
REVERT: B  124 MET cc_start: 0.7500 (tpp) cc_final: 0.7276 (tpp)
REVERT: B  387 MET cc_start: 0.8028 (mmm) cc_final: 0.7351 (tpp)
  outliers start: 33
  outliers final: 18
  residues processed: 90
  average time/residue: 0.0713
  time to fit residues: 9.1332
Evaluate side-chains
  75 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 54
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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  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  168 SER
Chi-restraints excluded: chain B residue  230 THR
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  340 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  417 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 78 optimal weight:    8.9990
   chunk 51 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 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 = 0.4197 r_free = 0.4197 target = 0.101814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.080182 restraints weight = 19236.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 4.64
r_work: 0.3607 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3608
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3608 r_free = 0.3608    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3608 r_free = 0.3608    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3608
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091   6712  Z= 0.164
  Angle     :  0.767  11.820   9139  Z= 0.365
  Chirality :  0.049   0.323   1027
  Planarity :  0.004   0.047   1175
  Dihedral  : 13.001 177.871   1153
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 16.16
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.15 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 22.11 %
    Favored  : 73.70 %
  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: -1.57 (0.29), residues: 816
  helix: -0.43 (0.53), residues: 103
  sheet: -0.69 (0.33), residues: 237
  loop : -1.38 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 303 
 TYR   0.023   0.002   TYR A 371 
 PHE   0.018   0.001   PHE B 248 
 TRP   0.016   0.002   TRP B 238 
 HIS   0.004   0.001   HIS B 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 6691)
  covalent geometry    : angle       0.73265 ( 9089)
  SS BOND              : bond        0.00162 (    6)
  SS BOND              : angle       1.04212 (   12)
  hydrogen bonds       : bond        0.03640 (  224)
  hydrogen bonds       : angle       6.20364 (  564)
  Misc. bond           : bond        0.00004 (    2)
  link_BETA1-4         : bond        0.01005 (    6)
  link_BETA1-4         : angle       3.65956 (   18)
  link_BETA1-6         : bond        0.00850 (    1)
  link_BETA1-6         : angle       2.05446 (    3)
  link_NAG-ASN         : bond        0.00720 (    5)
  link_NAG-ASN         : angle       3.93635 (   15)
  link_SS              : bond        0.00140 (    1)
  link_SS              : angle       0.37760 (    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
  85 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 56
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7244 (pp)
REVERT: A   27 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8304 (pptt)
REVERT: A   43 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7663 (tt)
REVERT: A   90 ARG cc_start: 0.8097 (ptm160) cc_final: 0.7377 (mmm160)
REVERT: A  363 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.5822 (tt)
REVERT: B  387 MET cc_start: 0.8075 (mmm) cc_final: 0.7590 (tpp)
  outliers start: 29
  outliers final: 16
  residues processed: 81
  average time/residue: 0.0743
  time to fit residues: 8.3981
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  : 0.175 
-------------------------------------------------------------------------------
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   43 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  293 VAL
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  347 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  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:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 46 optimal weight:    8.9990
   chunk 15 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    1.0784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.100692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.076438 restraints weight = 40614.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 6.85
r_work: 0.3492 rms_B_bonded: 6.73 restraints_weight: 2.0000
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3490
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3490 r_free = 0.3490    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 = 0.3490 r_free = 0.3490    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3490
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   6712  Z= 0.184
  Angle     :  0.771  11.713   9139  Z= 0.366
  Chirality :  0.048   0.312   1027
  Planarity :  0.004   0.049   1175
  Dihedral  : 12.590 174.260   1153
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 16.93
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.77 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 23.55 %
    Favored  : 72.40 %
  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: -1.53 (0.29), residues: 816
  helix: -0.33 (0.54), residues: 103
  sheet: -0.58 (0.34), residues: 222
  loop : -1.40 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 239 
 TYR   0.024   0.002   TYR A 166 
 PHE   0.027   0.002   PHE B 248 
 TRP   0.015   0.002   TRP B 238 
 HIS   0.003   0.001   HIS B 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 6691)
  covalent geometry    : angle       0.73884 ( 9089)
  SS BOND              : bond        0.00157 (    6)
  SS BOND              : angle       1.16303 (   12)
  hydrogen bonds       : bond        0.03718 (  224)
  hydrogen bonds       : angle       6.10351 (  564)
  Misc. bond           : bond        0.00002 (    2)
  link_BETA1-4         : bond        0.01078 (    6)
  link_BETA1-4         : angle       3.53447 (   18)
  link_BETA1-6         : bond        0.00732 (    1)
  link_BETA1-6         : angle       1.69630 (    3)
  link_NAG-ASN         : bond        0.00686 (    5)
  link_NAG-ASN         : angle       3.81488 (   15)
  link_SS              : bond        0.00191 (    1)
  link_SS              : angle       0.40410 (    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
  83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 55
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7361 (pp)
REVERT: A   27 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8352 (pptt)
REVERT: A   90 ARG cc_start: 0.8094 (ptm160) cc_final: 0.7379 (mmm160)
REVERT: A  197 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7119 (tm-30)
REVERT: A  363 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.5931 (tt)
REVERT: B  387 MET cc_start: 0.8160 (mmm) cc_final: 0.7724 (tpp)
  outliers start: 28
  outliers final: 18
  residues processed: 79
  average time/residue: 0.0742
  time to fit residues: 8.4034
Evaluate side-chains
  74 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 53
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
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 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  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  262 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 46 optimal weight:    9.9990
   chunk 67 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4172 r_free = 0.4172 target = 0.100492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.076178 restraints weight = 40947.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 6.95
r_work: 0.3484 rms_B_bonded: 6.80 restraints_weight: 2.0000
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3484
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    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 = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3484
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085   6712  Z= 0.182
  Angle     :  0.765  11.670   9139  Z= 0.363
  Chirality :  0.048   0.308   1027
  Planarity :  0.004   0.049   1175
  Dihedral  : 12.233 173.277   1153
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 17.09
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.27 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 24.13 %
    Favored  : 71.97 %
  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: -0.33 (0.54), residues: 103
  sheet: -0.58 (0.35), residues: 217
  loop : -1.38 (0.27), residues: 496

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   0.024   0.002   PHE B 248 
 TRP   0.029   0.002   TRP B 238 
 HIS   0.003   0.001   HIS B 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 6691)
  covalent geometry    : angle       0.73415 ( 9089)
  SS BOND              : bond        0.00199 (    6)
  SS BOND              : angle       1.07466 (   12)
  hydrogen bonds       : bond        0.03608 (  224)
  hydrogen bonds       : angle       6.12598 (  564)
  Misc. bond           : bond        0.00003 (    2)
  link_BETA1-4         : bond        0.01095 (    6)
  link_BETA1-4         : angle       3.42767 (   18)
  link_BETA1-6         : bond        0.00730 (    1)
  link_BETA1-6         : angle       1.62588 (    3)
  link_NAG-ASN         : bond        0.00662 (    5)
  link_NAG-ASN         : angle       3.75771 (   15)
  link_SS              : bond        0.00184 (    1)
  link_SS              : angle       0.35536 (    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
  82 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 55
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7421 (pp)
REVERT: A   27 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8337 (pptt)
REVERT: A   90 ARG cc_start: 0.8196 (ptm160) cc_final: 0.7419 (mmm160)
REVERT: A  197 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7069 (tm-30)
REVERT: B  387 MET cc_start: 0.8160 (mmm) cc_final: 0.7738 (tpp)
  outliers start: 27
  outliers final: 16
  residues processed: 80
  average time/residue: 0.0801
  time to fit residues: 8.8683
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  : 0.293 
-------------------------------------------------------------------------------
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  216 VAL
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  249 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  286 THR
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:    0.6980
   chunk 57 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 75 optimal weight:    7.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.098697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.074079 restraints weight = 44906.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 7.18
r_work: 0.3433 rms_B_bonded: 6.96 restraints_weight: 2.0000
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3435
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3435 r_free = 0.3435    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 = 0.3435 r_free = 0.3435    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3435
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.106   6712  Z= 0.229
  Angle     :  0.794  11.973   9139  Z= 0.380
  Chirality :  0.049   0.302   1027
  Planarity :  0.004   0.052   1175
  Dihedral  : 11.996 167.556   1152
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 19.26
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.26 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 25.43 %
    Favored  : 71.39 %
  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 (0.54), residues: 104
  sheet: -0.77 (0.34), residues: 225
  loop : -1.35 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 327 
 TYR   0.019   0.002   TYR A 380 
 PHE   0.021   0.002   PHE B 248 
 TRP   0.016   0.002   TRP B 238 
 HIS   0.004   0.001   HIS A  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 ( 6691)
  covalent geometry    : angle       0.76575 ( 9089)
  SS BOND              : bond        0.00236 (    6)
  SS BOND              : angle       1.23735 (   12)
  hydrogen bonds       : bond        0.03920 (  224)
  hydrogen bonds       : angle       6.21882 (  564)
  Misc. bond           : bond        0.00012 (    2)
  link_BETA1-4         : bond        0.01114 (    6)
  link_BETA1-4         : angle       3.34560 (   18)
  link_BETA1-6         : bond        0.00816 (    1)
  link_BETA1-6         : angle       1.72366 (    3)
  link_NAG-ASN         : bond        0.00649 (    5)
  link_NAG-ASN         : angle       3.69327 (   15)
  link_SS              : bond        0.00256 (    1)
  link_SS              : angle       0.51205 (    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
  78 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7528 (pp)
REVERT: A   27 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8365 (pptt)
REVERT: A   90 ARG cc_start: 0.8322 (ptm160) cc_final: 0.7499 (mmm160)
REVERT: A  197 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6890 (tm-30)
REVERT: B  387 MET cc_start: 0.8233 (mmm) cc_final: 0.7857 (tpp)
  outliers start: 22
  outliers final: 16
  residues processed: 75
  average time/residue: 0.0714
  time to fit residues: 7.6499
Evaluate side-chains
  71 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  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  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  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:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4180 r_free = 0.4180 target = 0.100952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.076708 restraints weight = 42289.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 7.03
r_work: 0.3490 rms_B_bonded: 6.85 restraints_weight: 2.0000
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3491
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3491 r_free = 0.3491    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 = 0.3491 r_free = 0.3491    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3491
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.2894

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= 0.162
  Angle     :  0.763  11.605   9139  Z= 0.363
  Chirality :  0.048   0.308   1027
  Planarity :  0.004   0.049   1175
  Dihedral  : 11.808 174.472   1150
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 17.01
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.64 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 24.86 %
    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: -1.48 (0.29), residues: 816
  helix: -0.35 (0.54), residues: 104
  sheet: -0.69 (0.34), residues: 229
  loop : -1.28 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 239 
 TYR   0.018   0.002   TYR A 380 
 PHE   0.024   0.002   PHE B 248 
 TRP   0.068   0.003   TRP B 238 
 HIS   0.003   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6691)
  covalent geometry    : angle       0.73495 ( 9089)
  SS BOND              : bond        0.00177 (    6)
  SS BOND              : angle       1.02478 (   12)
  hydrogen bonds       : bond        0.03551 (  224)
  hydrogen bonds       : angle       6.20528 (  564)
  Misc. bond           : bond        0.00004 (    2)
  link_BETA1-4         : bond        0.01137 (    6)
  link_BETA1-4         : angle       3.25984 (   18)
  link_BETA1-6         : bond        0.00779 (    1)
  link_BETA1-6         : angle       1.64247 (    3)
  link_NAG-ASN         : bond        0.00640 (    5)
  link_NAG-ASN         : angle       3.59233 (   15)
  link_SS              : bond        0.00108 (    1)
  link_SS              : angle       0.16729 (    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
  82 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 58
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8341 (pptt)
REVERT: A   90 ARG cc_start: 0.8267 (ptm160) cc_final: 0.7447 (mmm160)
REVERT: A  197 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7148 (tm-30)
REVERT: A  285 MET cc_start: 0.5624 (ttt) cc_final: 0.5381 (ttt)
REVERT: A  363 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.5959 (tt)
REVERT: B  266 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7518 (p)
REVERT: B  387 MET cc_start: 0.8189 (mmm) cc_final: 0.7812 (tpp)
  outliers start: 24
  outliers final: 15
  residues processed: 78
  average time/residue: 0.0685
  time to fit residues: 7.7630
Evaluate side-chains
  73 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
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  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  363 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  118 MET
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  266 VAL
Chi-restraints excluded: chain B residue  286 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:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   chunk 67 optimal weight:    0.7980
   chunk 61 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.101227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.077883 restraints weight = 29559.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 5.90
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3700
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3700 r_free = 0.3700    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 = 0.3700 r_free = 0.3700    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3700
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   6712  Z= 0.164
  Angle     :  0.759  11.387   9139  Z= 0.362
  Chirality :  0.048   0.303   1027
  Planarity :  0.004   0.048   1175
  Dihedral  : 11.656 175.840   1150
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 16.93
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.77 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 26.59 %
    Favored  : 70.81 %
  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: -1.41 (0.29), residues: 816
  helix: -0.40 (0.53), residues: 104
  sheet: -0.68 (0.32), residues: 244
  loop : -1.18 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 239 
 TYR   0.017   0.002   TYR A 380 
 PHE   0.030   0.002   PHE B 248 
 TRP   0.063   0.003   TRP A 113 
 HIS   0.004   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 6691)
  covalent geometry    : angle       0.73238 ( 9089)
  SS BOND              : bond        0.00181 (    6)
  SS BOND              : angle       0.99996 (   12)
  hydrogen bonds       : bond        0.03525 (  224)
  hydrogen bonds       : angle       6.17443 (  564)
  Misc. bond           : bond        0.00005 (    2)
  link_BETA1-4         : bond        0.01128 (    6)
  link_BETA1-4         : angle       3.20384 (   18)
  link_BETA1-6         : bond        0.00735 (    1)
  link_BETA1-6         : angle       1.59474 (    3)
  link_NAG-ASN         : bond        0.00621 (    5)
  link_NAG-ASN         : angle       3.57657 (   15)
  link_SS              : bond        0.00099 (    1)
  link_SS              : angle       0.15461 (    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
  71 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8208 (pptt)
REVERT: A   90 ARG cc_start: 0.8093 (ptm160) cc_final: 0.7374 (mmm160)
REVERT: A  197 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.7049 (tm-30)
REVERT: A  283 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7800 (tm-30)
REVERT: B  266 VAL cc_start: 0.7427 (OUTLIER) cc_final: 0.7122 (p)
REVERT: B  387 MET cc_start: 0.8111 (mmm) cc_final: 0.7410 (tpp)
  outliers start: 18
  outliers final: 12
  residues processed: 69
  average time/residue: 0.0738
  time to fit residues: 7.2215
Evaluate side-chains
  67 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 THR
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  283 GLU
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  161 VAL
Chi-restraints excluded: chain B residue  168 SER
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 46 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4172 r_free = 0.4172 target = 0.100403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.075373 restraints weight = 49309.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 7.59
r_work: 0.3459 rms_B_bonded: 7.30 restraints_weight: 2.0000
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3461
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3461 r_free = 0.3461    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3461 r_free = 0.3461    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3461
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   6712  Z= 0.187
  Angle     :  0.770  11.877   9139  Z= 0.368
  Chirality :  0.049   0.300   1027
  Planarity :  0.004   0.049   1175
  Dihedral  : 11.564 173.867   1150
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 18.49
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.01 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 27.17 %
    Favored  : 70.81 %
  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: -1.44 (0.29), residues: 816
  helix: -0.39 (0.53), residues: 104
  sheet: -0.73 (0.32), residues: 244
  loop : -1.18 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 327 
 TYR   0.022   0.002   TYR A 166 
 PHE   0.029   0.002   PHE B 248 
 TRP   0.044   0.003   TRP A 113 
 HIS   0.003   0.001   HIS A 278 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 6691)
  covalent geometry    : angle       0.74374 ( 9089)
  SS BOND              : bond        0.00194 (    6)
  SS BOND              : angle       1.03937 (   12)
  hydrogen bonds       : bond        0.03601 (  224)
  hydrogen bonds       : angle       6.14277 (  564)
  Misc. bond           : bond        0.00004 (    2)
  link_BETA1-4         : bond        0.01099 (    6)
  link_BETA1-4         : angle       3.15975 (   18)
  link_BETA1-6         : bond        0.00780 (    1)
  link_BETA1-6         : angle       1.61928 (    3)
  link_NAG-ASN         : bond        0.00599 (    5)
  link_NAG-ASN         : angle       3.54805 (   15)
  link_SS              : bond        0.00166 (    1)
  link_SS              : angle       0.24892 (    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
  64 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8940 (mtpp) cc_final: 0.8370 (pptt)
REVERT: A   90 ARG cc_start: 0.8296 (ptm160) cc_final: 0.7461 (mmm160)
REVERT: A  197 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7158 (tm-30)
REVERT: A  283 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7797 (tm-30)
REVERT: A  285 MET cc_start: 0.5742 (ttt) cc_final: 0.5472 (ttt)
REVERT: B  266 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7598 (p)
REVERT: B  387 MET cc_start: 0.8207 (mmm) cc_final: 0.7570 (tpp)
  outliers start: 14
  outliers final: 11
  residues processed: 63
  average time/residue: 0.0763
  time to fit residues: 6.7915
Evaluate side-chains
  64 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 THR
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  283 GLU
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  161 VAL
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  266 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:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0980
   chunk 64 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0870
   chunk 43 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4213 r_free = 0.4213 target = 0.102662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.078908 restraints weight = 33810.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 6.38
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6712  Z= 0.144
  Angle     :  0.749  11.575   9139  Z= 0.356
  Chirality :  0.048   0.305   1027
  Planarity :  0.004   0.046   1175
  Dihedral  : 11.389 176.420   1150
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 16.16
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.03 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 26.73 %
    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: -1.31 (0.29), residues: 816
  helix: -0.20 (0.55), residues: 102
  sheet: -0.59 (0.33), residues: 244
  loop : -1.16 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 239 
 TYR   0.016   0.002   TYR A 166 
 PHE   0.030   0.001   PHE B 248 
 TRP   0.046   0.003   TRP A 113 
 HIS   0.003   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6691)
  covalent geometry    : angle       0.72289 ( 9089)
  SS BOND              : bond        0.00167 (    6)
  SS BOND              : angle       0.88870 (   12)
  hydrogen bonds       : bond        0.03302 (  224)
  hydrogen bonds       : angle       6.10551 (  564)
  Misc. bond           : bond        0.00013 (    2)
  link_BETA1-4         : bond        0.01056 (    6)
  link_BETA1-4         : angle       3.09976 (   18)
  link_BETA1-6         : bond        0.00800 (    1)
  link_BETA1-6         : angle       1.52828 (    3)
  link_NAG-ASN         : bond        0.00602 (    5)
  link_NAG-ASN         : angle       3.52608 (   15)
  link_SS              : bond        0.00055 (    1)
  link_SS              : angle       0.04604 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2263.77 seconds
wall clock time: 39 minutes 29.53 seconds (2369.53 seconds total)