Starting phenix.real_space_refine
on Fri Sep 11 10:59:09 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7zn5_14801/09_2026/7zn5_14801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zn5_14801/09_2026/7zn5_14801.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7zn5_14801/09_2026/7zn5_14801.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7zn5_14801/09_2026/7zn5_14801.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zn5_14801/09_2026/7zn5_14801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zn5_14801/09_2026/7zn5_14801.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zn5_14801/09_2026/7zn5_14801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zn5_14801/09_2026/7zn5_14801.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      97      5.49       5
     S      18      5.16       5
     C    5500      2.51       5
     N    1562      2.21       5
     O    1869      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9046
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3533
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 430, 3525
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 411}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
      Conformer: "B"
        Number of residues, atoms: 430, 3525
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 411}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
          bond proxies already assigned to first conformer: 3601
    Chain: "B"
      Number of atoms: 3566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 435, 3566
          Classifications: {'peptide': 435}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 975
          Classifications: {'DNA': 48}
          Link IDs: {'rna3p': 47}
    Chain: "D"
      Number of atoms: 972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 972
          Classifications: {'DNA': 47}
          Link IDs: {'rna3p': 46}
  Time building chain proxies: 2.67, per 1000 atoms: 0.30
  Number of scatterers: 9046
  At special positions: 0
  Unit cell: (146.685, 98.679, 89.789, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     P      97     15.00
     O    1869      8.00
     N    1562      7.00
     C    5500      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 368.8 milliseconds
  

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1636

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 7 sheets defined
      46.8% alpha, 9.6% beta
      13 base pairs and 63 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 31
      removed outlier: 4.267A  pdb=" N   TYR A  21 " --> pdb=" O   TYR A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 52 through 66
      removed outlier: 3.580A  pdb=" N   VAL A  56 " --> pdb=" O   SER A  52 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.773A  pdb=" N   LYS A 126 " --> pdb=" O   GLU A 122 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   TYR A 127 " --> pdb=" O   GLN A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 163
    Processing helix  chain 'A' and resid 177 through 190
      removed outlier: 3.700A  pdb=" N   LEU A 181 " --> pdb=" O   GLY A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 212
      removed outlier: 4.153A  pdb=" N   HIS A 211 " --> pdb=" O   LYS A 207 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   TYR A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 233
    Processing helix  chain 'A' and resid 254 through 268
      removed outlier: 4.117A  pdb=" N   HIS A 268 " --> pdb=" O   TRP A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 296
    Processing helix  chain 'A' and resid 323 through 334
    Processing helix  chain 'A' and resid 342 through 356
      removed outlier: 3.927A  pdb=" N   GLN A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   GLY A 356 " --> pdb=" O   PHE A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 381
      removed outlier: 3.870A  pdb=" N   LYS A 360 " --> pdb=" O   GLY A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 418
    Processing helix  chain 'A' and resid 426 through 429
      removed outlier: 3.547A  pdb=" N   SER A 429 " --> pdb=" O   SER A 426 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 426 through 429'
    Processing helix  chain 'A' and resid 450 through 463
    Processing helix  chain 'B' and resid 15 through 31
      removed outlier: 4.349A  pdb=" N   TYR B  21 " --> pdb=" O   TYR B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 49
    Processing helix  chain 'B' and resid 52 through 67
      removed outlier: 3.615A  pdb=" N   VAL B  56 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 132
      removed outlier: 3.814A  pdb=" N   LYS B 126 " --> pdb=" O   GLU B 122 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   TYR B 127 " --> pdb=" O   GLN B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 164
      removed outlier: 3.659A  pdb=" N   GLY B 164 " --> pdb=" O   HIS B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 172
      removed outlier: 3.543A  pdb=" N   VAL B 172 " --> pdb=" O   PRO B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 190
      removed outlier: 4.374A  pdb=" N   THR B 180 " --> pdb=" O   ALA B 176 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LEU B 181 " --> pdb=" O   GLY B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 210
    Processing helix  chain 'B' and resid 227 through 233
    Processing helix  chain 'B' and resid 254 through 268
      removed outlier: 3.976A  pdb=" N   HIS B 268 " --> pdb=" O   TRP B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 296
    Processing helix  chain 'B' and resid 323 through 334
    Processing helix  chain 'B' and resid 342 through 355
      removed outlier: 3.693A  pdb=" N   GLN B 355 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 382
      removed outlier: 3.789A  pdb=" N   LYS B 360 " --> pdb=" O   GLY B 356 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   ARG B 382 " --> pdb=" O   SER B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 418
    Processing helix  chain 'B' and resid 450 through 462
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 71
    Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 109
      removed outlier: 3.822A  pdb=" N   PHE A 109 " --> pdb=" O   LYS A 421 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   TYR A 423 " --> pdb=" O   PHE A 109 " (cutoff:3.500A)
      removed outlier: 10.285A  pdb=" N   LYS A 421 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
      removed outlier: 8.273A  pdb=" N   GLY A 442 " --> pdb=" O   LYS A 421 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   TYR A 423 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL A 440 " --> pdb=" O   TYR A 423 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   VAL A 399 " --> pdb=" O   ILE A 390 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU A 388 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 175
      removed outlier: 6.698A  pdb=" N   VAL A 239 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   ASP A 276 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   THR A 241 " --> pdb=" O   ASP A 276 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   VAL A 194 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   TYR A 240 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   GLY A 196 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   TYR A 195 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   PHE A 219 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE A 197 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 222
      removed outlier: 3.552A  pdb=" N   GLY A 225 " --> pdb=" O   ASP A 222 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 71
    Processing sheet with id=AA6, first strand: chain 'B' and resid 173 through 175
      removed outlier: 3.597A  pdb=" N   GLY B 175 " --> pdb=" O   SER B 318 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL B 239 " --> pdb=" O   ILE B 274 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   ASP B 276 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   THR B 241 " --> pdb=" O   ASP B 276 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   VAL B 194 " --> pdb=" O   VAL B 238 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   TYR B 240 " --> pdb=" O   VAL B 194 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   GLY B 196 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 387 through 389
      removed outlier: 3.874A  pdb=" N   LEU B 388 " --> pdb=" O   VAL B 401 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL B 440 " --> pdb=" O   TYR B 423 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   TYR B 423 " --> pdb=" O   VAL B 440 " (cutoff:3.500A)

    292 hydrogen bonds defined for protein.
    846 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      32 hydrogen bonds
      64 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      63 stacking parallelities
  Total time for adding SS restraints: 1.47

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2318
        1.34 -     1.45: 2259
        1.45 -     1.57: 4657
        1.57 -     1.69: 190
        1.69 -     1.81: 32
  Bond restraints: 9456
  Sorted by residual:
  bond pdb=" OP4 LLP A 309 "
       pdb=" P   LLP A 309 "
    ideal  model  delta    sigma   weight residual
    1.726  1.544  0.182 2.00e-02 2.50e+03 8.32e+01
  bond pdb=" OP4 LLP B 309 "
       pdb=" P   LLP B 309 "
    ideal  model  delta    sigma   weight residual
    1.726  1.545  0.181 2.00e-02 2.50e+03 8.18e+01
  bond pdb=" NZ  LLP B 309 "
       pdb=" C4' LLP B 309 "
    ideal  model  delta    sigma   weight residual
    1.273  1.432 -0.159 2.00e-02 2.50e+03 6.30e+01
  bond pdb=" NZ  LLP A 309 "
       pdb=" C4' LLP A 309 "
    ideal  model  delta    sigma   weight residual
    1.273  1.432 -0.159 2.00e-02 2.50e+03 6.29e+01
  bond pdb=" C4  LLP B 309 "
       pdb=" C4' LLP B 309 "
    ideal  model  delta    sigma   weight residual
    1.464  1.615 -0.151 2.00e-02 2.50e+03 5.72e+01
  ... (remaining 9451 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 12983
        2.23 -     4.45: 195
        4.45 -     6.68: 28
        6.68 -     8.90: 3
        8.90 -    11.13: 6
  Bond angle restraints: 13215
  Sorted by residual:
  angle pdb=" N3   DT C  10 "
        pdb=" C4   DT C  10 "
        pdb=" O4   DT C  10 "
      ideal   model   delta    sigma   weight residual
     119.90  122.44   -2.54 6.00e-01 2.78e+00 1.79e+01
  angle pdb=" N3   DT D  40 "
        pdb=" C4   DT D  40 "
        pdb=" O4   DT D  40 "
      ideal   model   delta    sigma   weight residual
     119.90  122.42   -2.52 6.00e-01 2.78e+00 1.77e+01
  angle pdb=" N3   DT C  18 "
        pdb=" C4   DT C  18 "
        pdb=" O4   DT C  18 "
      ideal   model   delta    sigma   weight residual
     119.90  122.40   -2.50 6.00e-01 2.78e+00 1.74e+01
  angle pdb=" N3   DT C   7 "
        pdb=" C4   DT C   7 "
        pdb=" O4   DT C   7 "
      ideal   model   delta    sigma   weight residual
     119.90  122.40   -2.50 6.00e-01 2.78e+00 1.73e+01
  angle pdb=" N3   DT C  19 "
        pdb=" C4   DT C  19 "
        pdb=" O4   DT C  19 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.73e+01
  ... (remaining 13210 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.21: 4923
       28.21 -    56.42: 464
       56.42 -    84.63: 30
       84.63 -   112.84: 2
      112.84 -   141.06: 1
  Dihedral angle restraints: 5420
    sinusoidal: 2863
      harmonic: 2557
  Sorted by residual:
  dihedral pdb=" CA  ARG A  74 "
           pdb=" C   ARG A  74 "
           pdb=" N   LYS A  75 "
           pdb=" CA  LYS A  75 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.23  -20.77     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" C4'  DA D  33 "
           pdb=" C3'  DA D  33 "
           pdb=" O3'  DA D  33 "
           pdb=" P    DA D  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   78.94  141.06     1      3.50e+01 8.16e-04 1.39e+01
  dihedral pdb=" CA  PRO A  73 "
           pdb=" C   PRO A  73 "
           pdb=" N   ARG A  74 "
           pdb=" CA  ARG A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.36   18.64     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 5417 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 883
       0.032 -    0.064: 331
       0.064 -    0.096: 176
       0.096 -    0.128: 54
       0.128 -    0.159: 6
  Chirality restraints: 1450
  Sorted by residual:
  chirality pdb=" CA  ARG B 138 "
            pdb=" N   ARG B 138 "
            pdb=" C   ARG B 138 "
            pdb=" CB  ARG B 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CA  ILE A  72 "
            pdb=" N   ILE A  72 "
            pdb=" C   ILE A  72 "
            pdb=" CB  ILE A  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.93e-01
  chirality pdb=" CA  GLU B 154 "
            pdb=" N   GLU B 154 "
            pdb=" C   GLU B 154 "
            pdb=" CB  GLU B 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.85e-01
  ... (remaining 1447 not shown)

  Planarity restraints: 1348
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CE  LLP A 309 "   -0.156 2.00e-02 2.50e+03   2.55e-01 6.53e+02
        pdb=" NZ  LLP A 309 "    0.341 2.00e-02 2.50e+03
        pdb=" C4  LLP A 309 "    0.135 2.00e-02 2.50e+03
        pdb=" C4' LLP A 309 "   -0.320 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CE  LLP B 309 "    0.089 2.00e-02 2.50e+03   8.51e-02 7.24e+01
        pdb=" NZ  LLP B 309 "   -0.091 2.00e-02 2.50e+03
        pdb=" C4  LLP B 309 "    0.081 2.00e-02 2.50e+03
        pdb=" C4' LLP B 309 "   -0.079 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 168 "   -0.032 5.00e-02 4.00e+02   4.78e-02 3.66e+00
        pdb=" N   PRO A 169 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 169 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 169 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1345 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 804
        2.74 -     3.28: 8566
        3.28 -     3.82: 15123
        3.82 -     4.36: 16992
        4.36 -     4.90: 27837
  Nonbonded interactions: 69322
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 254 "
            pdb=" OD1 ASN A 256 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OG  SER A 162 "
            pdb=" OE2 GLU A 281 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OE1 GLN B 184 "
            pdb=" OH  TYR B 330 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   HIS B 145 "
            pdb=" OG  SER B 339 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   THR B 131 "
            pdb=" ND2 ASN B 136 "
     model   vdw
     2.302 3.120
  ... (remaining 69317 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 15 through 442 or resid 444 through 464))
  selection = (chain 'B' and (resid 15 through 442 or resid 444 through 464))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.960
  Find NCS groups from input model:        0.140
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
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      :  0.006   0.182   9456  Z= 0.418
  Angle     :  0.703  11.128  13215  Z= 0.510
  Chirality :  0.043   0.159   1450
  Planarity :  0.009   0.255   1348
  Dihedral  : 18.868 141.055   3784
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.52 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.18 (0.30), residues: 852
  helix:  1.18 (0.28), residues: 374
  sheet:  0.15 (0.52), residues: 106
  loop : -0.97 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 138 
 TYR   0.019   0.001   TYR A  82 
 PHE   0.011   0.001   PHE A 128 
 TRP   0.010   0.001   TRP A 264 
 HIS   0.003   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00617 /  0.42 ( 9456)
  covalent geometry    : angle       0.70349 /  0.51 (13215)
  hydrogen bonds       : bond        0.16656 / 10.58 (  324)
  hydrogen bonds       : angle       6.50322 /  4.51 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.8787 (pt) cc_final: 0.8580 (mt)
REVERT: A  270 ASN cc_start: 0.7690 (t0) cc_final: 0.7392 (t0)
REVERT: B  270 ASN cc_start: 0.7313 (t0) cc_final: 0.6885 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1152
  time to fit residues: 15.8412
Evaluate side-chains
  66 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0770
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.7542

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 ASN
A 183 GLN
B  53 GLN
B 142 ASN
B 183 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.133592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.097825 restraints weight = 15917.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.101034 restraints weight = 8138.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.103207 restraints weight = 5095.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.104667 restraints weight = 3667.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.105535 restraints weight = 2926.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9456  Z= 0.175
  Angle     :  0.664   7.024  13215  Z= 0.379
  Chirality :  0.046   0.242   1450
  Planarity :  0.005   0.050   1348
  Dihedral  : 20.547 141.551   2050
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  7.44 %
    Favored  : 90.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.06 (0.29), residues: 852
  helix:  1.08 (0.27), residues: 378
  sheet: -0.29 (0.49), residues: 113
  loop : -0.92 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 138 
 TYR   0.022   0.002   TYR B  21 
 PHE   0.012   0.002   PHE A 121 
 TRP   0.016   0.001   TRP B 264 
 HIS   0.007   0.001   HIS B  23 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.18 ( 9456)
  covalent geometry    : angle       0.66366 /  0.38 (13215)
  hydrogen bonds       : bond        0.05848 /  3.60 (  324)
  hydrogen bonds       : angle       4.22894 /  2.86 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7611 (pt0)
REVERT: A  237 ASP cc_start: 0.6188 (OUTLIER) cc_final: 0.5956 (m-30)
REVERT: A  270 ASN cc_start: 0.7859 (t0) cc_final: 0.7398 (t0)
REVERT: B   70 GLU cc_start: 0.8540 (tp30) cc_final: 0.8143 (pm20)
REVERT: B  268 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.7174 (t-90)
REVERT: B  270 ASN cc_start: 0.7506 (t0) cc_final: 0.6944 (t0)
  outliers start: 14
  outliers final: 9
  residues processed: 77
  average time/residue: 0.1003
  time to fit residues: 11.0549
Evaluate side-chains
  68 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  268 HIS
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 50 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:   20.0000
   chunk 19 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    1.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 HIS
B 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.132290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.096367 restraints weight = 16078.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.099506 restraints weight = 8391.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.101629 restraints weight = 5323.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.103066 restraints weight = 3864.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.103994 restraints weight = 3106.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3539
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3539 r_free = 0.3539    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3539 r_free = 0.3539    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3539
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9456  Z= 0.164
  Angle     :  0.597   6.153  13215  Z= 0.350
  Chirality :  0.043   0.162   1450
  Planarity :  0.005   0.050   1348
  Dihedral  : 20.691 141.424   2050
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  9.53 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.01 (0.29), residues: 852
  helix:  0.99 (0.27), residues: 379
  sheet: -0.25 (0.49), residues: 111
  loop : -0.92 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 138 
 TYR   0.013   0.001   TYR A 157 
 PHE   0.013   0.002   PHE B 352 
 TRP   0.007   0.001   TRP B 264 
 HIS   0.007   0.001   HIS B  23 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.16 ( 9456)
  covalent geometry    : angle       0.59676 /  0.35 (13215)
  hydrogen bonds       : bond        0.05056 /  3.18 (  324)
  hydrogen bonds       : angle       4.07911 /  2.74 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8312 (tm-30) cc_final: 0.6974 (tm-30)
REVERT: A   32 ARG cc_start: 0.7264 (mmp-170) cc_final: 0.7028 (mmm160)
REVERT: A   33 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7360 (tp)
REVERT: A  237 ASP cc_start: 0.6159 (OUTLIER) cc_final: 0.5949 (m-30)
REVERT: A  270 ASN cc_start: 0.7816 (t0) cc_final: 0.7323 (t0)
REVERT: B   70 GLU cc_start: 0.8501 (tp30) cc_final: 0.8174 (pm20)
REVERT: B  268 HIS cc_start: 0.7442 (OUTLIER) cc_final: 0.7156 (t-90)
REVERT: B  270 ASN cc_start: 0.7576 (t0) cc_final: 0.7165 (t0)
  outliers start: 20
  outliers final: 11
  residues processed: 81
  average time/residue: 0.0997
  time to fit residues: 11.4398
Evaluate side-chains
  74 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ILE
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  268 HIS
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 19 optimal weight:    0.3980
   chunk 37 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.0788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 ASN
B 183 GLN
** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.133241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.097006 restraints weight = 16147.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.100213 restraints weight = 8414.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.102384 restraints weight = 5326.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.103846 restraints weight = 3866.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.104713 restraints weight = 3103.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3549
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3549 r_free = 0.3549    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3549 r_free = 0.3549    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3549
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9456  Z= 0.135
  Angle     :  0.561   5.657  13215  Z= 0.334
  Chirality :  0.042   0.151   1450
  Planarity :  0.005   0.051   1348
  Dihedral  : 20.814 142.801   2050
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  :  9.66 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.15 (0.29), residues: 852
  helix:  1.11 (0.27), residues: 379
  sheet: -0.17 (0.49), residues: 111
  loop : -0.84 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 138 
 TYR   0.014   0.001   TYR B  17 
 PHE   0.008   0.001   PHE A 151 
 TRP   0.006   0.001   TRP B 264 
 HIS   0.007   0.001   HIS B  23 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.13 ( 9456)
  covalent geometry    : angle       0.56097 /  0.33 (13215)
  hydrogen bonds       : bond        0.04271 /  2.69 (  324)
  hydrogen bonds       : angle       3.87354 /  2.60 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 60
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7384 (tp)
REVERT: A  237 ASP cc_start: 0.6073 (OUTLIER) cc_final: 0.5866 (m-30)
REVERT: A  270 ASN cc_start: 0.7716 (t0) cc_final: 0.7219 (t0)
REVERT: B   70 GLU cc_start: 0.8455 (tp30) cc_final: 0.8192 (pm20)
REVERT: B  270 ASN cc_start: 0.7546 (t0) cc_final: 0.7134 (t0)
  outliers start: 21
  outliers final: 15
  residues processed: 75
  average time/residue: 0.1074
  time to fit residues: 11.3784
Evaluate side-chains
  72 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   33 ILE
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  399 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 71 optimal weight:    0.4980
   chunk 50 optimal weight:   10.0000
   chunk 41 optimal weight:    0.3980
   chunk 63 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 18 optimal weight:    0.5980
   chunk 61 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 82 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 ASN
B 142 ASN
B 346 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.134549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.098272 restraints weight = 15930.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.101505 restraints weight = 8292.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.103679 restraints weight = 5250.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.105151 restraints weight = 3809.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.106083 restraints weight = 3057.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3593
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3593 r_free = 0.3593    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3593 r_free = 0.3593    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3593
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9456  Z= 0.125
  Angle     :  0.548   6.186  13215  Z= 0.327
  Chirality :  0.041   0.144   1450
  Planarity :  0.005   0.051   1348
  Dihedral  : 20.915 143.951   2050
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 11.10 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.31 (0.30), residues: 852
  helix:  1.25 (0.27), residues: 378
  sheet:  0.06 (0.50), residues: 110
  loop : -0.82 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 138 
 TYR   0.015   0.001   TYR B  17 
 PHE   0.007   0.001   PHE A 151 
 TRP   0.006   0.001   TRP A 264 
 HIS   0.007   0.001   HIS B  23 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00218 /  0.12 ( 9456)
  covalent geometry    : angle       0.54802 /  0.33 (13215)
  hydrogen bonds       : bond        0.03837 /  2.42 (  324)
  hydrogen bonds       : angle       3.74882 /  2.51 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 61
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7272 (tp)
REVERT: A  237 ASP cc_start: 0.6066 (OUTLIER) cc_final: 0.5844 (m-30)
REVERT: A  270 ASN cc_start: 0.7737 (t0) cc_final: 0.7190 (t0)
REVERT: B  270 ASN cc_start: 0.7580 (t0) cc_final: 0.7162 (t0)
  outliers start: 22
  outliers final: 16
  residues processed: 78
  average time/residue: 0.0953
  time to fit residues: 10.7420
Evaluate side-chains
  74 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   33 ILE
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  399 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 93 optimal weight:   20.0000
   chunk 49 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0270
   chunk 90 optimal weight:   30.0000
   chunk 34 optimal weight:    0.4980
   chunk 15 optimal weight:    5.9990
   chunk 65 optimal weight:    7.9990
   chunk 79 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 78 optimal weight:    7.9990
   overall best weight:    2.5044

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 ASN
B 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.130132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.094053 restraints weight = 16139.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.096912 restraints weight = 8660.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.098885 restraints weight = 5607.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.100196 restraints weight = 4132.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.101097 restraints weight = 3348.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3494
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3494 r_free = 0.3494    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3494 r_free = 0.3494    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3494
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9456  Z= 0.180
  Angle     :  0.595   5.722  13215  Z= 0.349
  Chirality :  0.044   0.155   1450
  Planarity :  0.005   0.051   1348
  Dihedral  : 21.088 144.557   2050
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 12.14 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.09 (0.29), residues: 852
  helix:  1.03 (0.27), residues: 379
  sheet: -0.18 (0.50), residues: 111
  loop : -0.84 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 233 
 TYR   0.013   0.002   TYR B 319 
 PHE   0.016   0.002   PHE B 119 
 TRP   0.004   0.001   TRP B 124 
 HIS   0.007   0.001   HIS B  23 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.18 ( 9456)
  covalent geometry    : angle       0.59488 /  0.35 (13215)
  hydrogen bonds       : bond        0.04507 /  2.86 (  324)
  hydrogen bonds       : angle       3.85504 /  2.59 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 58
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6937 (pp)
REVERT: A  270 ASN cc_start: 0.7785 (t0) cc_final: 0.7220 (t0)
REVERT: B   17 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.6540 (t80)
REVERT: B   70 GLU cc_start: 0.8538 (tp30) cc_final: 0.8183 (pm20)
REVERT: B  270 ASN cc_start: 0.7633 (t0) cc_final: 0.7245 (t0)
REVERT: B  339 SER cc_start: 0.8331 (OUTLIER) cc_final: 0.8124 (t)
  outliers start: 25
  outliers final: 21
  residues processed: 76
  average time/residue: 0.0906
  time to fit residues: 10.0450
Evaluate side-chains
  82 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 58
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   33 ILE
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  399 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0040
   chunk 2 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0060
   chunk 33 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0070
   chunk 1 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 70 optimal weight:    5.9990
   overall best weight:    0.3626

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 ASN
B  23 HIS
B 142 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.133326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.096935 restraints weight = 15939.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.099948 restraints weight = 8494.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.101990 restraints weight = 5446.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.103257 restraints weight = 3983.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.104256 restraints weight = 3221.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3546
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3546 r_free = 0.3546    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3546 r_free = 0.3546    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3546
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9456  Z= 0.123
  Angle     :  0.543   6.380  13215  Z= 0.322
  Chirality :  0.042   0.185   1450
  Planarity :  0.005   0.050   1348
  Dihedral  : 21.153 145.343   2050
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 12.79 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.39 (0.30), residues: 852
  helix:  1.28 (0.27), residues: 378
  sheet:  0.09 (0.51), residues: 112
  loop : -0.73 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 283 
 TYR   0.015   0.001   TYR B  17 
 PHE   0.014   0.001   PHE B 119 
 TRP   0.006   0.001   TRP A 264 
 HIS   0.008   0.001   HIS B  23 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00208 /  0.12 ( 9456)
  covalent geometry    : angle       0.54322 /  0.32 (13215)
  hydrogen bonds       : bond        0.03674 /  2.31 (  324)
  hydrogen bonds       : angle       3.65690 /  2.45 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 62
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 ASN cc_start: 0.7695 (t0) cc_final: 0.7150 (t0)
REVERT: B   70 GLU cc_start: 0.8455 (tp30) cc_final: 0.8126 (pm20)
REVERT: B  270 ASN cc_start: 0.7613 (t0) cc_final: 0.7217 (t0)
REVERT: B  339 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.8093 (t)
  outliers start: 25
  outliers final: 16
  residues processed: 81
  average time/residue: 0.1102
  time to fit residues: 12.2530
Evaluate side-chains
  76 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  399 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 83 optimal weight:    7.9990
   chunk 73 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 ASN
B 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.129239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.092921 restraints weight = 16158.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.095771 restraints weight = 8714.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.097732 restraints weight = 5667.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.099058 restraints weight = 4186.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.099972 restraints weight = 3396.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3483
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3483
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9456  Z= 0.197
  Angle     :  0.627   8.718  13215  Z= 0.360
  Chirality :  0.044   0.174   1450
  Planarity :  0.005   0.051   1348
  Dihedral  : 21.370 145.698   2050
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 13.32 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.01 (0.29), residues: 852
  helix:  0.94 (0.26), residues: 378
  sheet: -0.22 (0.50), residues: 110
  loop : -0.89 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 138 
 TYR   0.016   0.002   TYR B 319 
 PHE   0.022   0.003   PHE A 352 
 TRP   0.004   0.001   TRP A 462 
 HIS   0.006   0.002   HIS A 145 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00428 /  0.20 ( 9456)
  covalent geometry    : angle       0.62718 /  0.36 (13215)
  hydrogen bonds       : bond        0.04697 /  2.98 (  324)
  hydrogen bonds       : angle       3.86848 /  2.61 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 60
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 ASN cc_start: 0.7801 (t0) cc_final: 0.7209 (t0)
REVERT: B   17 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6291 (t80)
REVERT: B  270 ASN cc_start: 0.7631 (t0) cc_final: 0.7180 (t0)
  outliers start: 26
  outliers final: 21
  residues processed: 78
  average time/residue: 0.0891
  time to fit residues: 10.0838
Evaluate side-chains
  80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 58
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   33 ILE
Chi-restraints excluded: chain A residue   35 TYR
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  399 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 2 optimal weight:    0.1980
   chunk 81 optimal weight:    6.9990
   chunk 29 optimal weight:    0.7980
   chunk 88 optimal weight:   30.0000
   chunk 71 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 91 optimal weight:   20.0000
   overall best weight:    1.7986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 142 ASN
B 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.129595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.093269 restraints weight = 16360.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.096175 restraints weight = 8840.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.098189 restraints weight = 5742.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.099536 restraints weight = 4229.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.100325 restraints weight = 3425.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3498
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9456  Z= 0.155
  Angle     :  0.589   6.603  13215  Z= 0.343
  Chirality :  0.043   0.145   1450
  Planarity :  0.005   0.051   1348
  Dihedral  : 21.419 145.987   2050
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 14.23 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.04 (0.29), residues: 852
  helix:  0.94 (0.26), residues: 379
  sheet: -0.18 (0.49), residues: 116
  loop : -0.83 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 138 
 TYR   0.016   0.001   TYR B  17 
 PHE   0.013   0.002   PHE A 352 
 TRP   0.004   0.001   TRP A 264 
 HIS   0.005   0.001   HIS A 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.16 ( 9456)
  covalent geometry    : angle       0.58864 /  0.34 (13215)
  hydrogen bonds       : bond        0.04296 /  2.74 (  324)
  hydrogen bonds       : angle       3.76777 /  2.54 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 57
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 ASN cc_start: 0.7766 (t0) cc_final: 0.7211 (t0)
REVERT: B   17 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6254 (t80)
REVERT: B   70 GLU cc_start: 0.8398 (tp30) cc_final: 0.8043 (pm20)
REVERT: B  270 ASN cc_start: 0.7624 (t0) cc_final: 0.7172 (t0)
  outliers start: 23
  outliers final: 20
  residues processed: 72
  average time/residue: 0.0937
  time to fit residues: 9.8188
Evaluate side-chains
  77 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 56
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   33 ILE
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  399 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 91 optimal weight:   20.0000
   chunk 24 optimal weight:    6.9990
   chunk 63 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 142 ASN
B 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.129814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.093453 restraints weight = 16048.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.096367 restraints weight = 8706.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.098343 restraints weight = 5673.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.099597 restraints weight = 4196.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.100598 restraints weight = 3410.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3501
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3501 r_free = 0.3501    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3501 r_free = 0.3501    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3501
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.161   9456  Z= 0.182
  Angle     :  0.872  59.200  13215  Z= 0.537
  Chirality :  0.045   0.565   1450
  Planarity :  0.005   0.051   1348
  Dihedral  : 21.422 145.999   2050
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.64 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 14.23 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.05 (0.29), residues: 852
  helix:  0.96 (0.26), residues: 379
  sheet: -0.18 (0.49), residues: 116
  loop : -0.83 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 138 
 TYR   0.016   0.001   TYR B  17 
 PHE   0.012   0.002   PHE A 352 
 TRP   0.004   0.001   TRP A 264 
 HIS   0.005   0.001   HIS A 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.18 ( 9456)
  covalent geometry    : angle       0.87212 /  0.54 (13215)
  hydrogen bonds       : bond        0.04261 /  2.71 (  324)
  hydrogen bonds       : angle       3.76239 /  2.53 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 ASN cc_start: 0.7759 (t0) cc_final: 0.7203 (t0)
REVERT: B   17 TYR cc_start: 0.6984 (OUTLIER) cc_final: 0.6247 (t80)
REVERT: B   70 GLU cc_start: 0.8386 (tp30) cc_final: 0.7994 (pm20)
REVERT: B  142 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.6329 (m-40)
REVERT: B  270 ASN cc_start: 0.7629 (t0) cc_final: 0.7170 (t0)
  outliers start: 23
  outliers final: 21
  residues processed: 71
  average time/residue: 0.0948
  time to fit residues: 9.7886
Evaluate side-chains
  79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   33 ILE
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  399 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 70 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 44 optimal weight:   10.0000
   chunk 76 optimal weight:    2.9990
   chunk 90 optimal weight:   30.0000
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0040
   chunk 14 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.3396

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.129793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.093460 restraints weight = 15958.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.096352 restraints weight = 8676.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.098233 restraints weight = 5664.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.099670 restraints weight = 4201.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.100513 restraints weight = 3402.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3497
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3497
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.154   9456  Z= 0.176
  Angle     :  0.789  46.670  13215  Z= 0.483
  Chirality :  0.044   0.517   1450
  Planarity :  0.005   0.051   1348
  Dihedral  : 21.422 145.999   2050
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.64 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 14.36 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.05 (0.29), residues: 852
  helix:  0.96 (0.26), residues: 379
  sheet: -0.18 (0.49), residues: 116
  loop : -0.83 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 138 
 TYR   0.016   0.001   TYR B  17 
 PHE   0.012   0.002   PHE A 352 
 TRP   0.004   0.001   TRP A 264 
 HIS   0.005   0.001   HIS A 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.18 ( 9456)
  covalent geometry    : angle       0.78865 /  0.48 (13215)
  hydrogen bonds       : bond        0.04261 /  2.71 (  324)
  hydrogen bonds       : angle       3.76239 /  2.53 (  910)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2201.61 seconds
wall clock time: 38 minutes 29.61 seconds (2309.61 seconds total)