Starting phenix.real_space_refine
on Thu Mar 13 17:28:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zn5_14801/03_2025/7zn5_14801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zn5_14801/03_2025/7zn5_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zn5_14801/03_2025/7zn5_14801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zn5_14801/03_2025/7zn5_14801.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zn5_14801/03_2025/7zn5_14801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zn5_14801/03_2025/7zn5_14801.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 7.54, per 1000 atoms: 0.83
  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: 2.43
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 2.93
  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: 2.75

  Time building geometry restraints manager: 2.66 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: 13059
        2.23 -     4.45: 119
        4.45 -     6.68: 28
        6.68 -     8.90: 3
        8.90 -    11.13: 6
  Bond angle restraints: 13215
  Sorted by residual:
  angle pdb=" CA  ARG B 138 "
        pdb=" CB  ARG B 138 "
        pdb=" CG  ARG B 138 "
      ideal   model   delta    sigma   weight residual
     114.10  121.66   -7.56 2.00e+00 2.50e-01 1.43e+01
  angle pdb=" NZ  LLP A 309 "
        pdb=" C4' LLP A 309 "
        pdb=" C4  LLP A 309 "
      ideal   model   delta    sigma   weight residual
     120.09  108.96   11.13 3.00e+00 1.11e-01 1.38e+01
  angle pdb=" NZ  LLP B 309 "
        pdb=" C4' LLP B 309 "
        pdb=" C4  LLP B 309 "
      ideal   model   delta    sigma   weight residual
     120.09  108.98   11.11 3.00e+00 1.11e-01 1.37e+01
  angle pdb=" CE  LLP A 309 "
        pdb=" NZ  LLP A 309 "
        pdb=" C4' LLP A 309 "
      ideal   model   delta    sigma   weight residual
     119.26  108.86   10.40 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" C   LEU A  49 "
        pdb=" N   LYS A  50 "
        pdb=" CA  LYS A  50 "
      ideal   model   delta    sigma   weight residual
     122.08  127.01   -4.93 1.47e+00 4.63e-01 1.12e+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: 1046
       0.032 -    0.064: 257
       0.064 -    0.096: 92
       0.096 -    0.128: 49
       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:             0.920
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.860
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
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      :  0.005   0.182   9456  Z= 0.316
  Angle     :  0.621  11.128  13215  Z= 0.319
  Chirality :  0.037   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.010   0.001   TRP A 264 
 HIS   0.003   0.001   HIS A 113 
 PHE   0.011   0.001   PHE A 128 
 TYR   0.019   0.001   TYR A  82 
 ARG   0.003   0.000   ARG B 138 

*********************** 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  : 0.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.8787 (pt) cc_final: 0.8579 (mt)
REVERT: A  270 ASN cc_start: 0.7690 (t0) cc_final: 0.7390 (t0)
REVERT: B  270 ASN cc_start: 0.7313 (t0) cc_final: 0.6887 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 101
  average time/residue: 0.2433
  time to fit residues: 33.0963
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  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    9.9990
   chunk 54 optimal weight:    6.9990
   chunk 85 optimal weight:    6.9990
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
A 183 GLN
B  53 GLN
B  62 GLN
** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.127976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.091985 restraints weight = 16103.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.094796 restraints weight = 8690.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.096702 restraints weight = 5655.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3423
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9456  Z= 0.313
  Angle     :  0.681   7.217  13215  Z= 0.380
  Chirality :  0.045   0.163   1450
  Planarity :  0.006   0.049   1348
  Dihedral  : 20.598 138.873   2050
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  :  7.96 %
    Favored  : 89.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.29), residues: 852
  helix:  0.66 (0.26), residues: 380
  sheet: -0.38 (0.47), residues: 119
  loop : -0.91 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 264 
 HIS   0.006   0.002   HIS A 110 
 PHE   0.019   0.003   PHE B 352 
 TYR   0.025   0.002   TYR B  21 
 ARG   0.003   0.001   ARG A 163 

*********************** 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
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7683 (pt0)
REVERT: A  270 ASN cc_start: 0.7861 (t0) cc_final: 0.7389 (t0)
REVERT: B   17 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.6402 (t80)
REVERT: B   62 GLN cc_start: 0.6146 (OUTLIER) cc_final: 0.5136 (tp40)
REVERT: B   70 GLU cc_start: 0.8556 (tp30) cc_final: 0.8140 (pm20)
REVERT: B  268 HIS cc_start: 0.7534 (OUTLIER) cc_final: 0.7231 (t-90)
REVERT: B  270 ASN cc_start: 0.7509 (t0) cc_final: 0.7039 (t0)
  outliers start: 18
  outliers final: 11
  residues processed: 81
  average time/residue: 0.2186
  time to fit residues: 24.8903
Evaluate side-chains
  72 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   17 TYR
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue   62 GLN
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 7 optimal weight:    4.9990
   chunk 60 optimal weight:    0.1980
   chunk 74 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.128904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.092782 restraints weight = 16284.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.095628 restraints weight = 8783.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.097579 restraints weight = 5717.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3448
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3448 r_free = 0.3448    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3448 r_free = 0.3448    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3448
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2125

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= 0.224
  Angle     :  0.605   5.680  13215  Z= 0.343
  Chirality :  0.042   0.152   1450
  Planarity :  0.005   0.050   1348
  Dihedral  : 20.809 142.211   2050
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 10.05 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.29), residues: 852
  helix:  0.76 (0.27), residues: 379
  sheet: -0.39 (0.48), residues: 115
  loop : -0.89 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 264 
 HIS   0.006   0.001   HIS B  23 
 PHE   0.011   0.002   PHE A 151 
 TYR   0.019   0.001   TYR B  21 
 ARG   0.002   0.000   ARG A 138 

*********************** 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
  90 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 ASN cc_start: 0.7796 (t0) cc_final: 0.7267 (t0)
REVERT: B   17 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6293 (t80)
REVERT: B  268 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.7140 (t-90)
REVERT: B  270 ASN cc_start: 0.7553 (t0) cc_final: 0.7023 (t0)
REVERT: B  339 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.8142 (t)
  outliers start: 25
  outliers final: 18
  residues processed: 83
  average time/residue: 0.2333
  time to fit residues: 26.8918
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  : 0.935 
-------------------------------------------------------------------------------
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  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   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  251 SER
Chi-restraints excluded: chain B residue  268 HIS
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 20 optimal weight:    0.1980
   chunk 31 optimal weight:    0.9980
   chunk 2 optimal weight:    0.2980
   chunk 84 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
A 183 GLN
B  62 GLN
** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.132531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.096366 restraints weight = 15863.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.099385 restraints weight = 8452.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.101429 restraints weight = 5412.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3519
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3519
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9456  Z= 0.161
  Angle     :  0.549   5.351  13215  Z= 0.316
  Chirality :  0.039   0.142   1450
  Planarity :  0.005   0.049   1348
  Dihedral  : 21.093 144.842   2050
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 12.27 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.30), residues: 852
  helix:  1.19 (0.27), residues: 379
  sheet: -0.14 (0.49), residues: 121
  loop : -0.85 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 264 
 HIS   0.006   0.001   HIS B  23 
 PHE   0.008   0.001   PHE A 151 
 TYR   0.016   0.001   TYR B  17 
 ARG   0.002   0.000   ARG A 283 

*********************** 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
  91 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7276 (pt0)
REVERT: A   33 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8078 (tt)
REVERT: A  270 ASN cc_start: 0.7764 (t0) cc_final: 0.7241 (t0)
REVERT: B   17 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.6317 (t80)
REVERT: B   70 GLU cc_start: 0.8438 (tp30) cc_final: 0.7997 (pm20)
REVERT: B  270 ASN cc_start: 0.7598 (t0) cc_final: 0.7104 (t0)
  outliers start: 23
  outliers final: 12
  residues processed: 83
  average time/residue: 0.2076
  time to fit residues: 24.4591
Evaluate side-chains
  76 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
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   82 TYR
Chi-restraints excluded: chain A residue  251 SER
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  251 SER
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 83 optimal weight:    0.0470
   chunk 39 optimal weight:    5.9990
   chunk 85 optimal weight:    4.9990
   chunk 90 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9980
   chunk 79 optimal weight:   10.0000
   chunk 66 optimal weight:    0.8980
   chunk 89 optimal weight:   10.0000
   chunk 61 optimal weight:    7.9990
   chunk 88 optimal weight:   10.0000
   overall best weight:    2.5882

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
A 183 GLN
B 142 ASN
B 183 GLN
B 361 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.127886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.091254 restraints weight = 16294.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.094040 restraints weight = 8954.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.095915 restraints weight = 5903.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3410
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3410 r_free = 0.3410    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3410 r_free = 0.3410    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3410
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9456  Z= 0.282
  Angle     :  0.630   5.311  13215  Z= 0.356
  Chirality :  0.042   0.164   1450
  Planarity :  0.006   0.051   1348
  Dihedral  : 21.502 145.355   2050
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 14.88 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.29), residues: 852
  helix:  0.82 (0.26), residues: 378
  sheet: -0.25 (0.48), residues: 116
  loop : -0.93 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 124 
 HIS   0.007   0.002   HIS B  23 
 PHE   0.016   0.002   PHE B 352 
 TYR   0.017   0.002   TYR B  17 
 ARG   0.006   0.000   ARG A  32 

*********************** 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
  91 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 63
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A  270 ASN cc_start: 0.7763 (t0) cc_final: 0.7226 (t0)
REVERT: B   17 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6456 (t80)
REVERT: B   70 GLU cc_start: 0.8505 (tp30) cc_final: 0.7960 (pm20)
REVERT: B  270 ASN cc_start: 0.7633 (t0) cc_final: 0.7130 (t0)
REVERT: B  339 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8192 (t)
  outliers start: 28
  outliers final: 18
  residues processed: 83
  average time/residue: 0.2202
  time to fit residues: 25.6040
Evaluate side-chains
  82 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
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   82 TYR
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  291 SER
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0030
   chunk 50 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
B  23 HIS
** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.131527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.095124 restraints weight = 16023.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.098049 restraints weight = 8633.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.100030 restraints weight = 5606.767|
|-----------------------------------------------------------------------------|
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 |
|-----------------------------------------------------------------------------|
r_final: 0.3494
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9456  Z= 0.162
  Angle     :  0.554   5.897  13215  Z= 0.316
  Chirality :  0.040   0.146   1450
  Planarity :  0.005   0.050   1348
  Dihedral  : 21.575 146.016   2050
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.93 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.30), residues: 852
  helix:  1.19 (0.27), residues: 379
  sheet: -0.01 (0.49), residues: 115
  loop : -0.90 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 264 
 HIS   0.008   0.001   HIS B  23 
 PHE   0.011   0.001   PHE B 119 
 TYR   0.017   0.001   TYR B  17 
 ARG   0.002   0.000   ARG A 283 

*********************** 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
  87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 67
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 ASN cc_start: 0.7677 (t0) cc_final: 0.7253 (t0)
REVERT: B   17 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6312 (t80)
REVERT: B   70 GLU cc_start: 0.8388 (tp30) cc_final: 0.7933 (pm20)
REVERT: B  270 ASN cc_start: 0.7609 (t0) cc_final: 0.7122 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 81
  average time/residue: 0.2120
  time to fit residues: 24.3748
Evaluate side-chains
  80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
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   82 TYR
Chi-restraints excluded: chain A residue  251 SER
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  251 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.130356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.094107 restraints weight = 16383.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.097039 restraints weight = 8789.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.099041 restraints weight = 5707.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3482
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3482
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.2796

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= 0.181
  Angle     :  0.558   6.204  13215  Z= 0.318
  Chirality :  0.040   0.177   1450
  Planarity :  0.005   0.049   1348
  Dihedral  : 21.762 145.994   2050
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 16.19 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.30), residues: 852
  helix:  1.22 (0.27), residues: 378
  sheet:  0.06 (0.49), residues: 116
  loop : -0.89 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 264 
 HIS   0.004   0.001   HIS A 110 
 PHE   0.009   0.001   PHE B 352 
 TYR   0.016   0.001   TYR B  17 
 ARG   0.001   0.000   ARG A  32 

*********************** 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
  90 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 67
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 ASN cc_start: 0.7668 (t0) cc_final: 0.7162 (t0)
REVERT: B   17 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6388 (t80)
REVERT: B   70 GLU cc_start: 0.8399 (tp30) cc_final: 0.7946 (pm20)
REVERT: B  270 ASN cc_start: 0.7661 (t0) cc_final: 0.7111 (t0)
REVERT: B  339 SER cc_start: 0.8325 (OUTLIER) cc_final: 0.8112 (t)
  outliers start: 23
  outliers final: 19
  residues processed: 83
  average time/residue: 0.2669
  time to fit residues: 32.9922
Evaluate side-chains
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
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  251 SER
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   72 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 13 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    0.7980
   chunk 86 optimal weight:   10.0000
   chunk 61 optimal weight:    0.0060
   chunk 3 optimal weight:   10.0000
   chunk 83 optimal weight:    6.9990
   chunk 37 optimal weight:    0.6980
   chunk 82 optimal weight:    4.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3959 r_free = 0.3959 target = 0.131986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.095801 restraints weight = 16422.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.098712 restraints weight = 8757.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.100788 restraints weight = 5682.869|
|-----------------------------------------------------------------------------|
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 |
|-----------------------------------------------------------------------------|
r_final: 0.3501
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9456  Z= 0.158
  Angle     :  0.541   6.446  13215  Z= 0.308
  Chirality :  0.039   0.148   1450
  Planarity :  0.005   0.049   1348
  Dihedral  : 21.808 145.681   2050
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.58 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.30), residues: 852
  helix:  1.36 (0.27), residues: 378
  sheet:  0.17 (0.51), residues: 111
  loop : -0.84 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 264 
 HIS   0.003   0.001   HIS A 110 
 PHE   0.009   0.001   PHE A 119 
 TYR   0.016   0.001   TYR B  17 
 ARG   0.002   0.000   ARG A  32 

*********************** 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
  90 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 ASN cc_start: 0.7597 (t0) cc_final: 0.7168 (t0)
REVERT: B   17 TYR cc_start: 0.7090 (OUTLIER) cc_final: 0.6363 (t80)
REVERT: B   70 GLU cc_start: 0.8360 (tp30) cc_final: 0.7922 (pm20)
REVERT: B  270 ASN cc_start: 0.7631 (t0) cc_final: 0.7073 (t0)
REVERT: B  339 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8138 (t)
  outliers start: 25
  outliers final: 20
  residues processed: 84
  average time/residue: 0.2015
  time to fit residues: 24.3608
Evaluate side-chains
  85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
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  251 SER
Chi-restraints excluded: chain A residue  291 SER
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   72 ILE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 92 optimal weight:    8.9990
   chunk 76 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3937 r_free = 0.3937 target = 0.130442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.094494 restraints weight = 16234.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.097372 restraints weight = 8752.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.099340 restraints weight = 5690.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3487
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3487 r_free = 0.3487    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 = 0.3487 r_free = 0.3487    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3487
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.2961

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= 0.188
  Angle     :  0.561   7.878  13215  Z= 0.317
  Chirality :  0.040   0.161   1450
  Planarity :  0.005   0.049   1348
  Dihedral  : 21.920 145.033   2050
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.23 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.30), residues: 852
  helix:  1.27 (0.27), residues: 378
  sheet:  0.16 (0.52), residues: 111
  loop : -0.81 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 264 
 HIS   0.004   0.001   HIS A 110 
 PHE   0.013   0.001   PHE A 119 
 TYR   0.016   0.001   TYR B  17 
 ARG   0.002   0.000   ARG B 138 

*********************** 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
  89 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 64
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 ASN cc_start: 0.7604 (t0) cc_final: 0.7175 (t0)
REVERT: B   17 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6454 (t80)
REVERT: B   70 GLU cc_start: 0.8381 (tp30) cc_final: 0.7987 (pm20)
REVERT: B  270 ASN cc_start: 0.7646 (t0) cc_final: 0.7211 (t0)
REVERT: B  339 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.8098 (t)
  outliers start: 25
  outliers final: 21
  residues processed: 83
  average time/residue: 0.2048
  time to fit residues: 24.6952
Evaluate side-chains
  86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 63
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
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  251 SER
Chi-restraints excluded: chain A residue  291 SER
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   72 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 39 optimal weight:    0.0470
   chunk 31 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 46 optimal weight:    8.9990
   chunk 64 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 43 optimal weight:    8.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3962 r_free = 0.3962 target = 0.132313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.096366 restraints weight = 16313.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.099339 restraints weight = 8716.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.101402 restraints weight = 5621.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3504
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3504 r_free = 0.3504    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 = 0.3504 r_free = 0.3504    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3504
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.3004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9456  Z= 0.160
  Angle     :  0.547   6.845  13215  Z= 0.309
  Chirality :  0.039   0.152   1450
  Planarity :  0.005   0.049   1348
  Dihedral  : 21.929 144.776   2050
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 16.71 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.30), residues: 852
  helix:  1.39 (0.27), residues: 378
  sheet:  0.22 (0.52), residues: 111
  loop : -0.78 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 264 
 HIS   0.003   0.001   HIS A 110 
 PHE   0.010   0.001   PHE A 119 
 TYR   0.016   0.001   TYR B  17 
 ARG   0.002   0.000   ARG B 138 

********************** 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
  89 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 63
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 ASN cc_start: 0.7571 (t0) cc_final: 0.7155 (t0)
REVERT: B   17 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6442 (t80)
REVERT: B   70 GLU cc_start: 0.8368 (tp30) cc_final: 0.7989 (pm20)
REVERT: B  270 ASN cc_start: 0.7647 (t0) cc_final: 0.7206 (t0)
REVERT: B  339 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.8120 (t)
  outliers start: 26
  outliers final: 22
  residues processed: 82
  average time/residue: 0.1911
  time to fit residues: 22.6182
Evaluate side-chains
  86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 62
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
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  251 SER
Chi-restraints excluded: chain A residue  291 SER
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   72 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0470
   chunk 18 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 91 optimal weight:    7.9990
   chunk 48 optimal weight:    8.9990
   chunk 28 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    1.2882

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3948 r_free = 0.3948 target = 0.131251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.095341 restraints weight = 16341.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.098253 restraints weight = 8821.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.100258 restraints weight = 5733.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3490
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3490 r_free = 0.3490    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 = 0.3490 r_free = 0.3490    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3490
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9456  Z= 0.187
  Angle     :  0.559   6.737  13215  Z= 0.315
  Chirality :  0.040   0.148   1450
  Planarity :  0.005   0.049   1348
  Dihedral  : 22.002 144.573   2050
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.97 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.30), residues: 852
  helix:  1.32 (0.27), residues: 378
  sheet:  0.11 (0.52), residues: 107
  loop : -0.73 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 264 
 HIS   0.004   0.001   HIS A 110 
 PHE   0.015   0.001   PHE B 119 
 TYR   0.016   0.001   TYR B  17 
 ARG   0.002   0.000   ARG B 138 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4080.64 seconds
wall clock time: 71 minutes 51.10 seconds (4311.10 seconds total)