Starting phenix.real_space_refine
on Tue Jan 14 08:20:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9enc_19831/01_2025/9enc_19831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9enc_19831/01_2025/9enc_19831.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9enc_19831/01_2025/9enc_19831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9enc_19831/01_2025/9enc_19831.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9enc_19831/01_2025/9enc_19831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9enc_19831/01_2025/9enc_19831.cif"
  }
  resolution = 3.36
  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=   0.002 sd=   0.030
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      74      5.49       5
     S      30      5.16       5
     C    3699      2.51       5
     N    1089      2.21       5
     O    1357      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6249
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2304
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 10, 'TRANS': 270}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2356
          Classifications: {'peptide': 285}
          Link IDs: {'PTRANS': 11, 'TRANS': 273}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 1589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1589
          Classifications: {'RNA': 75}
          Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 27, 'rna3p_pyr': 32}
          Link IDs: {'rna2p': 15, 'rna3p': 59}
  Time building chain proxies: 4.58, per 1000 atoms: 0.73
  Number of scatterers: 6249
  At special positions: 0
  Unit cell: (102.318, 127.686, 65.9568, 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      30     16.00
     P      74     15.00
     O    1357      8.00
     N    1089      7.00
     C    3699      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 114 " - pdb=" SG  CYS A 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 114 " - pdb=" SG  CYS B 327 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.50
  Conformation dependent library (CDL) restraints added in 663.6 milliseconds
  

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1080

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 4 sheets defined
      35.3% alpha, 25.1% beta
      22 base pairs and 25 stacking pairs defined.
    Time for finding SS restraints: 2.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 88 through 100
    Processing helix  chain 'A' and resid 105 through 109
    Processing helix  chain 'A' and resid 159 through 168
      removed outlier: 3.924A  pdb=" N   VAL A 167 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 214
      removed outlier: 3.766A  pdb=" N   TYR A 211 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 262
    Processing helix  chain 'A' and resid 277 through 292
    Processing helix  chain 'A' and resid 297 through 304
      removed outlier: 3.746A  pdb=" N   GLU A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 369
    Processing helix  chain 'B' and resid 88 through 100
      removed outlier: 3.503A  pdb=" N   LYS B  92 " --> pdb=" O   THR B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 109
    Processing helix  chain 'B' and resid 159 through 168
      removed outlier: 3.925A  pdb=" N   VAL B 167 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 214
      removed outlier: 3.667A  pdb=" N   GLN B 214 " --> pdb=" O   ASP B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 226
      removed outlier: 3.791A  pdb=" N   CYS B 226 " --> pdb=" O   ARG B 223 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 223 through 226'
    Processing helix  chain 'B' and resid 259 through 262
    Processing helix  chain 'B' and resid 277 through 291
      removed outlier: 3.659A  pdb=" N   LEU B 288 " --> pdb=" O   ALA B 284 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE B 289 " --> pdb=" O   ILE B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 303
      removed outlier: 3.518A  pdb=" N   GLU B 301 " --> pdb=" O   GLU B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 369
    Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113
      removed outlier: 5.122A  pdb=" N   PHE A 124 " --> pdb=" O   TYR A  71 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   TYR A  71 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ARG A  63 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   HIS A  64 " --> pdb=" O   PRO A 179 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ALA A  66 " --> pdb=" O   TRP A 177 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   TRP A 177 " --> pdb=" O   ALA A  66 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ARG A  68 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113
      removed outlier: 6.346A  pdb=" N   ASP A 326 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   GLN A 126 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
      removed outlier: 9.243A  pdb=" N   LYS A 328 " --> pdb=" O   GLN A 126 " (cutoff:3.500A)
      removed outlier: 11.007A  pdb=" N   ILE A 128 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   THR A 194 " --> pdb=" O   TYR A 325 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   CYS A 327 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   GLU A 192 " --> pdb=" O   CYS A 327 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   LEU A 264 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 5.173A  pdb=" N   LEU A 248 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   GLN A 266 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   VAL A 246 " --> pdb=" O   GLN A 266 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   GLU A 268 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ALA A 244 " --> pdb=" O   GLU A 268 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   THR A 270 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 113
      removed outlier: 5.056A  pdb=" N   PHE B 124 " --> pdb=" O   TYR B  71 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   TYR B  71 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLY B  61 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   HIS B  64 " --> pdb=" O   PRO B 179 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ALA B  66 " --> pdb=" O   TRP B 177 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   TRP B 177 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ARG B  68 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 113
      removed outlier: 7.226A  pdb=" N   SER B 122 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
      removed outlier: 8.631A  pdb=" N   ASP B 326 " --> pdb=" O   SER B 122 " (cutoff:3.500A)
      removed outlier: 8.588A  pdb=" N   PHE B 124 " --> pdb=" O   ASP B 326 " (cutoff:3.500A)
      removed outlier: 9.157A  pdb=" N   LYS B 328 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 10.704A  pdb=" N   GLN B 126 " --> pdb=" O   LYS B 328 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR B 194 " --> pdb=" O   TYR B 325 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   CYS B 327 " --> pdb=" O   GLU B 192 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLU B 192 " --> pdb=" O   CYS B 327 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   PHE B 199 " --> pdb=" O   CYS B 265 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   LEU B 264 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   LEU B 248 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLN B 266 " --> pdb=" O   VAL B 246 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   VAL B 246 " --> pdb=" O   GLN B 266 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   GLU B 268 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   ALA B 244 " --> pdb=" O   GLU B 268 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   THR B 270 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ARG B 239 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   HIS B 220 " --> pdb=" O   ARG B 239 " (cutoff:3.500A)

    185 hydrogen bonds defined for protein.
    516 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      58 hydrogen bonds
      102 hydrogen bond angles
      0 basepair planarities
      22 basepair parallelities
      25 stacking parallelities
  Total time for adding SS restraints: 1.98

  Time building geometry restraints manager: 1.72 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: 1690
        1.34 -     1.45: 1630
        1.45 -     1.57: 3030
        1.57 -     1.69: 148
        1.69 -     1.81: 48
  Bond restraints: 6546
  Sorted by residual:
  bond pdb=" C   GLU B 260 "
       pdb=" N   PRO B 261 "
    ideal  model  delta    sigma   weight residual
    1.334  1.352 -0.018 8.40e-03 1.42e+04 4.65e+00
  bond pdb=" C   GLU A 260 "
       pdb=" N   PRO A 261 "
    ideal  model  delta    sigma   weight residual
    1.337  1.351 -0.014 1.11e-02 8.12e+03 1.69e+00
  bond pdb=" C3'   G D  36 "
       pdb=" O3'   G D  36 "
    ideal  model  delta    sigma   weight residual
    1.427  1.443 -0.016 1.50e-02 4.44e+03 1.14e+00
  bond pdb=" CA  ASN A 232 "
       pdb=" C   ASN A 232 "
    ideal  model  delta    sigma   weight residual
    1.523  1.535 -0.013 1.41e-02 5.03e+03 8.00e-01
  bond pdb=" O3'   G D  36 "
       pdb=" P     A D  37 "
    ideal  model  delta    sigma   weight residual
    1.607  1.620 -0.013 1.50e-02 4.44e+03 7.47e-01
  ... (remaining 6541 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 9122
        2.07 -     4.14: 81
        4.14 -     6.20: 9
        6.20 -     8.27: 0
        8.27 -    10.34: 1
  Bond angle restraints: 9213
  Sorted by residual:
  angle pdb=" C3'   G D  36 "
        pdb=" O3'   G D  36 "
        pdb=" P     A D  37 "
      ideal   model   delta    sigma   weight residual
     120.20  125.79   -5.59 1.50e+00 4.44e-01 1.39e+01
  angle pdb=" O3'   G D  36 "
        pdb=" P     A D  37 "
        pdb=" OP1   A D  37 "
      ideal   model   delta    sigma   weight residual
     108.00  118.34  -10.34 3.00e+00 1.11e-01 1.19e+01
  angle pdb=" C4'   G D  36 "
        pdb=" C3'   G D  36 "
        pdb=" O3'   G D  36 "
      ideal   model   delta    sigma   weight residual
     109.40  113.35   -3.95 1.50e+00 4.44e-01 6.93e+00
  angle pdb=" CA  PHE A 320 "
        pdb=" C   PHE A 320 "
        pdb=" N   PRO A 321 "
      ideal   model   delta    sigma   weight residual
     118.44  122.46   -4.02 1.59e+00 3.96e-01 6.39e+00
  angle pdb=" N   PHE A 320 "
        pdb=" CA  PHE A 320 "
        pdb=" C   PHE A 320 "
      ideal   model   delta    sigma   weight residual
     109.81  114.97   -5.16 2.21e+00 2.05e-01 5.44e+00
  ... (remaining 9208 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.20: 3647
       31.20 -    62.40: 282
       62.40 -    93.60: 79
       93.60 -   124.80: 2
      124.80 -   156.00: 4
  Dihedral angle restraints: 4014
    sinusoidal: 2349
      harmonic: 1665
  Sorted by residual:
  dihedral pdb=" O4'   U D  35 "
           pdb=" C1'   U D  35 "
           pdb=" N1    U D  35 "
           pdb=" C2    U D  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   44.00  156.00     1      1.50e+01 4.44e-03 8.16e+01
  dihedral pdb=" O4'   C D  48 "
           pdb=" C1'   C D  48 "
           pdb=" N1    C D  48 "
           pdb=" C2    C D  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -25.27 -134.73     1      1.50e+01 4.44e-03 7.27e+01
  dihedral pdb=" O4'   A D  37 "
           pdb=" C1'   A D  37 "
           pdb=" N9    A D  37 "
           pdb=" C4    A D  37 "
      ideal   model   delta sinusoidal    sigma   weight residual
     254.00  175.33   78.67     1      1.70e+01 3.46e-03 2.67e+01
  ... (remaining 4011 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 870
       0.042 -    0.084: 148
       0.084 -    0.126: 40
       0.126 -    0.168: 3
       0.168 -    0.210: 2
  Chirality restraints: 1063
  Sorted by residual:
  chirality pdb=" P     A D  37 "
            pdb=" OP1   A D  37 "
            pdb=" OP2   A D  37 "
            pdb=" O5'   A D  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.62   -0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" C1'   A D  58 "
            pdb=" O4'   A D  58 "
            pdb=" C2'   A D  58 "
            pdb=" N9    A D  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.28    0.18 2.00e-01 2.50e+01 7.95e-01
  chirality pdb=" CA  PHE A 320 "
            pdb=" N   PHE A 320 "
            pdb=" C   PHE A 320 "
            pdb=" CB  PHE A 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.80e-01
  ... (remaining 1060 not shown)

  Planarity restraints: 907
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D  32 "    0.026 2.00e-02 2.50e+03   1.32e-02 3.94e+00
        pdb=" N1    C D  32 "   -0.029 2.00e-02 2.50e+03
        pdb=" C2    C D  32 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2    C D  32 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    C D  32 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    C D  32 "    0.004 2.00e-02 2.50e+03
        pdb=" N4    C D  32 "    0.007 2.00e-02 2.50e+03
        pdb=" C5    C D  32 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    C D  32 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  58 "   -0.017 2.00e-02 2.50e+03   8.90e-03 2.18e+00
        pdb=" N9    A D  58 "    0.023 2.00e-02 2.50e+03
        pdb=" C8    A D  58 "    0.000 2.00e-02 2.50e+03
        pdb=" N7    A D  58 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    A D  58 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A D  58 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6    A D  58 "   -0.001 2.00e-02 2.50e+03
        pdb=" N1    A D  58 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A D  58 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  58 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  58 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D  44 "   -0.018 2.00e-02 2.50e+03   9.34e-03 1.96e+00
        pdb=" N1    C D  44 "    0.020 2.00e-02 2.50e+03
        pdb=" C2    C D  44 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    C D  44 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    C D  44 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    C D  44 "   -0.001 2.00e-02 2.50e+03
        pdb=" N4    C D  44 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5    C D  44 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    C D  44 "    0.004 2.00e-02 2.50e+03
  ... (remaining 904 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1073
        2.77 -     3.30: 5518
        3.30 -     3.83: 10864
        3.83 -     4.37: 12384
        4.37 -     4.90: 20070
  Nonbonded interactions: 49909
  Sorted by model distance:
  nonbonded pdb=" OP2   G D  45 "
            pdb=" N2    G D  45 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" O2'   U D  35 "
            pdb=" OP1   A D  37 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG  SER B 105 "
            pdb=" OG1 THR B 108 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O2'   A D   7 "
            pdb=" O2    C D  48 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OH  TYR A 197 "
            pdb=" O   VAL A 318 "
     model   vdw
     2.305 3.040
  ... (remaining 49904 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 61 through 228 or resid 236 through 249 or resid 257 throu \ 
gh 369))
  selection = (chain 'B' and (resid 61 through 134 or resid 157 through 369))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.770
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
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      :  0.002   0.027   6546  Z= 0.153
  Angle     :  0.512  10.339   9213  Z= 0.292
  Chirality :  0.035   0.210   1063
  Planarity :  0.003   0.033    907
  Dihedral  : 21.396 156.003   2928
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 27.66 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.36), residues: 552
  helix:  1.24 (0.40), residues: 172
  sheet:  0.61 (0.57), residues: 87
  loop : -1.22 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 352 
 HIS   0.003   0.001   HIS B 360 
 PHE   0.017   0.001   PHE B 320 
 TYR   0.006   0.001   TYR A 216 
 ARG   0.003   0.000   ARG A 187 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.632 
Fit side-chains
REVERT: A  293 MET cc_start: 0.7799 (ttt) cc_final: 0.7592 (ttt)
REVERT: A  295 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8216 (ttpp)
  outliers start: 1
  outliers final: 0
  residues processed: 33
  average time/residue: 0.2623
  time to fit residues: 11.2916
Evaluate side-chains
  22 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 57 optimal weight:    6.9990
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.072373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.053141 restraints weight = 20555.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 3.04
r_work: 0.2962 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.1151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6546  Z= 0.217
  Angle     :  0.527  10.950   9213  Z= 0.275
  Chirality :  0.038   0.241   1063
  Planarity :  0.004   0.032    907
  Dihedral  : 20.786 154.016   1796
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 25.85 %
    Favored  : 72.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.20 (0.36), residues: 552
  helix:  2.07 (0.38), residues: 167
  sheet:  0.47 (0.58), residues: 84
  loop : -1.15 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 258 
 HIS   0.005   0.001   HIS B 360 
 PHE   0.016   0.001   PHE B 320 
 TYR   0.009   0.001   TYR A 195 
 ARG   0.003   0.001   ARG A 257 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8479 (mpp) cc_final: 0.8138 (mmm)
REVERT: A  258 TRP cc_start: 0.8126 (t60) cc_final: 0.7506 (t60)
REVERT: A  293 MET cc_start: 0.7780 (ttt) cc_final: 0.7577 (ttm)
  outliers start: 8
  outliers final: 2
  residues processed: 28
  average time/residue: 0.1797
  time to fit residues: 7.4380
Evaluate side-chains
  23 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  295 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0970
   chunk 12 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0170
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 8 optimal weight:    0.4980
   chunk 59 optimal weight:   10.0000
   overall best weight:    0.5018

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.074099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.054590 restraints weight = 20915.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 3.10
r_work: 0.3009 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6546  Z= 0.130
  Angle     :  0.470   9.360   9213  Z= 0.244
  Chirality :  0.036   0.217   1063
  Planarity :  0.003   0.031    907
  Dihedral  : 20.688 153.928   1796
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 24.05 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.51 (0.36), residues: 552
  helix:  2.53 (0.38), residues: 167
  sheet:  0.55 (0.57), residues: 91
  loop : -1.10 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 258 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.018   0.001   PHE B 320 
 TYR   0.008   0.001   TYR B 216 
 ARG   0.002   0.000   ARG A 223 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 23
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8505 (mpp) cc_final: 0.8126 (mmm)
REVERT: A  258 TRP cc_start: 0.8047 (t60) cc_final: 0.7526 (t60)
REVERT: A  293 MET cc_start: 0.7650 (ttt) cc_final: 0.7312 (ttm)
REVERT: B   72 MET cc_start: 0.8509 (mmm) cc_final: 0.7705 (mmm)
  outliers start: 10
  outliers final: 3
  residues processed: 29
  average time/residue: 0.1705
  time to fit residues: 7.3365
Evaluate side-chains
  24 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  295 LYS
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   chunk 57 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0020
   overall best weight:    1.7194

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

Flipped N/Q/H residues before XYZ refinement:
B 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.071557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.051763 restraints weight = 21042.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 3.09
r_work: 0.2932 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6546  Z= 0.272
  Angle     :  0.533   7.244   9213  Z= 0.276
  Chirality :  0.038   0.178   1063
  Planarity :  0.004   0.035    907
  Dihedral  : 20.822 156.659   1796
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 23.85 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.28 (0.36), residues: 552
  helix:  2.34 (0.38), residues: 167
  sheet:  0.25 (0.55), residues: 91
  loop : -1.18 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  74 
 HIS   0.005   0.001   HIS B 360 
 PHE   0.017   0.002   PHE B  94 
 TYR   0.011   0.001   TYR B 216 
 ARG   0.002   0.000   ARG A 201 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 21
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8608 (mpp) cc_final: 0.8223 (mmm)
REVERT: A  229 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8156 (t0)
REVERT: A  258 TRP cc_start: 0.8222 (t60) cc_final: 0.7747 (t60)
REVERT: A  293 MET cc_start: 0.7751 (ttt) cc_final: 0.7336 (ttm)
  outliers start: 10
  outliers final: 5
  residues processed: 29
  average time/residue: 0.1959
  time to fit residues: 7.9711
Evaluate side-chains
  27 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue  133 ARG
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 32 optimal weight:    0.2980
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.070977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.051091 restraints weight = 21224.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 3.10
r_work: 0.2900 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6546  Z= 0.283
  Angle     :  0.534   5.942   9213  Z= 0.276
  Chirality :  0.038   0.195   1063
  Planarity :  0.004   0.034    907
  Dihedral  : 20.968 159.419   1792
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 23.85 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.11 (0.36), residues: 552
  helix:  2.18 (0.38), residues: 167
  sheet:  0.03 (0.55), residues: 91
  loop : -1.21 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 352 
 HIS   0.005   0.001   HIS B 360 
 PHE   0.016   0.002   PHE B 320 
 TYR   0.011   0.001   TYR A 195 
 ARG   0.003   0.000   ARG A 201 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8720 (mpp) cc_final: 0.8317 (mmm)
REVERT: A  229 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8329 (t70)
REVERT: A  258 TRP cc_start: 0.8227 (t60) cc_final: 0.7748 (t60)
REVERT: A  293 MET cc_start: 0.7834 (ttt) cc_final: 0.7409 (ttm)
  outliers start: 8
  outliers final: 3
  residues processed: 29
  average time/residue: 0.1689
  time to fit residues: 7.3184
Evaluate side-chains
  26 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain B residue  133 ARG
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 19 optimal weight:    0.3980
   chunk 55 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 60 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0670
   chunk 0 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 62 optimal weight:    8.9990
   overall best weight:    0.8320

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.072827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.052972 restraints weight = 20827.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 3.10
r_work: 0.2955 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6546  Z= 0.155
  Angle     :  0.464   5.927   9213  Z= 0.240
  Chirality :  0.035   0.181   1063
  Planarity :  0.003   0.034    907
  Dihedral  : 20.909 158.603   1792
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 23.85 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.38 (0.36), residues: 552
  helix:  2.52 (0.38), residues: 167
  sheet:  0.23 (0.57), residues: 89
  loop : -1.14 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 352 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.021   0.001   PHE B 320 
 TYR   0.006   0.001   TYR B 216 
 ARG   0.001   0.000   ARG B 166 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.615 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8700 (mpp) cc_final: 0.8291 (mmm)
REVERT: A  229 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8174 (t0)
REVERT: A  258 TRP cc_start: 0.8198 (t60) cc_final: 0.7808 (t60)
REVERT: A  293 MET cc_start: 0.7804 (ttt) cc_final: 0.7449 (ttm)
  outliers start: 8
  outliers final: 4
  residues processed: 28
  average time/residue: 0.1859
  time to fit residues: 7.4898
Evaluate side-chains
  27 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  320 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0070
   chunk 30 optimal weight:    0.0980
   chunk 36 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 60 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.5600

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.073753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.054025 restraints weight = 21159.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 3.05
r_work: 0.2986 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6546  Z= 0.129
  Angle     :  0.446   5.956   9213  Z= 0.229
  Chirality :  0.035   0.167   1063
  Planarity :  0.003   0.034    907
  Dihedral  : 20.896 159.735   1792
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 24.05 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.53 (0.36), residues: 552
  helix:  2.63 (0.38), residues: 168
  sheet:  0.35 (0.58), residues: 89
  loop : -1.08 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  74 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.021   0.001   PHE B 320 
 TYR   0.006   0.001   TYR A 216 
 ARG   0.001   0.000   ARG B 280 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.654 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8714 (mpp) cc_final: 0.8287 (mmm)
REVERT: A  229 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8147 (t0)
REVERT: A  258 TRP cc_start: 0.8121 (t60) cc_final: 0.7706 (t60)
REVERT: A  293 MET cc_start: 0.7782 (ttt) cc_final: 0.7458 (ttm)
  outliers start: 5
  outliers final: 3
  residues processed: 26
  average time/residue: 0.1516
  time to fit residues: 6.2427
Evaluate side-chains
  26 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 52 optimal weight:    0.2980
   chunk 20 optimal weight:    0.0570
   chunk 29 optimal weight:    3.9990
   chunk 62 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    1.3902

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.072275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.052276 restraints weight = 20846.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 3.06
r_work: 0.2937 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6546  Z= 0.221
  Angle     :  0.483   6.034   9213  Z= 0.249
  Chirality :  0.036   0.175   1063
  Planarity :  0.004   0.034    907
  Dihedral  : 20.985 163.149   1792
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 23.65 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.38 (0.36), residues: 552
  helix:  2.48 (0.38), residues: 167
  sheet:  0.15 (0.56), residues: 89
  loop : -1.09 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  74 
 HIS   0.005   0.001   HIS B 360 
 PHE   0.021   0.001   PHE B 320 
 TYR   0.011   0.001   TYR A 216 
 ARG   0.002   0.000   ARG A 201 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.621 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8750 (mpp) cc_final: 0.8346 (mmm)
REVERT: A  229 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8142 (t0)
REVERT: A  258 TRP cc_start: 0.8188 (t60) cc_final: 0.7792 (t60)
REVERT: A  282 MET cc_start: 0.7911 (mtm) cc_final: 0.7531 (mtt)
REVERT: A  293 MET cc_start: 0.7801 (ttt) cc_final: 0.7434 (ttm)
REVERT: B  126 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8017 (tp-100)
  outliers start: 8
  outliers final: 4
  residues processed: 29
  average time/residue: 0.1304
  time to fit residues: 6.0979
Evaluate side-chains
  28 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 58 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 61 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    1.3182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.072282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.052309 restraints weight = 21035.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 3.09
r_work: 0.2936 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6546  Z= 0.212
  Angle     :  0.478   5.952   9213  Z= 0.246
  Chirality :  0.036   0.175   1063
  Planarity :  0.003   0.033    907
  Dihedral  : 21.048 165.842   1792
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 23.85 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.32 (0.36), residues: 552
  helix:  2.44 (0.38), residues: 167
  sheet:  0.10 (0.56), residues: 89
  loop : -1.13 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 352 
 HIS   0.004   0.001   HIS B 360 
 PHE   0.019   0.001   PHE B 320 
 TYR   0.009   0.001   TYR A 216 
 ARG   0.001   0.000   ARG B 159 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.568 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8735 (mpp) cc_final: 0.8324 (mmm)
REVERT: A  229 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8299 (t70)
REVERT: A  258 TRP cc_start: 0.8188 (t60) cc_final: 0.7746 (t60)
REVERT: A  293 MET cc_start: 0.7803 (ttt) cc_final: 0.7402 (ttm)
  outliers start: 7
  outliers final: 5
  residues processed: 27
  average time/residue: 0.1361
  time to fit residues: 5.9336
Evaluate side-chains
  28 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  320 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 59 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
B 126 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.072496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.052520 restraints weight = 21171.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 3.08
r_work: 0.2942 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6546  Z= 0.198
  Angle     :  0.477   5.911   9213  Z= 0.245
  Chirality :  0.035   0.175   1063
  Planarity :  0.003   0.032    907
  Dihedral  : 21.058 166.653   1792
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 23.85 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.30 (0.36), residues: 552
  helix:  2.37 (0.38), residues: 167
  sheet:  0.03 (0.56), residues: 90
  loop : -1.09 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 352 
 HIS   0.004   0.001   HIS B 360 
 PHE   0.019   0.001   PHE B 320 
 TYR   0.012   0.001   TYR A 216 
 ARG   0.001   0.000   ARG A 201 

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.621 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8732 (mpp) cc_final: 0.8325 (mmm)
REVERT: A  229 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8315 (t70)
REVERT: A  258 TRP cc_start: 0.8204 (t60) cc_final: 0.7780 (t60)
REVERT: A  293 MET cc_start: 0.7801 (ttt) cc_final: 0.7388 (ttm)
  outliers start: 7
  outliers final: 4
  residues processed: 28
  average time/residue: 0.1413
  time to fit residues: 6.3301
Evaluate side-chains
  27 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 56 optimal weight:    8.9990
   chunk 58 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 9 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 126 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.073293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.053329 restraints weight = 21177.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 3.08
r_work: 0.2964 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6546  Z= 0.157
  Angle     :  0.457   5.892   9213  Z= 0.234
  Chirality :  0.035   0.166   1063
  Planarity :  0.003   0.034    907
  Dihedral  : 21.010 166.684   1792
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 23.65 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.36), residues: 552
  helix:  2.43 (0.38), residues: 168
  sheet:  0.17 (0.57), residues: 89
  loop : -1.09 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 352 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.020   0.001   PHE B 320 
 TYR   0.005   0.001   TYR A 197 
 ARG   0.002   0.000   ARG A 280 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2811.28 seconds
wall clock time: 50 minutes 59.68 seconds (3059.68 seconds total)