Starting phenix.real_space_refine
on Wed Aug  5 09:15:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nzo_49954/08_2026/9nzo_49954.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nzo_49954/08_2026/9nzo_49954.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nzo_49954/08_2026/9nzo_49954.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nzo_49954/08_2026/9nzo_49954.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nzo_49954/08_2026/9nzo_49954.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nzo_49954/08_2026/9nzo_49954.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.029
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     168      5.49       5
     S      13      5.16       5
     C    5078      2.51       5
     N    1642      2.21       5
     O    2123      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9024
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 1994
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 1994
          Classifications: {'peptide': 249}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 9, 'TRANS': 239}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 72
          Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 5, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 56
    Chain: "D"
      Number of atoms: 668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 668
          Classifications: {'DNA': 33}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 32}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 345
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
    Chain: "C"
      Number of atoms: 2556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 2556
          Classifications: {'RNA': 119}
          Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 4, 'rna3p_pur': 61, 'rna3p_pyr': 45}
          Link IDs: {'rna2p': 13, 'rna3p': 105}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 3461
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 3461
          Classifications: {'peptide': 445}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 13, 'TRANS': 431}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 213
          Unresolved non-hydrogen angles: 261
          Unresolved non-hydrogen dihedrals: 182
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 9, 'TYR:plan': 2, 'PHE:plan': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 142
  Time building chain proxies: 1.70, per 1000 atoms: 0.19
  Number of scatterers: 9024
  At special positions: 0
  Unit cell: (120.357, 121.29, 102.63, 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      13     16.00
     P     168     15.00
     O    2123      8.00
     N    1642      7.00
     C    5078      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 132.0 milliseconds
  

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1310

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 7 sheets defined
      52.3% alpha, 15.9% beta
      64 base pairs and 111 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'B' and resid 24 through 68
      removed outlier: 4.877A  pdb=" N   TYR B  44 " --> pdb=" O   ASN B  40 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   LYS B  45 " --> pdb=" O   ASP B  41 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   GLU B  61 " --> pdb=" O   ASN B  57 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   TYR B  62 " --> pdb=" O   ASP B  58 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ARG B  63 " --> pdb=" O   ALA B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 80
      removed outlier: 3.589A  pdb=" N   TYR B  80 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 113
    Processing helix  chain 'B' and resid 128 through 137
    Processing helix  chain 'B' and resid 141 through 166
      removed outlier: 3.837A  pdb=" N   ASN B 147 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   LEU B 161 " --> pdb=" O   LYS B 157 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   ASP B 162 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 229
      removed outlier: 3.686A  pdb=" N   ILE B 223 " --> pdb=" O   ASN B 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 41
    Processing helix  chain 'A' and resid 42 through 68
      removed outlier: 3.699A  pdb=" N   GLU A  61 " --> pdb=" O   ASN A  57 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   HIS A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 80
      removed outlier: 3.917A  pdb=" N   TYR A  80 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 85
      removed outlier: 3.698A  pdb=" N   ASN A  84 " --> pdb=" O   TYR A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 115
    Processing helix  chain 'A' and resid 125 through 137
      removed outlier: 3.730A  pdb=" N   TYR A 129 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   VAL A 131 " --> pdb=" O   SER A 127 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU A 137 " --> pdb=" O   SER A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 158
      removed outlier: 3.925A  pdb=" N   ASN A 158 " --> pdb=" O   SER A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 165
    Processing helix  chain 'A' and resid 204 through 206
      No H-bonds generated for 'chain 'A' and resid 204 through 206'
    Processing helix  chain 'A' and resid 219 through 229
    Processing helix  chain 'A' and resid 299 through 308
      removed outlier: 4.223A  pdb=" N   MET A 303 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LYS A 308 " --> pdb=" O   ARG A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 316
      removed outlier: 3.955A  pdb=" N   GLN A 313 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 362
      removed outlier: 3.523A  pdb=" N   GLY A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ASN A 342 " --> pdb=" O   GLY A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 411
    Processing helix  chain 'A' and resid 450 through 455
    Processing helix  chain 'A' and resid 467 through 478
    Processing sheet with id=AA1, first strand: chain 'B' and resid 179 through 180
      removed outlier: 4.858A  pdb=" N   ARG B 247 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   ILE B 199 " --> pdb=" O   LEU B 211 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 179 through 180
    Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 181
      removed outlier: 3.816A  pdb=" N   SER A 237 " --> pdb=" O   PHE A 181 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   SER A 238 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   ARG A 247 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU A 251 " --> pdb=" O   ARG A  10 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   GLU A  13 " --> pdb=" O   SER A 212 " (cutoff:3.500A)
      removed outlier: 5.212A  pdb=" N   ILE A 199 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 181
      removed outlier: 3.816A  pdb=" N   SER A 237 " --> pdb=" O   PHE A 181 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   SER A 238 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 185
    Processing sheet with id=AA6, first strand: chain 'A' and resid 279 through 281
      removed outlier: 7.407A  pdb=" N   ALA A 364 " --> pdb=" O   PRO A 264 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ARG A 266 " --> pdb=" O   ALA A 364 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU A 370 " --> pdb=" O   VAL A 270 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   GLY A 365 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   ARG A 415 " --> pdb=" O   GLY A 365 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   ILE A 367 " --> pdb=" O   ARG A 415 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   VAL A 417 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   MET A 369 " --> pdb=" O   VAL A 417 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 437 through 439
      removed outlier: 6.560A  pdb=" N   THR A 442 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)

    319 hydrogen bonds defined for protein.
    924 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      158 hydrogen bonds
      288 hydrogen bond angles
      0 basepair planarities
      64 basepair parallelities
      111 stacking parallelities
  Total time for adding SS restraints: 1.87

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1960
        1.33 -     1.45: 2974
        1.45 -     1.57: 4270
        1.57 -     1.69: 331
        1.69 -     1.81: 19
  Bond restraints: 9554
  Sorted by residual:
  bond pdb=" C1'  DT D  12 "
       pdb=" N1   DT D  12 "
    ideal  model  delta    sigma   weight residual
    1.468  1.532 -0.064 1.40e-02 5.10e+03 2.06e+01
  bond pdb=" C3'  DT D   1 "
       pdb=" O3'  DT D   1 "
    ideal  model  delta    sigma   weight residual
    1.435  1.488 -0.053 1.30e-02 5.92e+03 1.65e+01
  bond pdb=" C3'  DC E   5 "
       pdb=" C2'  DC E   5 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.62e+00
  bond pdb=" C3'  DT E  12 "
       pdb=" C2'  DT E  12 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.34e+00
  bond pdb=" C1'  DC D   6 "
       pdb=" N1   DC D   6 "
    ideal  model  delta    sigma   weight residual
    1.468  1.511 -0.043 1.40e-02 5.10e+03 9.26e+00
  ... (remaining 9549 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 12969
        2.16 -     4.31: 663
        4.31 -     6.47: 58
        6.47 -     8.62: 15
        8.62 -    10.78: 5
  Bond angle restraints: 13710
  Sorted by residual:
  angle pdb=" O4'  DA E  16 "
        pdb=" C4'  DA E  16 "
        pdb=" C3'  DA E  16 "
      ideal   model   delta    sigma   weight residual
     106.00  102.62    3.38 6.00e-01 2.78e+00 3.17e+01
  angle pdb=" C3'   U C  39 "
        pdb=" O3'   U C  39 "
        pdb=" P     U C  40 "
      ideal   model   delta    sigma   weight residual
     119.70  126.13   -6.43 1.20e+00 6.94e-01 2.87e+01
  angle pdb=" O4'  DG E  15 "
        pdb=" C4'  DG E  15 "
        pdb=" C3'  DG E  15 "
      ideal   model   delta    sigma   weight residual
     106.00  102.82    3.18 6.00e-01 2.78e+00 2.81e+01
  angle pdb=" CA  GLU A 296 "
        pdb=" CB  GLU A 296 "
        pdb=" CG  GLU A 296 "
      ideal   model   delta    sigma   weight residual
     114.10  124.55  -10.45 2.00e+00 2.50e-01 2.73e+01
  angle pdb=" O5'   G C 135 "
        pdb=" C5'   G C 135 "
        pdb=" C4'   G C 135 "
      ideal   model   delta    sigma   weight residual
     109.40  113.37   -3.97 8.00e-01 1.56e+00 2.46e+01
  ... (remaining 13705 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.91: 5118
       33.91 -    67.82: 550
       67.82 -   101.73: 43
      101.73 -   135.64: 5
      135.64 -   169.55: 2
  Dihedral angle restraints: 5718
    sinusoidal: 3687
      harmonic: 2031
  Sorted by residual:
  dihedral pdb=" O4'   G C  75 "
           pdb=" C1'   G C  75 "
           pdb=" N9    G C  75 "
           pdb=" C4    G C  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -169.84   63.84     1      1.70e+01 3.46e-03 1.86e+01
  dihedral pdb=" C   ASP A 216 "
           pdb=" N   ASP A 216 "
           pdb=" CA  ASP A 216 "
           pdb=" CB  ASP A 216 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.16   10.56     0      2.50e+00 1.60e-01 1.78e+01
  dihedral pdb=" CA  ARG B 217 "
           pdb=" C   ARG B 217 "
           pdb=" N   SER B 218 "
           pdb=" CA  SER B 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.28   20.72     0      5.00e+00 4.00e-02 1.72e+01
  ... (remaining 5715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.116: 1456
       0.116 -    0.232: 153
       0.232 -    0.348: 4
       0.348 -    0.464: 0
       0.464 -    0.580: 2
  Chirality restraints: 1615
  Sorted by residual:
  chirality pdb=" P    DT D  17 "
            pdb=" OP1  DT D  17 "
            pdb=" OP2  DT D  17 "
            pdb=" O5'  DT D  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.91   -0.58 2.00e-01 2.50e+01 8.40e+00
  chirality pdb=" P    DC D  16 "
            pdb=" OP1  DC D  16 "
            pdb=" OP2  DC D  16 "
            pdb=" O5'  DC D  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.85   -0.51 2.00e-01 2.50e+01 6.57e+00
  chirality pdb=" CA  ASP A 216 "
            pdb=" N   ASP A 216 "
            pdb=" C   ASP A 216 "
            pdb=" CB  ASP A 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.59e+00
  ... (remaining 1612 not shown)

  Planarity restraints: 1152
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 263 "    0.059 5.00e-02 4.00e+02   8.97e-02 1.29e+01
        pdb=" N   PRO A 264 "   -0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO A 264 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO A 264 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  45 "    0.040 2.00e-02 2.50e+03   1.68e-02 8.49e+00
        pdb=" N9    G C  45 "   -0.036 2.00e-02 2.50e+03
        pdb=" C8    G C  45 "   -0.011 2.00e-02 2.50e+03
        pdb=" N7    G C  45 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G C  45 "    0.003 2.00e-02 2.50e+03
        pdb=" C6    G C  45 "    0.004 2.00e-02 2.50e+03
        pdb=" O6    G C  45 "    0.012 2.00e-02 2.50e+03
        pdb=" N1    G C  45 "    0.005 2.00e-02 2.50e+03
        pdb=" C2    G C  45 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G C  45 "   -0.009 2.00e-02 2.50e+03
        pdb=" N3    G C  45 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    G C  45 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 331 "   -0.015 2.00e-02 2.50e+03   2.88e-02 8.30e+00
        pdb=" C   GLN A 331 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLN A 331 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ALA A 332 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1149 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 933
        2.75 -     3.29: 8143
        3.29 -     3.82: 16982
        3.82 -     4.36: 19623
        4.36 -     4.90: 29294
  Nonbonded interactions: 74975
  Sorted by model distance:
  nonbonded pdb=" O   LEU B  29 "
            pdb=" CD2 TYR B  33 "
     model   vdw
     2.210 3.340
  nonbonded pdb=" N2   DG D  32 "
            pdb=" O2   DC E   2 "
     model   vdw
     2.253 2.496
  nonbonded pdb=" OH  TYR B 129 "
            pdb=" OG  SER B 142 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OP2   C C 131 "
            pdb=" NH2 ARG A 217 "
     model   vdw
     2.358 3.120
  nonbonded pdb=" N2    G C 135 "
            pdb=" OG1 THR A   9 "
     model   vdw
     2.368 3.120
  ... (remaining 74970 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             2.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.500
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
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   0.091   9554  Z= 0.367
  Angle     :  0.959  10.780  13710  Z= 0.734
  Chirality :  0.063   0.580   1615
  Planarity :  0.007   0.090   1152
  Dihedral  : 22.424 169.554   4408
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 13.69 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.29), residues: 686
  helix: -0.08 (0.25), residues: 346
  sheet: -0.16 (0.57), residues: 90
  loop : -1.44 (0.34), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 226 
 TYR   0.033   0.002   TYR B  80 
 PHE   0.025   0.003   PHE B 102 
 TRP   0.027   0.003   TRP B  36 
 HIS   0.009   0.001   HIS A  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00530 /  0.37 ( 9554)
  covalent geometry    : angle       0.95881 /  0.73 (13710)
  hydrogen bonds       : bond        0.13940 /  9.53 (  465)
  hydrogen bonds       : angle       6.15538 /  4.36 ( 1212)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 84
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: B   34 ARG cc_start: 0.7468 (tpp-160) cc_final: 0.6842 (ttm110)
REVERT: B   89 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8007 (tm-30)
REVERT: B   91 ILE cc_start: 0.8823 (mm) cc_final: 0.8617 (mt)
REVERT: B  213 PHE cc_start: 0.6979 (m-80) cc_final: 0.6774 (m-80)
REVERT: A   66 ILE cc_start: 0.8589 (tp) cc_final: 0.8364 (mt)
REVERT: A  111 THR cc_start: 0.8573 (m) cc_final: 0.8362 (m)
REVERT: A  190 MET cc_start: 0.8036 (mmp) cc_final: 0.7281 (mtm)
REVERT: A  216 ASP cc_start: 0.7565 (p0) cc_final: 0.7324 (p0)
REVERT: A  225 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7693 (tp30)
REVERT: A  226 ARG cc_start: 0.7441 (mtt-85) cc_final: 0.7183 (mtt180)
REVERT: A  229 SER cc_start: 0.8436 (m) cc_final: 0.8204 (p)
REVERT: A  392 ARG cc_start: 0.7236 (tpm170) cc_final: 0.5526 (ttt-90)
REVERT: A  416 TYR cc_start: 0.7434 (m-10) cc_final: 0.7118 (m-10)
  outliers start: 2
  outliers final: 2
  residues processed: 86
  average time/residue: 0.1168
  time to fit residues: 13.3040
Evaluate side-chains
  75 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 ILE
Chi-restraints excluded: chain A residue  333 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  42 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.219117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.158694 restraints weight = 11310.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 2.89
r_work: 0.3386 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.0988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   9554  Z= 0.161
  Angle     :  0.606   8.479  13710  Z= 0.350
  Chirality :  0.043   0.288   1615
  Planarity :  0.005   0.055   1152
  Dihedral  : 23.581 169.289   3136
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 11.71 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.31), residues: 686
  helix:  1.23 (0.26), residues: 341
  sheet: -0.38 (0.55), residues: 90
  loop : -1.31 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 226 
 TYR   0.022   0.002   TYR B  33 
 PHE   0.013   0.001   PHE A  56 
 TRP   0.011   0.001   TRP B  36 
 HIS   0.005   0.001   HIS A  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.16 ( 9554)
  covalent geometry    : angle       0.60622 /  0.35 (13710)
  hydrogen bonds       : bond        0.06316 /  4.42 (  465)
  hydrogen bonds       : angle       4.44449 /  3.16 ( 1212)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: B   34 ARG cc_start: 0.7529 (tpp-160) cc_final: 0.6936 (ttm110)
REVERT: B   89 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7899 (tm-30)
REVERT: A   66 ILE cc_start: 0.8672 (tp) cc_final: 0.8439 (mt)
REVERT: A   90 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6460 (p0)
REVERT: A  216 ASP cc_start: 0.7878 (p0) cc_final: 0.7568 (p0)
REVERT: A  222 GLU cc_start: 0.7816 (tt0) cc_final: 0.7401 (tp30)
REVERT: A  226 ARG cc_start: 0.7729 (mtt-85) cc_final: 0.7265 (mtt180)
REVERT: A  392 ARG cc_start: 0.7244 (tpm170) cc_final: 0.5481 (ttt-90)
REVERT: A  398 GLU cc_start: 0.7943 (tp30) cc_final: 0.7723 (tt0)
REVERT: A  416 TYR cc_start: 0.7518 (m-10) cc_final: 0.7273 (m-10)
  outliers start: 17
  outliers final: 9
  residues processed: 78
  average time/residue: 0.0905
  time to fit residues: 9.6175
Evaluate side-chains
  72 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 ILE
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  401 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 13 optimal weight:    0.0670
   chunk 9 optimal weight:    0.8980
   chunk 31 optimal weight:   50.0000
   chunk 54 optimal weight:    0.4980
   chunk 56 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 69 optimal weight:    9.9990
   overall best weight:    0.6920

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 315 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.217909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.144824 restraints weight = 11287.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 1.75
r_work: 0.3482 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9554  Z= 0.143
  Angle     :  0.547   7.239  13710  Z= 0.319
  Chirality :  0.040   0.309   1615
  Planarity :  0.004   0.044   1152
  Dihedral  : 23.443 166.993   3134
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 12.61 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.31), residues: 686
  helix:  1.71 (0.27), residues: 343
  sheet: -0.73 (0.52), residues: 97
  loop : -1.13 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 221 
 TYR   0.020   0.002   TYR B  33 
 PHE   0.013   0.002   PHE A  56 
 TRP   0.008   0.001   TRP B  36 
 HIS   0.006   0.001   HIS A  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.14 ( 9554)
  covalent geometry    : angle       0.54676 /  0.32 (13710)
  hydrogen bonds       : bond        0.05504 /  3.86 (  465)
  hydrogen bonds       : angle       4.10571 /  2.95 ( 1212)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: B   34 ARG cc_start: 0.7590 (tpp-160) cc_final: 0.7049 (ttm110)
REVERT: B   72 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7076 (mt0)
REVERT: A   66 ILE cc_start: 0.8810 (tp) cc_final: 0.8535 (mt)
REVERT: A  216 ASP cc_start: 0.7814 (p0) cc_final: 0.7510 (p0)
REVERT: A  222 GLU cc_start: 0.7865 (tt0) cc_final: 0.7486 (tp30)
REVERT: A  225 GLU cc_start: 0.8234 (tp30) cc_final: 0.7886 (tt0)
REVERT: A  226 ARG cc_start: 0.7896 (mtt-85) cc_final: 0.7466 (mtt180)
REVERT: A  392 ARG cc_start: 0.7260 (tpm170) cc_final: 0.5623 (ttt-90)
REVERT: A  398 GLU cc_start: 0.8046 (tp30) cc_final: 0.7767 (tt0)
  outliers start: 15
  outliers final: 12
  residues processed: 72
  average time/residue: 0.0974
  time to fit residues: 9.4700
Evaluate side-chains
  76 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 ILE
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  401 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 8 optimal weight:    0.1980
   chunk 60 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 24 optimal weight:   20.0000
   chunk 9 optimal weight:    0.8980
   chunk 27 optimal weight:   10.0000
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  67 HIS
B 236 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.217427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.142024 restraints weight = 11321.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 2.08
r_work: 0.3439 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.1812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9554  Z= 0.137
  Angle     :  0.530   7.377  13710  Z= 0.308
  Chirality :  0.039   0.302   1615
  Planarity :  0.004   0.047   1152
  Dihedral  : 23.417 167.839   3134
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 12.07 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.32), residues: 686
  helix:  2.03 (0.27), residues: 343
  sheet: -0.69 (0.52), residues: 96
  loop : -1.08 (0.38), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  70 
 TYR   0.013   0.001   TYR A 129 
 PHE   0.014   0.001   PHE A  56 
 TRP   0.006   0.001   TRP B  36 
 HIS   0.006   0.001   HIS A  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.14 ( 9554)
  covalent geometry    : angle       0.53012 /  0.31 (13710)
  hydrogen bonds       : bond        0.05255 /  3.67 (  465)
  hydrogen bonds       : angle       4.00003 /  2.87 ( 1212)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: B   34 ARG cc_start: 0.7614 (tpp-160) cc_final: 0.7028 (ttm110)
REVERT: B   72 GLN cc_start: 0.7582 (mm-40) cc_final: 0.6995 (mt0)
REVERT: B  150 GLN cc_start: 0.8071 (tt0) cc_final: 0.7551 (mm110)
REVERT: A    8 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7917 (pt)
REVERT: A   66 ILE cc_start: 0.8816 (tp) cc_final: 0.8518 (mt)
REVERT: A  160 SER cc_start: 0.8796 (t) cc_final: 0.8517 (p)
REVERT: A  216 ASP cc_start: 0.7801 (p0) cc_final: 0.7510 (p0)
REVERT: A  226 ARG cc_start: 0.7903 (mtt-85) cc_final: 0.7570 (mtt180)
REVERT: A  392 ARG cc_start: 0.7378 (tpm170) cc_final: 0.5725 (ttt-90)
REVERT: A  398 GLU cc_start: 0.7964 (tp30) cc_final: 0.7710 (tt0)
  outliers start: 20
  outliers final: 15
  residues processed: 76
  average time/residue: 0.0835
  time to fit residues: 8.6572
Evaluate side-chains
  78 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 ILE
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  405 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 35 optimal weight:   20.0000
   chunk 6 optimal weight:    0.6980
   chunk 32 optimal weight:   30.0000
   chunk 72 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0670
   chunk 41 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.6720

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  15 HIS
A  17 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.217380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.143495 restraints weight = 11373.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 1.76
r_work: 0.3411 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9554  Z= 0.136
  Angle     :  0.523   7.260  13710  Z= 0.304
  Chirality :  0.039   0.304   1615
  Planarity :  0.004   0.047   1152
  Dihedral  : 23.365 166.427   3134
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 13.87 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.32), residues: 686
  helix:  2.16 (0.27), residues: 344
  sheet: -0.66 (0.51), residues: 98
  loop : -0.99 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  70 
 TYR   0.014   0.001   TYR A 358 
 PHE   0.013   0.001   PHE A  56 
 TRP   0.007   0.001   TRP B  36 
 HIS   0.007   0.001   HIS A  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.14 ( 9554)
  covalent geometry    : angle       0.52344 /  0.30 (13710)
  hydrogen bonds       : bond        0.05211 /  3.66 (  465)
  hydrogen bonds       : angle       3.91700 /  2.82 ( 1212)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: B   34 ARG cc_start: 0.7774 (tpp-160) cc_final: 0.7162 (ttm110)
REVERT: B   72 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7006 (mt0)
REVERT: B  150 GLN cc_start: 0.8147 (tt0) cc_final: 0.7613 (mm110)
REVERT: A    8 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7968 (pt)
REVERT: A   66 ILE cc_start: 0.8780 (tp) cc_final: 0.8514 (mt)
REVERT: A  160 SER cc_start: 0.8800 (t) cc_final: 0.8511 (p)
REVERT: A  216 ASP cc_start: 0.7805 (p0) cc_final: 0.7529 (p0)
REVERT: A  226 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7579 (mtt180)
REVERT: A  339 LYS cc_start: 0.8441 (ptpp) cc_final: 0.7982 (ptmm)
REVERT: A  392 ARG cc_start: 0.7457 (tpm170) cc_final: 0.5692 (ttt-90)
REVERT: A  398 GLU cc_start: 0.7911 (tp30) cc_final: 0.7671 (tt0)
  outliers start: 17
  outliers final: 12
  residues processed: 75
  average time/residue: 0.0871
  time to fit residues: 9.0351
Evaluate side-chains
  76 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  405 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 36 optimal weight:   30.0000
   chunk 38 optimal weight:    6.9990
   chunk 1 optimal weight:    8.9990
   chunk 78 optimal weight:    0.3980
   chunk 62 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.9182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.216080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.142785 restraints weight = 11313.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 1.78
r_work: 0.3382 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9554  Z= 0.154
  Angle     :  0.531   7.579  13710  Z= 0.307
  Chirality :  0.039   0.303   1615
  Planarity :  0.004   0.047   1152
  Dihedral  : 23.353 166.244   3132
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 14.77 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.32), residues: 686
  helix:  2.21 (0.27), residues: 344
  sheet: -0.65 (0.51), residues: 98
  loop : -1.00 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  70 
 TYR   0.014   0.002   TYR A 129 
 PHE   0.014   0.001   PHE A  56 
 TRP   0.007   0.001   TRP B  36 
 HIS   0.006   0.001   HIS A  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.15 ( 9554)
  covalent geometry    : angle       0.53149 /  0.31 (13710)
  hydrogen bonds       : bond        0.05159 /  3.59 (  465)
  hydrogen bonds       : angle       3.93672 /  2.84 ( 1212)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: B   34 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.7130 (ttm110)
REVERT: B   72 GLN cc_start: 0.7623 (mm-40) cc_final: 0.6940 (mt0)
REVERT: B  150 GLN cc_start: 0.8128 (tt0) cc_final: 0.7582 (mm110)
REVERT: A    8 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7965 (pt)
REVERT: A   66 ILE cc_start: 0.8795 (tp) cc_final: 0.8513 (mt)
REVERT: A  160 SER cc_start: 0.8806 (t) cc_final: 0.8503 (p)
REVERT: A  216 ASP cc_start: 0.7864 (p0) cc_final: 0.7570 (p0)
REVERT: A  358 TYR cc_start: 0.8246 (t80) cc_final: 0.7845 (t80)
REVERT: A  392 ARG cc_start: 0.7533 (tpm170) cc_final: 0.5745 (ttt-90)
REVERT: A  398 GLU cc_start: 0.7913 (tp30) cc_final: 0.7638 (tt0)
  outliers start: 16
  outliers final: 12
  residues processed: 76
  average time/residue: 0.1126
  time to fit residues: 11.6582
Evaluate side-chains
  78 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  405 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 34 optimal weight:   50.0000
   chunk 27 optimal weight:    9.9990
   chunk 30 optimal weight:   20.0000
   chunk 22 optimal weight:    5.9990
   chunk 75 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 37 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   chunk 69 optimal weight:   10.0000
   chunk 5 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.216305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.142218 restraints weight = 11267.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 1.79
r_work: 0.3382 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   9554  Z= 0.148
  Angle     :  0.527   7.648  13710  Z= 0.305
  Chirality :  0.039   0.304   1615
  Planarity :  0.004   0.047   1152
  Dihedral  : 23.321 164.706   3132
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.32 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.32), residues: 686
  helix:  2.17 (0.27), residues: 344
  sheet: -0.68 (0.50), residues: 99
  loop : -0.99 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  70 
 TYR   0.013   0.001   TYR A 129 
 PHE   0.014   0.001   PHE A  56 
 TRP   0.006   0.001   TRP B  36 
 HIS   0.006   0.001   HIS A  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.15 ( 9554)
  covalent geometry    : angle       0.52680 /  0.30 (13710)
  hydrogen bonds       : bond        0.05150 /  3.59 (  465)
  hydrogen bonds       : angle       3.86658 /  2.80 ( 1212)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: B   34 ARG cc_start: 0.7780 (tpp-160) cc_final: 0.7154 (ttm110)
REVERT: B   72 GLN cc_start: 0.7674 (mm-40) cc_final: 0.6994 (mt0)
REVERT: B  150 GLN cc_start: 0.8120 (tt0) cc_final: 0.7594 (mm110)
REVERT: A    8 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8004 (pt)
REVERT: A   19 HIS cc_start: 0.7494 (OUTLIER) cc_final: 0.7231 (m90)
REVERT: A   66 ILE cc_start: 0.8813 (tp) cc_final: 0.8526 (mt)
REVERT: A  160 SER cc_start: 0.8808 (t) cc_final: 0.8512 (p)
REVERT: A  216 ASP cc_start: 0.7872 (p0) cc_final: 0.7572 (p0)
REVERT: A  392 ARG cc_start: 0.7590 (tpm170) cc_final: 0.5778 (ttt-90)
REVERT: A  398 GLU cc_start: 0.7926 (tp30) cc_final: 0.7635 (tt0)
  outliers start: 16
  outliers final: 10
  residues processed: 75
  average time/residue: 0.1022
  time to fit residues: 10.5213
Evaluate side-chains
  76 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue   19 HIS
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  405 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 81 optimal weight:   20.0000
   chunk 10 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9990
   chunk 32 optimal weight:   40.0000
   chunk 22 optimal weight:    6.9990
   chunk 35 optimal weight:   20.0000
   chunk 27 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 347 GLN
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 GLN ** 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 = 0.4366 r_free = 0.4366 target = 0.208761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.131446 restraints weight = 11201.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 1.70
r_work: 0.3310 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.107   9554  Z= 0.356
  Angle     :  0.732   9.333  13710  Z= 0.404
  Chirality :  0.051   0.357   1615
  Planarity :  0.007   0.123   1152
  Dihedral  : 23.528 164.168   3132
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 16.04 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.30), residues: 686
  helix:  1.39 (0.26), residues: 344
  sheet: -0.65 (0.50), residues: 94
  loop : -1.24 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 168 
 TYR   0.027   0.003   TYR A 173 
 PHE   0.019   0.003   PHE A 203 
 TRP   0.011   0.002   TRP B  36 
 HIS   0.007   0.001   HIS A  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00831 /  0.36 ( 9554)
  covalent geometry    : angle       0.73193 /  0.40 (13710)
  hydrogen bonds       : bond        0.06591 /  4.51 (  465)
  hydrogen bonds       : angle       4.32061 /  3.11 ( 1212)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: B   34 ARG cc_start: 0.7920 (tpp-160) cc_final: 0.7340 (ttm110)
REVERT: B   72 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7288 (mt0)
REVERT: B  150 GLN cc_start: 0.8343 (tt0) cc_final: 0.7763 (mm110)
REVERT: B  242 SER cc_start: 0.8038 (t) cc_final: 0.7796 (m)
REVERT: A    8 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7993 (pt)
REVERT: A   66 ILE cc_start: 0.8906 (tp) cc_final: 0.8582 (mt)
REVERT: A  392 ARG cc_start: 0.7774 (tpm170) cc_final: 0.5975 (ttt-90)
  outliers start: 14
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0875
  time to fit residues: 9.2606
Evaluate side-chains
  65 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain A residue    8 ILE
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  405 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 21 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 66 optimal weight:    0.1980
   chunk 63 optimal weight:    0.5980
   chunk 25 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 362 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.214301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.139591 restraints weight = 11057.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 1.58
r_work: 0.3406 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.3216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   9554  Z= 0.141
  Angle     :  0.544   7.648  13710  Z= 0.315
  Chirality :  0.040   0.304   1615
  Planarity :  0.004   0.050   1152
  Dihedral  : 23.402 161.718   3132
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 17.12 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.31), residues: 686
  helix:  1.91 (0.27), residues: 345
  sheet: -0.90 (0.49), residues: 101
  loop : -1.07 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 226 
 TYR   0.014   0.001   TYR A 358 
 PHE   0.015   0.001   PHE A  56 
 TRP   0.006   0.001   TRP A 343 
 HIS   0.005   0.001   HIS A  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.14 ( 9554)
  covalent geometry    : angle       0.54357 /  0.31 (13710)
  hydrogen bonds       : bond        0.05203 /  3.63 (  465)
  hydrogen bonds       : angle       3.96414 /  2.88 ( 1212)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: B   34 ARG cc_start: 0.7876 (tpp-160) cc_final: 0.7283 (ttm110)
REVERT: B   72 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7346 (mt0)
REVERT: B  150 GLN cc_start: 0.8337 (tt0) cc_final: 0.7872 (mm110)
REVERT: B  242 SER cc_start: 0.8108 (t) cc_final: 0.7894 (m)
REVERT: A   66 ILE cc_start: 0.8855 (tp) cc_final: 0.8593 (mt)
REVERT: A  160 SER cc_start: 0.8904 (t) cc_final: 0.8655 (p)
REVERT: A  190 MET cc_start: 0.8663 (mmp) cc_final: 0.7871 (mmm)
REVERT: A  216 ASP cc_start: 0.8301 (p0) cc_final: 0.7939 (p0)
REVERT: A  392 ARG cc_start: 0.7727 (tpm170) cc_final: 0.5841 (ttt-90)
  outliers start: 8
  outliers final: 6
  residues processed: 68
  average time/residue: 0.0783
  time to fit residues: 7.3608
Evaluate side-chains
  68 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  405 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 31 optimal weight:   50.0000
   chunk 45 optimal weight:    0.6980
   chunk 38 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0980
   chunk 17 optimal weight:    0.6980
   chunk 34 optimal weight:   50.0000
   chunk 52 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   chunk 24 optimal weight:    9.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 362 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.214764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.140700 restraints weight = 11057.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.53
r_work: 0.3419 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9554  Z= 0.134
  Angle     :  0.525   7.524  13710  Z= 0.305
  Chirality :  0.038   0.300   1615
  Planarity :  0.004   0.048   1152
  Dihedral  : 23.329 160.660   3132
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 17.48 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.32), residues: 686
  helix:  2.18 (0.27), residues: 344
  sheet: -0.65 (0.49), residues: 99
  loop : -1.11 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 226 
 TYR   0.015   0.001   TYR A 129 
 PHE   0.013   0.001   PHE A  56 
 TRP   0.005   0.001   TRP B  36 
 HIS   0.006   0.001   HIS A  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.13 ( 9554)
  covalent geometry    : angle       0.52514 /  0.31 (13710)
  hydrogen bonds       : bond        0.05151 /  3.59 (  465)
  hydrogen bonds       : angle       3.83715 /  2.79 ( 1212)

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: B   34 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.7284 (ttm110)
REVERT: B   72 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7357 (mt0)
REVERT: B  150 GLN cc_start: 0.8342 (tt0) cc_final: 0.7883 (mm110)
REVERT: A   66 ILE cc_start: 0.8870 (tp) cc_final: 0.8592 (mt)
REVERT: A  160 SER cc_start: 0.8905 (t) cc_final: 0.8637 (p)
REVERT: A  190 MET cc_start: 0.8614 (mmp) cc_final: 0.7835 (mmm)
REVERT: A  216 ASP cc_start: 0.8212 (p0) cc_final: 0.7870 (p0)
REVERT: A  339 LYS cc_start: 0.8620 (ptpp) cc_final: 0.8110 (ptmm)
REVERT: A  363 ASN cc_start: 0.8682 (t0) cc_final: 0.8274 (t0)
REVERT: A  392 ARG cc_start: 0.7667 (tpm170) cc_final: 0.5837 (ttt-90)
  outliers start: 6
  outliers final: 6
  residues processed: 67
  average time/residue: 0.0878
  time to fit residues: 7.9877
Evaluate side-chains
  65 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  405 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 11 optimal weight:    8.9990
   chunk 53 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 36 optimal weight:   30.0000
   chunk 82 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 362 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.214500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.142952 restraints weight = 10977.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 1.70
r_work: 0.3383 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9554  Z= 0.148
  Angle     :  0.544  12.877  13710  Z= 0.310
  Chirality :  0.039   0.298   1615
  Planarity :  0.004   0.049   1152
  Dihedral  : 23.292 158.790   3132
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 17.48 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.32), residues: 686
  helix:  2.18 (0.27), residues: 345
  sheet: -0.58 (0.49), residues: 102
  loop : -1.07 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 392 
 TYR   0.014   0.002   TYR A 129 
 PHE   0.013   0.001   PHE A  56 
 TRP   0.006   0.001   TRP B  36 
 HIS   0.006   0.001   HIS A  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.15 ( 9554)
  covalent geometry    : angle       0.54385 /  0.31 (13710)
  hydrogen bonds       : bond        0.05093 /  3.54 (  465)
  hydrogen bonds       : angle       3.79145 /  2.76 ( 1212)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2536.92 seconds
wall clock time: 43 minutes 53.76 seconds (2633.76 seconds total)