Starting phenix.real_space_refine
on Tue Apr 29 05:32:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ene_19832/04_2025/9ene_19832.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ene_19832/04_2025/9ene_19832.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ene_19832/04_2025/9ene_19832.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ene_19832/04_2025/9ene_19832.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ene_19832/04_2025/9ene_19832.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ene_19832/04_2025/9ene_19832.cif"
  }
  resolution = 3.15
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.012
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     144      5.49       5
     S      36      5.16       5
     C    4824      2.51       5
     N    1494      2.21       5
     O    1986      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8484
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2686
          Classifications: {'peptide': 329}
          Link IDs: {'PTRANS': 15, 'TRANS': 313}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2686
          Classifications: {'peptide': 329}
          Link IDs: {'PTRANS': 15, 'TRANS': 313}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 1556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1556
          Classifications: {'RNA': 73}
          Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 29}
          Link IDs: {'rna2p': 11, 'rna3p': 61}
    Chain: "D"
      Number of atoms: 1556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1556
          Classifications: {'RNA': 73}
          Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 29}
          Link IDs: {'rna2p': 11, 'rna3p': 61}
  Time building chain proxies: 6.31, per 1000 atoms: 0.74
  Number of scatterers: 8484
  At special positions: 0
  Unit cell: (102.34, 152.22, 68.8, 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      36     16.00
     P     144     15.00
     O    1986      8.00
     N    1494      7.00
     C    4824      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.31
  Conformation dependent library (CDL) restraints added in 662.8 milliseconds
  

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1248

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 4 sheets defined
      34.5% alpha, 16.1% beta
      44 base pairs and 57 stacking pairs defined.
    Time for finding SS restraints: 3.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 60
      removed outlier: 3.590A  pdb=" N   ALA A  59 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 100
    Processing helix  chain 'A' and resid 105 through 110
      removed outlier: 3.513A  pdb=" N   SER A 109 " --> pdb=" O   ARG A 106 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   ASN A 110 " --> pdb=" O   GLN A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 168
      removed outlier: 3.655A  pdb=" N   ARG A 166 " --> pdb=" O   HIS A 162 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   VAL A 167 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 213
    Processing helix  chain 'A' and resid 214 through 217
      removed outlier: 3.505A  pdb=" N   VAL A 217 " --> pdb=" O   GLN A 214 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 214 through 217'
    Processing helix  chain 'A' and resid 229 through 233
    Processing helix  chain 'A' and resid 259 through 263
    Processing helix  chain 'A' and resid 277 through 291
    Processing helix  chain 'A' and resid 297 through 304
      removed outlier: 3.625A  pdb=" N   GLU A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 370
      removed outlier: 3.944A  pdb=" N   LYS A 358 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASP A 370 " --> pdb=" O   LEU A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 417
    Processing helix  chain 'B' and resid 56 through 60
      removed outlier: 3.720A  pdb=" N   ALA B  59 " --> pdb=" O   ASP B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 76
    Processing helix  chain 'B' and resid 88 through 100
      removed outlier: 4.230A  pdb=" N   LYS B  92 " --> pdb=" O   THR B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 110
      removed outlier: 4.321A  pdb=" N   ASN B 110 " --> pdb=" O   GLN B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 166
      removed outlier: 3.749A  pdb=" N   ARG B 166 " --> pdb=" O   HIS B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 213
    Processing helix  chain 'B' and resid 214 through 217
      removed outlier: 3.758A  pdb=" N   VAL B 217 " --> pdb=" O   GLN B 214 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 214 through 217'
    Processing helix  chain 'B' and resid 277 through 291
      removed outlier: 3.557A  pdb=" N   CYS B 281 " --> pdb=" O   HIS B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 303
      removed outlier: 3.610A  pdb=" N   GLU B 301 " --> pdb=" O   GLU B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 368
      removed outlier: 3.510A  pdb=" N   GLU B 342 " --> pdb=" O   GLN B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 372
    Processing helix  chain 'B' and resid 398 through 402
      removed outlier: 4.398A  pdb=" N   ALA B 401 " --> pdb=" O   GLN B 398 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113
      removed outlier: 3.652A  pdb=" N   GLY A  61 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 174
      removed outlier: 6.413A  pdb=" N   TYR A  71 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      removed outlier: 5.306A  pdb=" N   PHE A 124 " --> pdb=" O   TYR A  71 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   ASP A 326 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   GLN A 126 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
      removed outlier: 9.323A  pdb=" N   LYS A 328 " --> pdb=" O   GLN A 126 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   THR A 194 " --> pdb=" O   TYR A 325 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   CYS A 327 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   GLU A 192 " --> pdb=" O   CYS A 327 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL A 269 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   GLN A 266 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   VAL A 246 " --> pdb=" O   GLN A 266 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   GLU A 268 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   ALA A 244 " --> pdb=" O   GLU A 268 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   THR A 270 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   HIS A 220 " --> pdb=" O   ARG A 239 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 113
      removed outlier: 3.714A  pdb=" N   GLY B  61 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 172 through 174
      removed outlier: 6.511A  pdb=" N   TYR B  71 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 5.493A  pdb=" N   PHE B 124 " --> pdb=" O   TYR B  71 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   ASP B 326 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   GLN B 126 " --> pdb=" O   ASP B 326 " (cutoff:3.500A)
      removed outlier: 9.370A  pdb=" N   LYS B 328 " --> pdb=" O   GLN B 126 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   THR B 194 " --> pdb=" O   TYR B 325 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   CYS B 327 " --> pdb=" O   GLU B 192 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   GLU B 192 " --> pdb=" O   CYS B 327 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL B 269 " --> pdb=" O   TYR B 195 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER B 243 " --> pdb=" O   THR B 270 " (cutoff:3.500A)

    189 hydrogen bonds defined for protein.
    492 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      114 hydrogen bonds
      200 hydrogen bond angles
      0 basepair planarities
      44 basepair parallelities
      57 stacking parallelities
  Total time for adding SS restraints: 2.71

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1020
        1.27 -     1.40: 2627
        1.40 -     1.54: 4958
        1.54 -     1.67: 315
        1.67 -     1.81: 58
  Bond restraints: 8978
  Sorted by residual:
  bond pdb=" C   CYS A 226 "
       pdb=" O   CYS A 226 "
    ideal  model  delta    sigma   weight residual
    1.234  1.133  0.102 1.20e-02 6.94e+03 7.19e+01
  bond pdb=" C   CYS A 226 "
       pdb=" N   LYS A 227 "
    ideal  model  delta    sigma   weight residual
    1.334  1.389 -0.056 1.79e-02 3.12e+03 9.62e+00
  bond pdb=" N   VAL A 230 "
       pdb=" CA  VAL A 230 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.033 1.19e-02 7.06e+03 7.57e+00
  bond pdb=" N   MET A 228 "
       pdb=" CA  MET A 228 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.27e-02 6.20e+03 6.75e+00
  bond pdb=" N   LYS A 227 "
       pdb=" CA  LYS A 227 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.27e-02 6.20e+03 6.55e+00
  ... (remaining 8973 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.56: 12838
        5.56 -    11.13: 9
       11.13 -    16.69: 1
       16.69 -    22.26: 1
       22.26 -    27.82: 1
  Bond angle restraints: 12850
  Sorted by residual:
  angle pdb=" O   CYS A 226 "
        pdb=" C   CYS A 226 "
        pdb=" N   LYS A 227 "
      ideal   model   delta    sigma   weight residual
     122.92  109.61   13.31 1.17e+00 7.31e-01 1.29e+02
  angle pdb=" O3'   A D  38 "
        pdb=" P     U D  39 "
        pdb=" OP1   U D  39 "
      ideal   model   delta    sigma   weight residual
     108.00   80.18   27.82 3.00e+00 1.11e-01 8.60e+01
  angle pdb=" O3'   A D  38 "
        pdb=" P     U D  39 "
        pdb=" OP2   U D  39 "
      ideal   model   delta    sigma   weight residual
     108.00   85.94   22.06 3.00e+00 1.11e-01 5.41e+01
  angle pdb=" CA  CYS A 226 "
        pdb=" C   CYS A 226 "
        pdb=" N   LYS A 227 "
      ideal   model   delta    sigma   weight residual
     115.67  106.99    8.68 1.36e+00 5.41e-01 4.08e+01
  angle pdb=" O3'   A D  38 "
        pdb=" P     U D  39 "
        pdb=" O5'   U D  39 "
      ideal   model   delta    sigma   weight residual
     104.00   98.05    5.95 1.50e+00 4.44e-01 1.57e+01
  ... (remaining 12845 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.86: 4502
       18.86 -    37.73: 603
       37.73 -    56.59: 225
       56.59 -    75.45: 239
       75.45 -    94.32: 21
  Dihedral angle restraints: 5590
    sinusoidal: 3664
      harmonic: 1926
  Sorted by residual:
  dihedral pdb=" O4'   U C  40 "
           pdb=" C1'   U C  40 "
           pdb=" N1    U C  40 "
           pdb=" C2    U C  40 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -56.88  -71.12     1      1.70e+01 3.46e-03 2.25e+01
  dihedral pdb=" O4'   U D  40 "
           pdb=" C1'   U D  40 "
           pdb=" N1    U D  40 "
           pdb=" C2    U D  40 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -60.45  -67.55     1      1.70e+01 3.46e-03 2.05e+01
  dihedral pdb=" CA  ARG B  68 "
           pdb=" C   ARG B  68 "
           pdb=" N   ILE B  69 "
           pdb=" CA  ILE B  69 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.95  -17.05     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 5587 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.401: 1519
       0.401 -    0.801: 0
       0.801 -    1.202: 0
       1.202 -    1.602: 0
       1.602 -    2.003: 1
  Chirality restraints: 1520
  Sorted by residual:
  chirality pdb=" P     U D  39 "
            pdb=" OP1   U D  39 "
            pdb=" OP2   U D  39 "
            pdb=" O5'   U D  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    0.41    2.00 2.00e-01 2.50e+01 1.00e+02
  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    2.35    0.16 2.00e-01 2.50e+01 6.67e-01
  chirality pdb=" CA  PHE B 320 "
            pdb=" N   PHE B 320 "
            pdb=" C   PHE B 320 "
            pdb=" CB  PHE B 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.05e-01
  ... (remaining 1517 not shown)

  Planarity restraints: 1108
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 226 "    0.084 2.00e-02 2.50e+03   1.69e-01 2.87e+02
        pdb=" C   CYS A 226 "   -0.292 2.00e-02 2.50e+03
        pdb=" O   CYS A 226 "    0.124 2.00e-02 2.50e+03
        pdb=" N   LYS A 227 "    0.083 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G D  18 "    0.025 2.00e-02 2.50e+03   1.07e-02 3.43e+00
        pdb=" N9    G D  18 "   -0.025 2.00e-02 2.50e+03
        pdb=" C8    G D  18 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G D  18 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G D  18 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G D  18 "    0.003 2.00e-02 2.50e+03
        pdb=" O6    G D  18 "    0.007 2.00e-02 2.50e+03
        pdb=" N1    G D  18 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G D  18 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G D  18 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G D  18 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    G D  18 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  18 "   -0.025 2.00e-02 2.50e+03   1.06e-02 3.40e+00
        pdb=" N9    G C  18 "    0.025 2.00e-02 2.50e+03
        pdb=" C8    G C  18 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    G C  18 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G C  18 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    G C  18 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6    G C  18 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1    G C  18 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    G C  18 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G C  18 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G C  18 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    G C  18 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1105 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1664
        2.77 -     3.30: 7418
        3.30 -     3.83: 15035
        3.83 -     4.37: 17014
        4.37 -     4.90: 26709
  Nonbonded interactions: 67840
  Sorted by model distance:
  nonbonded pdb=" N7    G D  22 "
            pdb=" N2    G D  46 "
     model   vdw
     2.233 2.560
  nonbonded pdb=" N7    G C  22 "
            pdb=" N2    G C  46 "
     model   vdw
     2.233 2.560
  nonbonded pdb=" OH  TYR B 197 "
            pdb=" O   VAL B 318 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OH  TYR A 197 "
            pdb=" O   VAL A 318 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OE2 GLU A 294 "
            pdb=" OH  TYR A 411 "
     model   vdw
     2.236 3.040
  ... (remaining 67835 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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:             2.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     26.070
  Find NCS groups from input model:        0.270
  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:             0.010
  Load rotamer database and sin/cos tables:3.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
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      :  0.004   0.102   8978  Z= 0.208
  Angle     :  0.642  27.822  12850  Z= 0.321
  Chirality :  0.063   2.003   1520
  Planarity :  0.006   0.169   1108
  Dihedral  : 22.563  94.318   4342
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 25.43 %
    Favored  : 73.53 %
  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: -0.77 (0.32), residues: 642
  helix:  1.27 (0.40), residues: 176
  sheet: -0.57 (0.58), residues: 64
  loop : -1.40 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 352 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.017   0.001   PHE A 320 
 TYR   0.013   0.001   TYR A 276 
 ARG   0.001   0.000   ARG B 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18488 (  303)
  hydrogen bonds       : angle       5.01962 (  692)
  covalent geometry    : bond        0.00412 ( 8978)
  covalent geometry    : angle       0.64249 (12850)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.684 
Fit side-chains
REVERT: B  293 MET cc_start: 0.8314 (ptp) cc_final: 0.8060 (ptp)
REVERT: B  361 MET cc_start: 0.9179 (ttm) cc_final: 0.8937 (ttm)
  outliers start: 6
  outliers final: 1
  residues processed: 37
  average time/residue: 0.2510
  time to fit residues: 12.7311
Evaluate side-chains
  31 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  279 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 59 optimal weight:    0.6980
   chunk 32 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A  64 HIS
A 266 GLN
B 367 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.086406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.060479 restraints weight = 22787.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.60
r_work: 0.2933 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.0898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8978  Z= 0.126
  Angle     :  0.600  27.751  12850  Z= 0.278
  Chirality :  0.062   2.026   1520
  Planarity :  0.004   0.042   1108
  Dihedral  : 22.420  95.482   3019
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 25.43 %
    Favored  : 73.18 %
  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: -0.73 (0.33), residues: 642
  helix:  1.16 (0.39), residues: 184
  sheet: -0.47 (0.59), residues: 60
  loop : -1.35 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 352 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.017   0.001   PHE B 320 
 TYR   0.011   0.001   TYR B 276 
 ARG   0.004   0.000   ARG B 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05354 (  303)
  hydrogen bonds       : angle       3.80186 (  692)
  covalent geometry    : bond        0.00272 ( 8978)
  covalent geometry    : angle       0.60006 (12850)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.727 
Fit side-chains
  outliers start: 8
  outliers final: 4
  residues processed: 39
  average time/residue: 0.2284
  time to fit residues: 12.6464
Evaluate side-chains
  35 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   85 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 69 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 20 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   overall best weight:    2.5186

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.084838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.058242 restraints weight = 23212.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 2.61
r_work: 0.2868 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.1006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8978  Z= 0.234
  Angle     :  0.660  28.020  12850  Z= 0.313
  Chirality :  0.063   2.004   1520
  Planarity :  0.004   0.045   1108
  Dihedral  : 22.388  95.107   3018
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 25.26 %
    Favored  : 72.15 %
  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: -0.97 (0.32), residues: 642
  helix:  1.03 (0.39), residues: 182
  sheet: -0.77 (0.59), residues: 60
  loop : -1.50 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 352 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.019   0.002   PHE A 320 
 TYR   0.021   0.002   TYR A 276 
 ARG   0.006   0.001   ARG B 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06739 (  303)
  hydrogen bonds       : angle       3.92606 (  692)
  covalent geometry    : bond        0.00531 ( 8978)
  covalent geometry    : angle       0.65994 (12850)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 30
  time to evaluate  : 0.685 
Fit side-chains
REVERT: A  163 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9043 (mp)
REVERT: B  257 ARG cc_start: 0.8581 (mmp80) cc_final: 0.8371 (mmp80)
  outliers start: 15
  outliers final: 7
  residues processed: 43
  average time/residue: 0.2436
  time to fit residues: 14.5706
Evaluate side-chains
  38 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  234 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.086126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.059750 restraints weight = 22979.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 2.62
r_work: 0.2908 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8978  Z= 0.148
  Angle     :  0.601  27.817  12850  Z= 0.279
  Chirality :  0.062   2.032   1520
  Planarity :  0.004   0.042   1108
  Dihedral  : 22.276  94.411   3018
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 25.95 %
    Favored  : 71.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.82 (0.33), residues: 642
  helix:  1.15 (0.40), residues: 182
  sheet: -0.54 (0.60), residues: 60
  loop : -1.43 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 352 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.018   0.001   PHE A 320 
 TYR   0.013   0.001   TYR A 276 
 ARG   0.004   0.000   ARG B 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05392 (  303)
  hydrogen bonds       : angle       3.64943 (  692)
  covalent geometry    : bond        0.00331 ( 8978)
  covalent geometry    : angle       0.60146 (12850)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 30
  time to evaluate  : 0.658 
Fit side-chains
REVERT: A  163 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9001 (mp)
REVERT: A  257 ARG cc_start: 0.8342 (tmt170) cc_final: 0.8064 (tmt170)
REVERT: B  257 ARG cc_start: 0.8522 (mmp80) cc_final: 0.8234 (mmp80)
  outliers start: 13
  outliers final: 8
  residues processed: 42
  average time/residue: 0.2236
  time to fit residues: 13.4140
Evaluate side-chains
  39 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  327 CYS
Chi-restraints excluded: chain B residue  408 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 63 optimal weight:   20.0000
   chunk 66 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   chunk 68 optimal weight:    8.9990
   overall best weight:    3.1588

-------------------------------------------------------------------------------
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 = 0.3624 r_free = 0.3624 target = 0.084228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.057536 restraints weight = 23035.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 2.64
r_work: 0.2848 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.1213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   8978  Z= 0.281
  Angle     :  0.689  28.116  12850  Z= 0.329
  Chirality :  0.064   1.992   1520
  Planarity :  0.004   0.048   1108
  Dihedral  : 22.376  96.625   3018
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.81 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 23.53 %
    Favored  : 72.15 %
  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: -1.12 (0.32), residues: 642
  helix:  0.83 (0.39), residues: 182
  sheet: -1.00 (0.57), residues: 64
  loop : -1.53 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  74 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.021   0.002   PHE A 320 
 TYR   0.017   0.002   TYR A 276 
 ARG   0.005   0.001   ARG B 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07183 (  303)
  hydrogen bonds       : angle       3.98195 (  692)
  covalent geometry    : bond        0.00641 ( 8978)
  covalent geometry    : angle       0.68910 (12850)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 31
  time to evaluate  : 0.706 
Fit side-chains
REVERT: A  116 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8179 (ptp-170)
REVERT: A  163 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9040 (mp)
REVERT: A  257 ARG cc_start: 0.8446 (tmt170) cc_final: 0.8129 (tmt170)
REVERT: B   72 MET cc_start: 0.8837 (mpp) cc_final: 0.8633 (mmp)
REVERT: B  293 MET cc_start: 0.8359 (ptp) cc_final: 0.8106 (ptp)
  outliers start: 25
  outliers final: 18
  residues processed: 54
  average time/residue: 0.2122
  time to fit residues: 16.1991
Evaluate side-chains
  49 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 29
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  116 ARG
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain B residue  327 CYS
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0470
   chunk 16 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   chunk 75 optimal weight:    9.9990
   overall best weight:    0.9682

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

Flipped N/Q/H residues before XYZ refinement:
B  64 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.086824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.060435 restraints weight = 23204.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 2.65
r_work: 0.2929 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.1340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8978  Z= 0.114
  Angle     :  0.586  27.653  12850  Z= 0.270
  Chirality :  0.062   2.032   1520
  Planarity :  0.004   0.041   1108
  Dihedral  : 22.192  93.855   3018
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 27.16 %
    Favored  : 70.76 %
  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: -0.76 (0.33), residues: 642
  helix:  1.12 (0.40), residues: 182
  sheet: -0.37 (0.61), residues: 60
  loop : -1.38 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  74 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.017   0.001   PHE B 320 
 TYR   0.011   0.001   TYR B 276 
 ARG   0.012   0.000   ARG B 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04808 (  303)
  hydrogen bonds       : angle       3.55305 (  692)
  covalent geometry    : bond        0.00249 ( 8978)
  covalent geometry    : angle       0.58647 (12850)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 30
  time to evaluate  : 0.745 
Fit side-chains
REVERT: A  116 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7864 (ptp-170)
REVERT: A  163 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8992 (mp)
REVERT: A  257 ARG cc_start: 0.8314 (tmt170) cc_final: 0.7965 (tmt170)
REVERT: B  257 ARG cc_start: 0.8534 (mmp80) cc_final: 0.8284 (mmp80)
REVERT: B  293 MET cc_start: 0.8330 (ptp) cc_final: 0.8092 (ptp)
  outliers start: 12
  outliers final: 7
  residues processed: 42
  average time/residue: 0.2462
  time to fit residues: 14.3447
Evaluate side-chains
  39 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 ARG
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  327 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.3657 r_free = 0.3657 target = 0.085894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.059485 restraints weight = 23189.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 2.62
r_work: 0.2901 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8978  Z= 0.168
  Angle     :  0.613  27.607  12850  Z= 0.285
  Chirality :  0.062   2.011   1520
  Planarity :  0.004   0.045   1108
  Dihedral  : 22.207  94.806   3018
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 26.12 %
    Favored  : 70.76 %
  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: -0.82 (0.33), residues: 642
  helix:  1.05 (0.40), residues: 182
  sheet: -0.43 (0.62), residues: 60
  loop : -1.39 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 352 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.019   0.001   PHE A 320 
 TYR   0.014   0.001   TYR A 216 
 ARG   0.005   0.000   ARG B 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05575 (  303)
  hydrogen bonds       : angle       3.66036 (  692)
  covalent geometry    : bond        0.00380 ( 8978)
  covalent geometry    : angle       0.61293 (12850)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 30
  time to evaluate  : 0.677 
Fit side-chains
REVERT: A  116 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7982 (ptp-170)
REVERT: A  163 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.9017 (mp)
REVERT: A  257 ARG cc_start: 0.8399 (tmt170) cc_final: 0.8048 (tmt170)
REVERT: B  293 MET cc_start: 0.8334 (ptp) cc_final: 0.8093 (ptp)
  outliers start: 18
  outliers final: 13
  residues processed: 47
  average time/residue: 0.2238
  time to fit residues: 14.6472
Evaluate side-chains
  44 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 29
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  116 ARG
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  327 CYS
Chi-restraints excluded: chain B residue  408 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
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 = 0.3653 r_free = 0.3653 target = 0.085785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.059223 restraints weight = 23088.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 2.61
r_work: 0.2895 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8978  Z= 0.178
  Angle     :  0.621  27.676  12850  Z= 0.291
  Chirality :  0.062   2.016   1520
  Planarity :  0.004   0.042   1108
  Dihedral  : 22.207  95.202   3018
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 26.30 %
    Favored  : 70.59 %
  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: -0.87 (0.33), residues: 642
  helix:  0.99 (0.40), residues: 182
  sheet: -0.46 (0.61), residues: 60
  loop : -1.42 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 352 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.018   0.001   PHE A 320 
 TYR   0.017   0.002   TYR B 276 
 ARG   0.006   0.000   ARG B 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05730 (  303)
  hydrogen bonds       : angle       3.64948 (  692)
  covalent geometry    : bond        0.00404 ( 8978)
  covalent geometry    : angle       0.62134 (12850)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 29
  time to evaluate  : 0.681 
Fit side-chains
REVERT: A  116 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7968 (ptp-170)
REVERT: A  163 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9015 (mp)
REVERT: A  257 ARG cc_start: 0.8410 (tmt170) cc_final: 0.8120 (tmt170)
REVERT: B  293 MET cc_start: 0.8338 (ptp) cc_final: 0.8081 (ptp)
  outliers start: 18
  outliers final: 14
  residues processed: 46
  average time/residue: 0.2056
  time to fit residues: 13.5328
Evaluate side-chains
  45 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 29
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  116 ARG
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  327 CYS
Chi-restraints excluded: chain B residue  408 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 67 optimal weight:    9.9990
   chunk 57 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0670
   chunk 65 optimal weight:    7.9990
   chunk 53 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.2722

-------------------------------------------------------------------------------
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 = 0.3671 r_free = 0.3671 target = 0.086667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.060148 restraints weight = 23110.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 2.60
r_work: 0.2920 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.1441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8978  Z= 0.131
  Angle     :  0.594  27.631  12850  Z= 0.274
  Chirality :  0.062   2.032   1520
  Planarity :  0.004   0.042   1108
  Dihedral  : 22.152  94.417   3018
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 26.64 %
    Favored  : 70.76 %
  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: -0.77 (0.33), residues: 642
  helix:  1.04 (0.40), residues: 182
  sheet: -0.30 (0.62), residues: 60
  loop : -1.35 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 352 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.018   0.001   PHE A 320 
 TYR   0.017   0.001   TYR B 276 
 ARG   0.004   0.000   ARG B 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05038 (  303)
  hydrogen bonds       : angle       3.54928 (  692)
  covalent geometry    : bond        0.00292 ( 8978)
  covalent geometry    : angle       0.59394 (12850)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 29
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A  116 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7857 (ptp-170)
REVERT: A  163 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8993 (mp)
REVERT: A  257 ARG cc_start: 0.8386 (tmt170) cc_final: 0.8080 (tmt170)
REVERT: B  293 MET cc_start: 0.8344 (ptp) cc_final: 0.8105 (ptp)
  outliers start: 15
  outliers final: 13
  residues processed: 43
  average time/residue: 0.2167
  time to fit residues: 13.3497
Evaluate side-chains
  44 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 29
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  116 ARG
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  327 CYS
Chi-restraints excluded: chain B residue  408 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 50 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 42 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0970
   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 = 0.3674 r_free = 0.3674 target = 0.086822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.060461 restraints weight = 22857.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 2.59
r_work: 0.2925 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8978  Z= 0.135
  Angle     :  0.595  27.527  12850  Z= 0.275
  Chirality :  0.062   2.034   1520
  Planarity :  0.004   0.042   1108
  Dihedral  : 22.132  94.518   3018
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 25.95 %
    Favored  : 71.11 %
  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: -0.78 (0.33), residues: 642
  helix:  1.01 (0.40), residues: 182
  sheet: -0.28 (0.62), residues: 60
  loop : -1.35 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 352 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.018   0.001   PHE A 320 
 TYR   0.017   0.001   TYR A 216 
 ARG   0.004   0.000   ARG B 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05066 (  303)
  hydrogen bonds       : angle       3.54317 (  692)
  covalent geometry    : bond        0.00302 ( 8978)
  covalent geometry    : angle       0.59526 (12850)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 31
  time to evaluate  : 0.745 
Fit side-chains
REVERT: A  116 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7849 (ptp-170)
REVERT: A  163 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8996 (mp)
REVERT: A  257 ARG cc_start: 0.8390 (tmt170) cc_final: 0.8110 (tmt170)
REVERT: B  257 ARG cc_start: 0.8430 (mmp80) cc_final: 0.8208 (mmp80)
REVERT: B  293 MET cc_start: 0.8336 (ptp) cc_final: 0.8092 (ptp)
  outliers start: 17
  outliers final: 13
  residues processed: 47
  average time/residue: 0.2389
  time to fit residues: 15.6838
Evaluate side-chains
  46 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 31
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  116 ARG
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  327 CYS
Chi-restraints excluded: chain B residue  408 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 74 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   chunk 27 optimal weight:    0.5980
   chunk 76 optimal weight:    6.9990
   chunk 22 optimal weight:    0.2980
   chunk 61 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 14 optimal weight:    0.6980
   chunk 75 optimal weight:    7.9990
   overall best weight:    1.2582

-------------------------------------------------------------------------------
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 = 0.3666 r_free = 0.3666 target = 0.086844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.060403 restraints weight = 23138.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 2.68
r_work: 0.2915 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8978  Z= 0.130
  Angle     :  0.592  27.851  12850  Z= 0.272
  Chirality :  0.061   2.013   1520
  Planarity :  0.004   0.043   1108
  Dihedral  : 22.097  94.460   3018
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 26.30 %
    Favored  : 70.93 %
  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: -0.76 (0.33), residues: 642
  helix:  1.01 (0.40), residues: 182
  sheet: -0.26 (0.62), residues: 60
  loop : -1.33 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 352 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.017   0.001   PHE A 320 
 TYR   0.015   0.001   TYR B 276 
 ARG   0.005   0.000   ARG B 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04956 (  303)
  hydrogen bonds       : angle       3.53496 (  692)
  covalent geometry    : bond        0.00291 ( 8978)
  covalent geometry    : angle       0.59215 (12850)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4026.59 seconds
wall clock time: 69 minutes 46.64 seconds (4186.64 seconds total)