Starting phenix.real_space_refine
on Fri May 16 06:17:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8omr_16976/05_2025/8omr_16976.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8omr_16976/05_2025/8omr_16976.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8omr_16976/05_2025/8omr_16976.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8omr_16976/05_2025/8omr_16976.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8omr_16976/05_2025/8omr_16976.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8omr_16976/05_2025/8omr_16976.cif"
  }
  resolution = 3.3
  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=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7626 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      75      5.49       5
     S      48      5.16       5
     C    4520      2.51       5
     N    1341      2.21       5
     O    1640      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7626
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3010
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 390, 3000
          Classifications: {'peptide': 390}
          Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 368}
      Conformer: "B"
        Number of residues, atoms: 390, 3000
          Classifications: {'peptide': 390}
          Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 368}
          bond proxies already assigned to first conformer: 3053
    Chain: "B"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 3014
          Classifications: {'peptide': 382}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 365}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1589
          Classifications: {'RNA': 75}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 33, 'rna3p_pyr': 31}
          Link IDs: {'rna2p': 11, 'rna3p': 63}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'  G%rna3p_pur:plan2': 1, '  G%rna3p_pur:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 12
          Unusual residues: {' ZN': 1, '9DG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2336  SG  CYS A 317      50.960  46.783  79.155  1.00 71.53           S
  ATOM   2349  SG  CYS A 319      48.135  45.426  76.966  1.00 57.96           S
  ATOM   2369  SG  CYS A 322      51.015  47.274  75.471  1.00 66.05           S
  ATOM   5496  SG  CYS B 351      26.013  26.939  71.448  1.00 61.72           S
  ATOM   5508  SG  CYS B 353      27.602  29.987  72.683  1.00 70.08           S
  ATOM   5532  SG  CYS B 356      24.182  29.011  73.915  1.00 67.56           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS A 335 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 335 " occ=0.50
  Time building chain proxies: 6.42, per 1000 atoms: 0.84
  Number of scatterers: 7626
  At special positions: 0
  Unit cell: (72.54, 99.06, 124.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      48     16.00
     P      75     15.00
     O    1640      8.00
     N    1341      7.00
     C    4520      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: 1.96
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" ND1 HIS A 348 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 319 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 322 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 317 "
      pdb="  ZN B 501 "
        pdb="ZN    ZN B 501 " - pdb=" ND1 HIS B 382 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B 351 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B 356 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B 353 "
      Number of angles added : 6


  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1428

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      47.9% alpha, 11.8% beta
      23 base pairs and 34 stacking pairs defined.
    Time for finding SS restraints: 2.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 66
      removed outlier: 3.581A  pdb=" N   GLY A  66 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 80
    Processing helix  chain 'A' and resid 82 through 89
      removed outlier: 3.571A  pdb=" N   ILE A  86 " --> pdb=" O   GLY A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 97
    Processing helix  chain 'A' and resid 109 through 114
    Processing helix  chain 'A' and resid 139 through 151
    Processing helix  chain 'A' and resid 169 through 189
    Processing helix  chain 'A' and resid 206 through 218
    Processing helix  chain 'A' and resid 235 through 250
      removed outlier: 3.649A  pdb=" N   ARG A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ARG A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 274
    Processing helix  chain 'A' and resid 281 through 288
      removed outlier: 3.554A  pdb=" N   ARG A 288 " --> pdb=" O   THR A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 307
      removed outlier: 3.911A  pdb=" N   PHE A 306 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 325
      removed outlier: 4.065A  pdb=" N   LYS A 324 " --> pdb=" O   PRO A 320 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   HIS A 325 " --> pdb=" O   THR A 321 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 320 through 325'
    Processing helix  chain 'A' and resid 326 through 335
      removed outlier: 3.625A  pdb=" N   LEU A 330 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N  AHIS A 335 " --> pdb=" O   HIS A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 340
      No H-bonds generated for 'chain 'A' and resid 338 through 340'
    Processing helix  chain 'A' and resid 341 through 366
      removed outlier: 4.244A  pdb=" N   LEU A 345 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   THR A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   VAL A 347 " --> pdb=" O   HIS A 343 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 356 " --> pdb=" O   TYR A 352 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   MET A 357 " --> pdb=" O   GLN A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 382
      removed outlier: 3.555A  pdb=" N   VAL A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ARG A 374 " --> pdb=" O   PRO A 370 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ASP A 375 " --> pdb=" O   ASP A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
      removed outlier: 4.216A  pdb=" N   CYS A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 399
      removed outlier: 3.639A  pdb=" N   ASP A 393 " --> pdb=" O   THR A 389 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ALA A 394 " --> pdb=" O   TRP A 390 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   VAL A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 51
    Processing helix  chain 'B' and resid 64 through 68
    Processing helix  chain 'B' and resid 73 through 78
    Processing helix  chain 'B' and resid 125 through 137
      removed outlier: 3.521A  pdb=" N   PHE B 129 " --> pdb=" O   THR B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 151
      removed outlier: 4.071A  pdb=" N   SER B 150 " --> pdb=" O   GLY B 147 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   CYS B 151 " --> pdb=" O   GLU B 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 147 through 151'
    Processing helix  chain 'B' and resid 156 through 181
      removed outlier: 3.820A  pdb=" N   VAL B 160 " --> pdb=" O   SER B 156 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   SER B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 187
      removed outlier: 3.718A  pdb=" N   LYS B 186 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 210
      removed outlier: 4.159A  pdb=" N   ALA B 206 " --> pdb=" O   ARG B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 240
      removed outlier: 3.830A  pdb=" N   SER B 237 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 264
      removed outlier: 3.987A  pdb=" N   LEU B 261 " --> pdb=" O   PRO B 257 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   GLU B 262 " --> pdb=" O   ASP B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 267
      No H-bonds generated for 'chain 'B' and resid 265 through 267'
    Processing helix  chain 'B' and resid 274 through 282
    Processing helix  chain 'B' and resid 353 through 359
    Processing helix  chain 'B' and resid 360 through 370
    Processing helix  chain 'B' and resid 373 through 401
      removed outlier: 3.844A  pdb=" N   VAL B 377 " --> pdb=" O   LEU B 373 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   HIS B 382 " --> pdb=" O   LEU B 378 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLU B 385 " --> pdb=" O   MET B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 412
      removed outlier: 3.874A  pdb=" N   LEU B 406 " --> pdb=" O   LYS B 402 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 22
      removed outlier: 6.732A  pdb=" N   MET A  17 " --> pdb=" O   TRP A  34 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   TRP A  34 " --> pdb=" O   MET A  17 " (cutoff:3.500A)
      removed outlier: 5.645A  pdb=" N   LEU A  19 " --> pdb=" O   GLU A  32 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   GLU A  32 " --> pdb=" O   LEU A  19 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46
      removed outlier: 3.546A  pdb=" N   PHE A 278 " --> pdb=" O   VAL A  44 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   MET A  46 " --> pdb=" O   PHE A 278 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 72
      removed outlier: 3.562A  pdb=" N   ILE A 154 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   MET A 156 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   GLY A 224 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA A 199 " --> pdb=" O   GLY A 224 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 121
    Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 294
    Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 9
      removed outlier: 5.665A  pdb=" N   LEU B   5 " --> pdb=" O   LYS B  16 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   LYS B  16 " --> pdb=" O   LEU B   5 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LYS B   7 " --> pdb=" O   LEU B  14 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL B   9 " --> pdb=" O   CYS B  12 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY B  15 " --> pdb=" O   ILE B  30 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 33
      removed outlier: 6.825A  pdb=" N   GLY B  32 " --> pdb=" O   PHE B 271 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 36
      removed outlier: 6.917A  pdb=" N   LEU B  35 " --> pdb=" O   GLN B  61 " (cutoff:3.500A)
      removed outlier: 8.425A  pdb=" N   THR B  63 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   TYR B  93 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   CYS B  94 " --> pdb=" O   TRP B 140 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLN B 142 " --> pdb=" O   CYS B  94 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   PHE B 141 " --> pdb=" O   ILE B 190 " (cutoff:3.500A)
      removed outlier: 8.696A  pdb=" N   VAL B 192 " --> pdb=" O   PHE B 141 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 113 through 117
    Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 286

    244 hydrogen bonds defined for protein.
    699 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      61 hydrogen bonds
      102 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      34 stacking parallelities
  Total time for adding SS restraints: 2.26

  Time building geometry restraints manager: 2.23 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1581
        1.33 -     1.45: 2123
        1.45 -     1.57: 4014
        1.57 -     1.69: 149
        1.69 -     1.81: 71
  Bond restraints: 7938
  Sorted by residual:
  bond pdb=" CG  ASP A 279 "
       pdb=" OD2 ASP A 279 "
    ideal  model  delta    sigma   weight residual
    1.249  1.359 -0.110 1.90e-02 2.77e+03 3.34e+01
  bond pdb=" O5'   C C  48 "
       pdb=" C5'   C C  48 "
    ideal  model  delta    sigma   weight residual
    1.420  1.454 -0.034 1.50e-02 4.44e+03 5.29e+00
  bond pdb=" O5'   A C   1 "
       pdb=" C5'   A C   1 "
    ideal  model  delta    sigma   weight residual
    1.420  1.449 -0.029 1.50e-02 4.44e+03 3.83e+00
  bond pdb=" O5'   U C  58 "
       pdb=" C5'   U C  58 "
    ideal  model  delta    sigma   weight residual
    1.420  1.449 -0.029 1.50e-02 4.44e+03 3.68e+00
  bond pdb=" O5'   G C  15 "
       pdb=" C5'   G C  15 "
    ideal  model  delta    sigma   weight residual
    1.420  1.449 -0.029 1.50e-02 4.44e+03 3.63e+00
  ... (remaining 7933 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 10715
        2.42 -     4.83: 345
        4.83 -     7.25: 41
        7.25 -     9.66: 4
        9.66 -    12.08: 1
  Bond angle restraints: 11106
  Sorted by residual:
  angle pdb=" O3'   A C  57 "
        pdb=" P     U C  58 "
        pdb=" O5'   U C  58 "
      ideal   model   delta    sigma   weight residual
     104.00   95.43    8.57 1.50e+00 4.44e-01 3.26e+01
  angle pdb=" O3'   U C  58 "
        pdb=" P     U C  59 "
        pdb=" O5'   U C  59 "
      ideal   model   delta    sigma   weight residual
     104.00   96.91    7.09 1.50e+00 4.44e-01 2.23e+01
  angle pdb=" C4'   G C  56 "
        pdb=" C3'   G C  56 "
        pdb=" O3'   G C  56 "
      ideal   model   delta    sigma   weight residual
     113.00  106.87    6.13 1.50e+00 4.44e-01 1.67e+01
  angle pdb=" O3'   A C  57 "
        pdb=" P     U C  58 "
        pdb=" OP1   U C  58 "
      ideal   model   delta    sigma   weight residual
     108.00  120.08  -12.08 3.00e+00 1.11e-01 1.62e+01
  angle pdb=" C2'   A C  12 "
        pdb=" C1'   A C  12 "
        pdb=" N9    A C  12 "
      ideal   model   delta    sigma   weight residual
     112.00  117.40   -5.40 1.50e+00 4.44e-01 1.30e+01
  ... (remaining 11101 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.64: 4618
       29.64 -    59.28: 208
       59.28 -    88.93: 81
       88.93 -   118.57: 0
      118.57 -   148.21: 1
  Dihedral angle restraints: 4908
    sinusoidal: 2691
      harmonic: 2217
  Sorted by residual:
  dihedral pdb=" C4'   G C  34 "
           pdb=" C3'   G C  34 "
           pdb=" C2'   G C  34 "
           pdb=" C1'   G C  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.00  -21.05   57.05     1      8.00e+00 1.56e-02 6.84e+01
  dihedral pdb=" O4'   G C  34 "
           pdb=" C2'   G C  34 "
           pdb=" C1'   G C  34 "
           pdb=" C3'   G C  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00  -30.91   55.91     1      8.00e+00 1.56e-02 6.59e+01
  dihedral pdb=" C5'   G C  34 "
           pdb=" C4'   G C  34 "
           pdb=" C3'   G C  34 "
           pdb=" O3'   G C  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      82.00  123.89  -41.89     1      8.00e+00 1.56e-02 3.83e+01
  ... (remaining 4905 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.114: 1215
       0.114 -    0.227: 85
       0.227 -    0.341: 4
       0.341 -    0.454: 3
       0.454 -    0.568: 6
  Chirality restraints: 1313
  Sorted by residual:
  chirality pdb=" P     A C   1 "
            pdb=" OP1   A C   1 "
            pdb=" OP2   A C   1 "
            pdb=" O5'   A C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.98   -0.57 2.00e-01 2.50e+01 8.06e+00
  chirality pdb=" P     C C  47 "
            pdb=" OP1   C C  47 "
            pdb=" OP2   C C  47 "
            pdb=" O5'   C C  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.93   -0.52 2.00e-01 2.50e+01 6.84e+00
  chirality pdb=" P     U C  16 "
            pdb=" OP1   U C  16 "
            pdb=" OP2   U C  16 "
            pdb=" O5'   U C  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.93   -0.52 2.00e-01 2.50e+01 6.64e+00
  ... (remaining 1310 not shown)

  Planarity restraints: 1148
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  21 "   -0.037 2.00e-02 2.50e+03   2.20e-02 1.33e+01
        pdb=" N9    A C  21 "    0.061 2.00e-02 2.50e+03
        pdb=" C8    A C  21 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    A C  21 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5    A C  21 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A C  21 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6    A C  21 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    A C  21 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A C  21 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A C  21 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    A C  21 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  12 "    0.037 2.00e-02 2.50e+03   1.98e-02 1.07e+01
        pdb=" N9    A C  12 "   -0.052 2.00e-02 2.50e+03
        pdb=" C8    A C  12 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A C  12 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    A C  12 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A C  12 "    0.003 2.00e-02 2.50e+03
        pdb=" N6    A C  12 "    0.009 2.00e-02 2.50e+03
        pdb=" N1    A C  12 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2    A C  12 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    A C  12 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A C  12 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  42 "    0.015 2.00e-02 2.50e+03   3.07e-02 9.42e+00
        pdb=" C   THR A  42 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   THR A  42 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PRO A  43 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1145 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.19: 1
        2.19 -     2.87: 2730
        2.87 -     3.54: 10057
        3.54 -     4.22: 17336
        4.22 -     4.90: 28650
  Nonbonded interactions: 58774
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 279 "
            pdb=" C1'   G C  34 "
     model   vdw
     1.512 3.470
  nonbonded pdb=" OD2 ASP A 279 "
            pdb=" O4'   G C  34 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG  SER B 181 "
            pdb=" N   GLU B 182 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" O   MET A 175 "
            pdb=" OG  SER A 178 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OD1 ASN B 110 "
            pdb=" NE  ARG B 166 "
     model   vdw
     2.232 3.120
  ... (remaining 58769 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=0.50 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:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     25.680
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
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      :  0.010   0.110   7946  Z= 0.428
  Angle     :  1.009  12.077  11112  Z= 0.570
  Chirality :  0.073   0.568   1313
  Planarity :  0.008   0.075   1148
  Dihedral  : 17.486 148.211   3480
  Min Nonbonded Distance : 1.512

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  6.62 %
    Allowed  :  7.67 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -1.83 (0.28), residues: 769
  helix: -0.33 (0.28), residues: 325
  sheet: -1.15 (0.61), residues: 70
  loop : -2.04 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 240 
 HIS   0.008   0.002   HIS B 359 
 PHE   0.028   0.003   PHE B 331 
 TYR   0.018   0.004   TYR B 354 
 ARG   0.018   0.003   ARG A 285 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16748 (  305)
  hydrogen bonds       : angle       6.65423 (  801)
  metal coordination   : bond        0.02265 (    8)
  metal coordination   : angle       4.59186 (    6)
  covalent geometry    : bond        0.00951 ( 7938)
  covalent geometry    : angle       1.00378 (11106)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 51
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6854 (mp)
REVERT: A  197 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8583 (tt)
REVERT: A  368 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7145 (ptm160)
REVERT: B    1 MET cc_start: 0.4226 (mtm) cc_final: 0.3501 (mtp)
REVERT: B   97 HIS cc_start: 0.8290 (OUTLIER) cc_final: 0.7507 (p90)
REVERT: B  123 GLU cc_start: 0.8388 (pm20) cc_final: 0.7945 (pt0)
REVERT: B  228 THR cc_start: 0.7697 (OUTLIER) cc_final: 0.7371 (p)
REVERT: B  249 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.6373 (mtt-85)
REVERT: B  393 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7009 (t80)
REVERT: B  405 GLN cc_start: 0.7883 (tp40) cc_final: 0.7663 (tm-30)
  outliers start: 44
  outliers final: 32
  residues processed: 90
  average time/residue: 0.2183
  time to fit residues: 26.0996
Evaluate side-chains
  79 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 40
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue   99 PRO
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   22 LYS
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  249 ARG
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  393 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 157 GLN
** B  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.111713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.081970 restraints weight = 35631.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 3.57
r_work: 0.3008 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3016
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3016
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7946  Z= 0.148
  Angle     :  0.599   7.031  11112  Z= 0.308
  Chirality :  0.040   0.208   1313
  Planarity :  0.004   0.038   1148
  Dihedral  : 19.085 132.675   2095
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 10.83 %
    Favored  : 85.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.85 (0.30), residues: 769
  helix:  0.62 (0.30), residues: 325
  sheet: -0.81 (0.54), residues: 100
  loop : -1.66 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 240 
 HIS   0.004   0.001   HIS B 365 
 PHE   0.014   0.001   PHE A 127 
 TYR   0.012   0.001   TYR B 354 
 ARG   0.010   0.000   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05987 (  305)
  hydrogen bonds       : angle       4.91636 (  801)
  metal coordination   : bond        0.01117 (    8)
  metal coordination   : angle       2.57529 (    6)
  covalent geometry    : bond        0.00314 ( 7938)
  covalent geometry    : angle       0.59569 (11106)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 48
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  368 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6719 (ptm160)
REVERT: B    1 MET cc_start: 0.5438 (mtm) cc_final: 0.4469 (mtp)
REVERT: B   97 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7361 (p90)
REVERT: B  173 ASN cc_start: 0.8714 (m-40) cc_final: 0.8461 (m-40)
REVERT: B  249 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7448 (mmt-90)
REVERT: B  393 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.7307 (t80)
  outliers start: 25
  outliers final: 16
  residues processed: 70
  average time/residue: 0.2039
  time to fit residues: 19.8468
Evaluate side-chains
  57 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 37
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain B residue   22 LYS
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  249 ARG
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  393 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 83 optimal weight:   20.0000
   chunk 8 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0170
   chunk 47 optimal weight:    0.8980
   chunk 16 optimal weight:    9.9990
   chunk 77 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   chunk 74 optimal weight:    0.0870
   chunk 30 optimal weight:    0.0040
   overall best weight:    0.6010

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

Flipped N/Q/H residues before XYZ refinement:
B 366 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.113301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.084083 restraints weight = 46096.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 4.12
r_work: 0.3022 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3026
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3026
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7946  Z= 0.097
  Angle     :  0.512   6.260  11112  Z= 0.259
  Chirality :  0.036   0.198   1313
  Planarity :  0.004   0.033   1148
  Dihedral  : 18.898 101.369   2067
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 11.88 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.48 (0.31), residues: 769
  helix:  0.87 (0.31), residues: 338
  sheet: -0.80 (0.50), residues: 112
  loop : -1.40 (0.32), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 240 
 HIS   0.003   0.000   HIS B 365 
 PHE   0.013   0.001   PHE A 127 
 TYR   0.008   0.001   TYR B 354 
 ARG   0.006   0.000   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04458 (  305)
  hydrogen bonds       : angle       4.31971 (  801)
  metal coordination   : bond        0.00414 (    8)
  metal coordination   : angle       1.40353 (    6)
  covalent geometry    : bond        0.00200 ( 7938)
  covalent geometry    : angle       0.51090 (11106)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 48
  time to evaluate  : 0.791 
Fit side-chains
REVERT: A  197 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8561 (tt)
REVERT: B    1 MET cc_start: 0.5374 (mtm) cc_final: 0.4472 (mtp)
REVERT: B  230 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8157 (mm-30)
REVERT: B  249 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.5717 (mmt-90)
REVERT: B  341 GLN cc_start: 0.7729 (pt0) cc_final: 0.7444 (tt0)
REVERT: B  393 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7154 (t80)
  outliers start: 20
  outliers final: 12
  residues processed: 65
  average time/residue: 0.1888
  time to fit residues: 17.3346
Evaluate side-chains
  60 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain B residue   22 LYS
Chi-restraints excluded: chain B residue  249 ARG
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  393 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 53 optimal weight:    0.3980
   chunk 40 optimal weight:   20.0000
   chunk 67 optimal weight:    7.9990
   chunk 50 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 80 optimal weight:   10.0000
   chunk 83 optimal weight:   20.0000
   chunk 65 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   overall best weight:    3.4788

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.108921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.079239 restraints weight = 48338.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 4.16
r_work: 0.2918 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2920
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2920 r_free = 0.2920    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2920 r_free = 0.2920    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2920
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7946  Z= 0.230
  Angle     :  0.623   6.524  11112  Z= 0.320
  Chirality :  0.041   0.212   1313
  Planarity :  0.004   0.035   1148
  Dihedral  : 18.954  87.807   2053
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 13.38 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 (0.30), residues: 769
  helix:  0.74 (0.30), residues: 335
  sheet: -0.81 (0.57), residues: 86
  loop : -1.70 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  98 
 HIS   0.005   0.001   HIS B 359 
 PHE   0.017   0.002   PHE B 331 
 TYR   0.013   0.002   TYR B 354 
 ARG   0.005   0.000   ARG A  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06852 (  305)
  hydrogen bonds       : angle       4.74978 (  801)
  metal coordination   : bond        0.01605 (    8)
  metal coordination   : angle       2.76452 (    6)
  covalent geometry    : bond        0.00531 ( 7938)
  covalent geometry    : angle       0.62031 (11106)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.697 
Fit side-chains
REVERT: B    1 MET cc_start: 0.5411 (mtm) cc_final: 0.4509 (mtp)
REVERT: B   97 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7362 (p90)
REVERT: B  230 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8148 (mm-30)
REVERT: B  249 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.5618 (mmt-90)
REVERT: B  393 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7273 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 61
  average time/residue: 0.2043
  time to fit residues: 16.9258
Evaluate side-chains
  60 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 41
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain B residue   22 LYS
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  249 ARG
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  393 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 80 optimal weight:    8.9990
   chunk 2 optimal weight:   20.0000
   chunk 50 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 11 optimal weight:    6.9990
   chunk 4 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3698 r_free = 0.3698 target = 0.111846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.083548 restraints weight = 25733.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.96
r_work: 0.3045 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7946  Z= 0.106
  Angle     :  0.503   6.256  11112  Z= 0.257
  Chirality :  0.036   0.216   1313
  Planarity :  0.004   0.034   1148
  Dihedral  : 18.920  73.976   2053
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 13.98 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.31), residues: 769
  helix:  1.07 (0.31), residues: 332
  sheet: -0.69 (0.49), residues: 112
  loop : -1.45 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 240 
 HIS   0.002   0.001   HIS B 365 
 PHE   0.011   0.001   PHE A 127 
 TYR   0.009   0.001   TYR B 354 
 ARG   0.004   0.000   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04931 (  305)
  hydrogen bonds       : angle       4.29203 (  801)
  metal coordination   : bond        0.00668 (    8)
  metal coordination   : angle       1.72450 (    6)
  covalent geometry    : bond        0.00224 ( 7938)
  covalent geometry    : angle       0.50167 (11106)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.750 
Fit side-chains
REVERT: A  197 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8517 (tt)
REVERT: B    1 MET cc_start: 0.5483 (mtm) cc_final: 0.4612 (mtp)
REVERT: B   97 HIS cc_start: 0.8019 (OUTLIER) cc_final: 0.7273 (p90)
REVERT: B  230 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8129 (mm-30)
REVERT: B  249 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.6205 (mmt-90)
REVERT: B  393 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7209 (t80)
  outliers start: 16
  outliers final: 12
  residues processed: 57
  average time/residue: 0.2086
  time to fit residues: 16.4258
Evaluate side-chains
  58 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain B residue   22 LYS
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  249 ARG
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  393 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 83 optimal weight:   20.0000
   chunk 52 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 67 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3697 r_free = 0.3697 target = 0.111735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.084030 restraints weight = 21205.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.68
r_work: 0.3060 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7946  Z= 0.113
  Angle     :  0.496   6.280  11112  Z= 0.252
  Chirality :  0.036   0.224   1313
  Planarity :  0.004   0.033   1148
  Dihedral  : 18.880  73.974   2053
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.38 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.34 (0.31), residues: 769
  helix:  1.10 (0.31), residues: 335
  sheet: -0.71 (0.49), residues: 112
  loop : -1.47 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 240 
 HIS   0.003   0.001   HIS B 359 
 PHE   0.011   0.001   PHE A 127 
 TYR   0.009   0.001   TYR B 354 
 ARG   0.005   0.000   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04945 (  305)
  hydrogen bonds       : angle       4.20017 (  801)
  metal coordination   : bond        0.00826 (    8)
  metal coordination   : angle       1.84936 (    6)
  covalent geometry    : bond        0.00247 ( 7938)
  covalent geometry    : angle       0.49384 (11106)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A  197 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8501 (tt)
REVERT: B    1 MET cc_start: 0.5436 (mtm) cc_final: 0.4589 (mtp)
REVERT: B   97 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.7253 (p90)
REVERT: B  230 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8126 (mm-30)
REVERT: B  249 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.6152 (mmt-90)
REVERT: B  341 GLN cc_start: 0.7730 (pt0) cc_final: 0.7473 (tt0)
REVERT: B  393 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7161 (t80)
  outliers start: 19
  outliers final: 15
  residues processed: 62
  average time/residue: 0.1984
  time to fit residues: 17.1361
Evaluate side-chains
  62 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 43
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain B residue   22 LYS
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  249 ARG
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  393 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 45 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 75 optimal weight:    8.9990
   chunk 79 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3716 r_free = 0.3716 target = 0.112960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.084935 restraints weight = 24810.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 2.92
r_work: 0.3077 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3076
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3076
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7946  Z= 0.096
  Angle     :  0.470   6.153  11112  Z= 0.237
  Chirality :  0.036   0.235   1313
  Planarity :  0.004   0.033   1148
  Dihedral  : 18.850  73.938   2053
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.38 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.24 (0.31), residues: 769
  helix:  1.08 (0.31), residues: 342
  sheet: -0.79 (0.47), residues: 119
  loop : -1.27 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 240 
 HIS   0.002   0.001   HIS B 359 
 PHE   0.011   0.001   PHE A 127 
 TYR   0.008   0.001   TYR B 354 
 ARG   0.005   0.000   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04383 (  305)
  hydrogen bonds       : angle       4.03864 (  801)
  metal coordination   : bond        0.00571 (    8)
  metal coordination   : angle       1.53979 (    6)
  covalent geometry    : bond        0.00205 ( 7938)
  covalent geometry    : angle       0.46831 (11106)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A  197 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8478 (tt)
REVERT: B    1 MET cc_start: 0.5439 (mtm) cc_final: 0.4602 (mtp)
REVERT: B   97 HIS cc_start: 0.8090 (OUTLIER) cc_final: 0.7371 (p90)
REVERT: B  230 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8177 (mm-30)
REVERT: B  341 GLN cc_start: 0.7739 (pt0) cc_final: 0.7505 (tt0)
REVERT: B  393 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7096 (t80)
  outliers start: 19
  outliers final: 15
  residues processed: 62
  average time/residue: 0.1735
  time to fit residues: 15.5998
Evaluate side-chains
  60 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain B residue   22 LYS
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  393 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0670
   chunk 72 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 49 optimal weight:    0.5980
   overall best weight:    1.1324

-------------------------------------------------------------------------------
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 = 0.3710 r_free = 0.3710 target = 0.112534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.083727 restraints weight = 31291.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 3.33
r_work: 0.3043 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7946  Z= 0.101
  Angle     :  0.470   6.241  11112  Z= 0.238
  Chirality :  0.036   0.228   1313
  Planarity :  0.004   0.033   1148
  Dihedral  : 18.811  73.953   2048
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 13.83 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.23 (0.31), residues: 769
  helix:  1.09 (0.31), residues: 342
  sheet: -0.74 (0.50), residues: 107
  loop : -1.28 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 240 
 HIS   0.003   0.001   HIS B 359 
 PHE   0.010   0.001   PHE A 127 
 TYR   0.008   0.001   TYR B 354 
 ARG   0.005   0.000   ARG A  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04583 (  305)
  hydrogen bonds       : angle       4.04284 (  801)
  metal coordination   : bond        0.00730 (    8)
  metal coordination   : angle       1.71058 (    6)
  covalent geometry    : bond        0.00220 ( 7938)
  covalent geometry    : angle       0.46870 (11106)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.741 
Fit side-chains
REVERT: A  197 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8476 (tt)
REVERT: B    1 MET cc_start: 0.5406 (mtm) cc_final: 0.4534 (mtp)
REVERT: B   97 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7325 (p90)
REVERT: B  230 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8201 (mm-30)
REVERT: B  249 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.6360 (mmt-90)
REVERT: B  341 GLN cc_start: 0.7726 (pt0) cc_final: 0.7507 (tt0)
REVERT: B  393 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.7100 (t80)
  outliers start: 18
  outliers final: 14
  residues processed: 58
  average time/residue: 0.1952
  time to fit residues: 15.9520
Evaluate side-chains
  60 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain B residue   22 LYS
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  249 ARG
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  393 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 63 optimal weight:    0.4980
   chunk 18 optimal weight:    4.9990
   chunk 68 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 23 optimal weight:    0.0770
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.9144

-------------------------------------------------------------------------------
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 = 0.3682 r_free = 0.3682 target = 0.110843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.082027 restraints weight = 29670.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 3.22
r_work: 0.3005 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3007
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7946  Z= 0.140
  Angle     :  0.517   6.333  11112  Z= 0.263
  Chirality :  0.037   0.234   1313
  Planarity :  0.004   0.032   1148
  Dihedral  : 18.821  74.020   2048
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.83 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.31), residues: 769
  helix:  1.12 (0.31), residues: 336
  sheet: -0.76 (0.50), residues: 107
  loop : -1.31 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 240 
 HIS   0.004   0.001   HIS A 344 
 PHE   0.011   0.001   PHE A 127 
 TYR   0.010   0.001   TYR B 354 
 ARG   0.004   0.000   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05523 (  305)
  hydrogen bonds       : angle       4.24981 (  801)
  metal coordination   : bond        0.01138 (    8)
  metal coordination   : angle       2.14269 (    6)
  covalent geometry    : bond        0.00315 ( 7938)
  covalent geometry    : angle       0.51438 (11106)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 43
  time to evaluate  : 0.800 
Fit side-chains
REVERT: B    1 MET cc_start: 0.5358 (mtm) cc_final: 0.4499 (mtp)
REVERT: B   97 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7318 (p90)
REVERT: B  230 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8223 (mm-30)
REVERT: B  249 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.6492 (mmt-90)
REVERT: B  341 GLN cc_start: 0.7769 (pt0) cc_final: 0.7506 (tt0)
REVERT: B  393 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.7179 (t80)
  outliers start: 19
  outliers final: 16
  residues processed: 60
  average time/residue: 0.1868
  time to fit residues: 15.8443
Evaluate side-chains
  61 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 42
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain B residue   22 LYS
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  249 ARG
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  393 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 64 optimal weight:    9.9990
   chunk 83 optimal weight:   20.0000
   chunk 46 optimal weight:    5.9990
   chunk 76 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    2.8988

-------------------------------------------------------------------------------
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 = 0.3656 r_free = 0.3656 target = 0.109162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.079562 restraints weight = 42960.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 3.94
r_work: 0.2932 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2935
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2935
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7946  Z= 0.192
  Angle     :  0.569   6.395  11112  Z= 0.293
  Chirality :  0.039   0.229   1313
  Planarity :  0.004   0.041   1148
  Dihedral  : 18.876  74.123   2048
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 13.83 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.54 (0.30), residues: 769
  helix:  0.91 (0.30), residues: 335
  sheet: -0.72 (0.53), residues: 97
  loop : -1.56 (0.31), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  98 
 HIS   0.005   0.001   HIS A 344 
 PHE   0.014   0.002   PHE B 331 
 TYR   0.011   0.001   TYR B 354 
 ARG   0.008   0.000   ARG A  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06596 (  305)
  hydrogen bonds       : angle       4.53518 (  801)
  metal coordination   : bond        0.01403 (    8)
  metal coordination   : angle       2.43995 (    6)
  covalent geometry    : bond        0.00440 ( 7938)
  covalent geometry    : angle       0.56659 (11106)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 42
  time to evaluate  : 0.720 
Fit side-chains
REVERT: A   18 ARG cc_start: 0.8113 (tmm160) cc_final: 0.7813 (ppt170)
REVERT: B    1 MET cc_start: 0.5292 (mtm) cc_final: 0.4436 (mtp)
REVERT: B   97 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7372 (p90)
REVERT: B  249 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.6563 (mmt-90)
REVERT: B  341 GLN cc_start: 0.7779 (pt0) cc_final: 0.7464 (tt0)
REVERT: B  393 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7248 (t80)
  outliers start: 20
  outliers final: 17
  residues processed: 60
  average time/residue: 0.2098
  time to fit residues: 17.1888
Evaluate side-chains
  61 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 41
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain B residue   22 LYS
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  249 ARG
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  393 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 41 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 0 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 81 optimal weight:    8.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    2.9588

-------------------------------------------------------------------------------
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 = 0.108949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.080268 restraints weight = 27154.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 3.06
r_work: 0.2974 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2978
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2978 r_free = 0.2978    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2978 r_free = 0.2978    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2978
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7946  Z= 0.192
  Angle     :  0.570   6.405  11112  Z= 0.293
  Chirality :  0.039   0.226   1313
  Planarity :  0.004   0.036   1148
  Dihedral  : 18.913  74.078   2048
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 13.68 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.67 (0.30), residues: 769
  helix:  0.82 (0.30), residues: 335
  sheet: -0.83 (0.51), residues: 102
  loop : -1.64 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  98 
 HIS   0.005   0.001   HIS A 344 
 PHE   0.014   0.002   PHE A 127 
 TYR   0.011   0.001   TYR B 354 
 ARG   0.008   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06570 (  305)
  hydrogen bonds       : angle       4.58951 (  801)
  metal coordination   : bond        0.01315 (    8)
  metal coordination   : angle       2.33267 (    6)
  covalent geometry    : bond        0.00440 ( 7938)
  covalent geometry    : angle       0.56782 (11106)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3877.70 seconds
wall clock time: 67 minutes 48.16 seconds (4068.16 seconds total)