Starting phenix.real_space_refine
on Tue Nov 18 08:10:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6c70_7352/11_2025/6c70_7352_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6c70_7352/11_2025/6c70_7352.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6c70_7352/11_2025/6c70_7352_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6c70_7352/11_2025/6c70_7352_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6c70_7352/11_2025/6c70_7352.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6c70_7352/11_2025/6c70_7352.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.159 sd=   0.641
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     108      5.16       5
     C    8152      2.51       5
     N    1992      2.21       5
     O    2116      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12368
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3092
          Classifications: {'peptide': 388}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 377}
          Chain breaks: 2
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 2.73, per 1000 atoms: 0.22
  Number of scatterers: 12368
  At special positions: 0
  Unit cell: (121, 121, 101, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     108     16.00
     O    2116      8.00
     N    1992      7.00
     C    8152      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: 1.11
  Conformation dependent library (CDL) restraints added in 644.6 milliseconds
  

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2952

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 4 sheets defined
      81.4% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 11
    Processing helix  chain 'A' and resid 12 through 23
      removed outlier: 3.560A  pdb=" N   MET A  19 " --> pdb=" O   ASN A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 33
      No H-bonds generated for 'chain 'A' and resid 31 through 33'
    Processing helix  chain 'A' and resid 34 through 63
      removed outlier: 3.533A  pdb=" N   ILE A  40 " --> pdb=" O   PHE A  36 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   TYR A  41 " --> pdb=" O   PRO A  37 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ALA A  57 " --> pdb=" O   TYR A  53 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL A  58 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN A  59 " --> pdb=" O   MET A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 80
    Processing helix  chain 'A' and resid 81 through 93
      removed outlier: 3.696A  pdb=" N   MET A  87 " --> pdb=" O   PRO A  83 " (cutoff:3.500A)
      Proline residue:  A  91  - end of helix
    Processing helix  chain 'A' and resid 94 through 102
    Processing helix  chain 'A' and resid 113 through 115
      No H-bonds generated for 'chain 'A' and resid 113 through 115'
    Processing helix  chain 'A' and resid 116 through 151
      removed outlier: 3.589A  pdb=" N   PHE A 120 " --> pdb=" O   SER A 116 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A 123 " --> pdb=" O   ARG A 119 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 132 " --> pdb=" O   MET A 128 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   ILE A 149 " --> pdb=" O   SER A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 190
      No H-bonds generated for 'chain 'A' and resid 188 through 190'
    Processing helix  chain 'A' and resid 191 through 233
      removed outlier: 3.907A  pdb=" N   ASN A 210 " --> pdb=" O   MET A 206 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU A 212 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU A 221 " --> pdb=" O   CYS A 217 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA A 232 " --> pdb=" O   GLN A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 315 through 347
      removed outlier: 3.522A  pdb=" N   ALA A 342 " --> pdb=" O   ARG A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 371
      removed outlier: 3.530A  pdb=" N   ILE A 360 " --> pdb=" O   LEU A 356 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU A 364 " --> pdb=" O   ILE A 360 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   TYR A 367 " --> pdb=" O   THR A 363 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LYS A 371 " --> pdb=" O   TYR A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 416
      removed outlier: 4.305A  pdb=" N   TYR A 388 " --> pdb=" O   GLY A 384 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A 393 " --> pdb=" O   THR A 389 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE A 396 " --> pdb=" O   GLN A 392 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   PHE A 399 " --> pdb=" O   LEU A 395 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET A 411 " --> pdb=" O   SER A 407 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU A 412 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 422
      removed outlier: 3.541A  pdb=" N   ASP A 421 " --> pdb=" O   HIS A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 437
      removed outlier: 3.605A  pdb=" N   ILE A 432 " --> pdb=" O   THR A 428 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN A 435 " --> pdb=" O   GLN A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 471
      removed outlier: 3.717A  pdb=" N   PHE A 456 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 11
    Processing helix  chain 'B' and resid 12 through 23
      removed outlier: 3.560A  pdb=" N   MET B  19 " --> pdb=" O   ASN B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 33
      No H-bonds generated for 'chain 'B' and resid 31 through 33'
    Processing helix  chain 'B' and resid 34 through 63
      removed outlier: 3.534A  pdb=" N   ILE B  40 " --> pdb=" O   PHE B  36 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   TYR B  41 " --> pdb=" O   PRO B  37 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN B  52 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA B  57 " --> pdb=" O   TYR B  53 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL B  58 " --> pdb=" O   GLY B  54 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ASN B  59 " --> pdb=" O   MET B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 80
    Processing helix  chain 'B' and resid 81 through 93
      removed outlier: 3.696A  pdb=" N   MET B  87 " --> pdb=" O   PRO B  83 " (cutoff:3.500A)
      Proline residue:  B  91  - end of helix
    Processing helix  chain 'B' and resid 94 through 102
    Processing helix  chain 'B' and resid 113 through 115
      No H-bonds generated for 'chain 'B' and resid 113 through 115'
    Processing helix  chain 'B' and resid 116 through 151
      removed outlier: 3.589A  pdb=" N   PHE B 120 " --> pdb=" O   SER B 116 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU B 123 " --> pdb=" O   ARG B 119 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU B 132 " --> pdb=" O   MET B 128 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY B 137 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   ILE B 149 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 190
      No H-bonds generated for 'chain 'B' and resid 188 through 190'
    Processing helix  chain 'B' and resid 191 through 233
      removed outlier: 3.908A  pdb=" N   ASN B 210 " --> pdb=" O   MET B 206 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU B 212 " --> pdb=" O   VAL B 208 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU B 221 " --> pdb=" O   CYS B 217 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA B 232 " --> pdb=" O   GLN B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 239
    Processing helix  chain 'B' and resid 315 through 347
      removed outlier: 3.522A  pdb=" N   ALA B 342 " --> pdb=" O   ARG B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 371
      removed outlier: 3.530A  pdb=" N   ILE B 360 " --> pdb=" O   LEU B 356 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU B 364 " --> pdb=" O   ILE B 360 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   TYR B 367 " --> pdb=" O   THR B 363 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LYS B 371 " --> pdb=" O   TYR B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 378 through 416
      removed outlier: 4.305A  pdb=" N   TYR B 388 " --> pdb=" O   GLY B 384 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL B 393 " --> pdb=" O   THR B 389 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE B 396 " --> pdb=" O   GLN B 392 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   PHE B 399 " --> pdb=" O   LEU B 395 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET B 411 " --> pdb=" O   SER B 407 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLU B 412 " --> pdb=" O   SER B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 422
      removed outlier: 3.541A  pdb=" N   ASP B 421 " --> pdb=" O   HIS B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 437
      removed outlier: 3.605A  pdb=" N   ILE B 432 " --> pdb=" O   THR B 428 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLN B 435 " --> pdb=" O   GLN B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 471
      removed outlier: 3.717A  pdb=" N   PHE B 456 " --> pdb=" O   SER B 452 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 11
    Processing helix  chain 'C' and resid 12 through 23
      removed outlier: 3.561A  pdb=" N   MET C  19 " --> pdb=" O   ASN C  15 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 33
      No H-bonds generated for 'chain 'C' and resid 31 through 33'
    Processing helix  chain 'C' and resid 34 through 63
      removed outlier: 3.534A  pdb=" N   ILE C  40 " --> pdb=" O   PHE C  36 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   TYR C  41 " --> pdb=" O   PRO C  37 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN C  52 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA C  57 " --> pdb=" O   TYR C  53 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL C  58 " --> pdb=" O   GLY C  54 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN C  59 " --> pdb=" O   MET C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 80
    Processing helix  chain 'C' and resid 81 through 93
      removed outlier: 3.697A  pdb=" N   MET C  87 " --> pdb=" O   PRO C  83 " (cutoff:3.500A)
      Proline residue:  C  91  - end of helix
    Processing helix  chain 'C' and resid 94 through 102
    Processing helix  chain 'C' and resid 113 through 115
      No H-bonds generated for 'chain 'C' and resid 113 through 115'
    Processing helix  chain 'C' and resid 116 through 151
      removed outlier: 3.589A  pdb=" N   PHE C 120 " --> pdb=" O   SER C 116 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU C 123 " --> pdb=" O   ARG C 119 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU C 132 " --> pdb=" O   MET C 128 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY C 137 " --> pdb=" O   PHE C 133 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   ILE C 149 " --> pdb=" O   SER C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 188 through 190
      No H-bonds generated for 'chain 'C' and resid 188 through 190'
    Processing helix  chain 'C' and resid 191 through 233
      removed outlier: 3.907A  pdb=" N   ASN C 210 " --> pdb=" O   MET C 206 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU C 212 " --> pdb=" O   VAL C 208 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU C 221 " --> pdb=" O   CYS C 217 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA C 232 " --> pdb=" O   GLN C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 239
    Processing helix  chain 'C' and resid 315 through 347
      removed outlier: 3.522A  pdb=" N   ALA C 342 " --> pdb=" O   ARG C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 347 through 371
      removed outlier: 3.530A  pdb=" N   ILE C 360 " --> pdb=" O   LEU C 356 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU C 364 " --> pdb=" O   ILE C 360 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   TYR C 367 " --> pdb=" O   THR C 363 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LYS C 371 " --> pdb=" O   TYR C 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 378 through 416
      removed outlier: 4.305A  pdb=" N   TYR C 388 " --> pdb=" O   GLY C 384 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL C 393 " --> pdb=" O   THR C 389 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE C 396 " --> pdb=" O   GLN C 392 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   PHE C 399 " --> pdb=" O   LEU C 395 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET C 411 " --> pdb=" O   SER C 407 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU C 412 " --> pdb=" O   SER C 408 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 418 through 422
      removed outlier: 3.541A  pdb=" N   ASP C 421 " --> pdb=" O   HIS C 418 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 423 through 437
      removed outlier: 3.606A  pdb=" N   ILE C 432 " --> pdb=" O   THR C 428 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN C 435 " --> pdb=" O   GLN C 431 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 471
      removed outlier: 3.717A  pdb=" N   PHE C 456 " --> pdb=" O   SER C 452 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 11
    Processing helix  chain 'D' and resid 12 through 23
      removed outlier: 3.560A  pdb=" N   MET D  19 " --> pdb=" O   ASN D  15 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 33
      No H-bonds generated for 'chain 'D' and resid 31 through 33'
    Processing helix  chain 'D' and resid 34 through 63
      removed outlier: 3.534A  pdb=" N   ILE D  40 " --> pdb=" O   PHE D  36 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   TYR D  41 " --> pdb=" O   PRO D  37 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN D  52 " --> pdb=" O   LEU D  48 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA D  57 " --> pdb=" O   TYR D  53 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL D  58 " --> pdb=" O   GLY D  54 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN D  59 " --> pdb=" O   MET D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 80
    Processing helix  chain 'D' and resid 81 through 93
      removed outlier: 3.696A  pdb=" N   MET D  87 " --> pdb=" O   PRO D  83 " (cutoff:3.500A)
      Proline residue:  D  91  - end of helix
    Processing helix  chain 'D' and resid 94 through 102
    Processing helix  chain 'D' and resid 113 through 115
      No H-bonds generated for 'chain 'D' and resid 113 through 115'
    Processing helix  chain 'D' and resid 116 through 151
      removed outlier: 3.589A  pdb=" N   PHE D 120 " --> pdb=" O   SER D 116 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU D 123 " --> pdb=" O   ARG D 119 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU D 132 " --> pdb=" O   MET D 128 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLY D 137 " --> pdb=" O   PHE D 133 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   ILE D 149 " --> pdb=" O   SER D 145 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 190
      No H-bonds generated for 'chain 'D' and resid 188 through 190'
    Processing helix  chain 'D' and resid 191 through 233
      removed outlier: 3.908A  pdb=" N   ASN D 210 " --> pdb=" O   MET D 206 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU D 212 " --> pdb=" O   VAL D 208 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU D 221 " --> pdb=" O   CYS D 217 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA D 232 " --> pdb=" O   GLN D 228 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 239
    Processing helix  chain 'D' and resid 315 through 347
      removed outlier: 3.522A  pdb=" N   ALA D 342 " --> pdb=" O   ARG D 338 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 347 through 371
      removed outlier: 3.530A  pdb=" N   ILE D 360 " --> pdb=" O   LEU D 356 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU D 364 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   TYR D 367 " --> pdb=" O   THR D 363 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LYS D 371 " --> pdb=" O   TYR D 367 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 378 through 416
      removed outlier: 4.305A  pdb=" N   TYR D 388 " --> pdb=" O   GLY D 384 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL D 393 " --> pdb=" O   THR D 389 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE D 396 " --> pdb=" O   GLN D 392 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   PHE D 399 " --> pdb=" O   LEU D 395 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET D 411 " --> pdb=" O   SER D 407 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU D 412 " --> pdb=" O   SER D 408 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 418 through 422
      removed outlier: 3.540A  pdb=" N   ASP D 421 " --> pdb=" O   HIS D 418 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 423 through 437
      removed outlier: 3.604A  pdb=" N   ILE D 432 " --> pdb=" O   THR D 428 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLN D 435 " --> pdb=" O   GLN D 431 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 452 through 471
      removed outlier: 3.716A  pdb=" N   PHE D 456 " --> pdb=" O   SER D 452 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 444 through 445
      removed outlier: 4.079A  pdb=" N   PHE A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 444 through 445
      removed outlier: 4.079A  pdb=" N   PHE B 449 " --> pdb=" O   GLY B 445 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 444 through 445
      removed outlier: 4.080A  pdb=" N   PHE C 449 " --> pdb=" O   GLY C 445 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 444 through 445
      removed outlier: 4.079A  pdb=" N   PHE D 449 " --> pdb=" O   GLY D 445 " (cutoff:3.500A)

    860 hydrogen bonds defined for protein.
    2544 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.02

  Time building geometry restraints manager: 1.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3655
        1.34 -     1.45: 2438
        1.45 -     1.57: 6391
        1.57 -     1.69: 0
        1.69 -     1.80: 184
  Bond restraints: 12668
  Sorted by residual:
  bond pdb=" CG  GLN A 436 "
       pdb=" CD  GLN A 436 "
    ideal  model  delta    sigma   weight residual
    1.516  1.450  0.066 2.50e-02 1.60e+03 7.01e+00
  bond pdb=" CG  GLN B 436 "
       pdb=" CD  GLN B 436 "
    ideal  model  delta    sigma   weight residual
    1.516  1.450  0.066 2.50e-02 1.60e+03 6.95e+00
  bond pdb=" CG  GLN C 436 "
       pdb=" CD  GLN C 436 "
    ideal  model  delta    sigma   weight residual
    1.516  1.450  0.066 2.50e-02 1.60e+03 6.89e+00
  bond pdb=" CG  GLN D 436 "
       pdb=" CD  GLN D 436 "
    ideal  model  delta    sigma   weight residual
    1.516  1.451  0.065 2.50e-02 1.60e+03 6.83e+00
  bond pdb=" CB  TRP B 219 "
       pdb=" CG  TRP B 219 "
    ideal  model  delta    sigma   weight residual
    1.498  1.425  0.073 3.10e-02 1.04e+03 5.56e+00
  ... (remaining 12663 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 16076
        1.98 -     3.96: 863
        3.96 -     5.93: 173
        5.93 -     7.91: 36
        7.91 -     9.89: 24
  Bond angle restraints: 17172
  Sorted by residual:
  angle pdb=" CA  PRO B  83 "
        pdb=" N   PRO B  83 "
        pdb=" CD  PRO B  83 "
      ideal   model   delta    sigma   weight residual
     112.00  107.81    4.19 1.40e+00 5.10e-01 8.96e+00
  angle pdb=" N   CYS A 417 "
        pdb=" CA  CYS A 417 "
        pdb=" C   CYS A 417 "
      ideal   model   delta    sigma   weight residual
     109.81  105.27    4.54 1.53e+00 4.27e-01 8.80e+00
  angle pdb=" CA  PRO A  83 "
        pdb=" N   PRO A  83 "
        pdb=" CD  PRO A  83 "
      ideal   model   delta    sigma   weight residual
     112.00  107.85    4.15 1.40e+00 5.10e-01 8.77e+00
  angle pdb=" CA  PRO D  83 "
        pdb=" N   PRO D  83 "
        pdb=" CD  PRO D  83 "
      ideal   model   delta    sigma   weight residual
     112.00  107.85    4.15 1.40e+00 5.10e-01 8.77e+00
  angle pdb=" N   CYS B 417 "
        pdb=" CA  CYS B 417 "
        pdb=" C   CYS B 417 "
      ideal   model   delta    sigma   weight residual
     109.81  105.30    4.51 1.53e+00 4.27e-01 8.67e+00
  ... (remaining 17167 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.37: 6895
       15.37 -    30.73: 421
       30.73 -    46.10: 84
       46.10 -    61.47: 4
       61.47 -    76.84: 12
  Dihedral angle restraints: 7416
    sinusoidal: 2848
      harmonic: 4568
  Sorted by residual:
  dihedral pdb=" CA  MET C 468 "
           pdb=" C   MET C 468 "
           pdb=" N   VAL C 469 "
           pdb=" CA  VAL C 469 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.96   23.04     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  MET D 468 "
           pdb=" C   MET D 468 "
           pdb=" N   VAL D 469 "
           pdb=" CA  VAL D 469 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.96   23.04     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  MET A 468 "
           pdb=" C   MET A 468 "
           pdb=" N   VAL A 469 "
           pdb=" CA  VAL A 469 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.99   23.01     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 7413 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1113
       0.043 -    0.085: 658
       0.085 -    0.128: 175
       0.128 -    0.171: 57
       0.171 -    0.213: 5
  Chirality restraints: 2008
  Sorted by residual:
  chirality pdb=" CG  LEU A 230 "
            pdb=" CB  LEU A 230 "
            pdb=" CD1 LEU A 230 "
            pdb=" CD2 LEU A 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.80    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CG  LEU C 230 "
            pdb=" CB  LEU C 230 "
            pdb=" CD1 LEU C 230 "
            pdb=" CD2 LEU C 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.80    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CG  LEU B 230 "
            pdb=" CB  LEU B 230 "
            pdb=" CD1 LEU B 230 "
            pdb=" CD2 LEU B 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.80    0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 2005 not shown)

  Planarity restraints: 2080
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 329 "   -0.004 2.00e-02 2.50e+03   1.38e-02 4.77e+00
        pdb=" CG  TRP D 329 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 329 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 329 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 329 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 329 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 329 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 329 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 329 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 329 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 329 "   -0.004 2.00e-02 2.50e+03   1.36e-02 4.63e+00
        pdb=" CG  TRP C 329 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 329 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 329 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 329 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 329 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 329 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 329 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 329 "   -0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 329 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 329 "    0.004 2.00e-02 2.50e+03   1.35e-02 4.59e+00
        pdb=" CG  TRP B 329 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 329 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 329 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 329 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 329 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 329 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 329 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 329 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 329 "    0.006 2.00e-02 2.50e+03
  ... (remaining 2077 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1571
        2.74 -     3.28: 12895
        3.28 -     3.82: 21457
        3.82 -     4.36: 25337
        4.36 -     4.90: 42002
  Nonbonded interactions: 103262
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B  68 "
            pdb=" NZ  LYS B 371 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" OD1 ASP C  68 "
            pdb=" NZ  LYS C 371 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" OD1 ASP A  68 "
            pdb=" NZ  LYS A 371 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" OD1 ASP D  68 "
            pdb=" NZ  LYS D 371 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" NE2 GLN C 436 "
            pdb=" O   MET D 411 "
     model   vdw
     2.263 3.120
  ... (remaining 103257 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.970
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
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   0.073  12668  Z= 0.469
  Angle     :  1.093   9.890  17172  Z= 0.565
  Chirality :  0.057   0.213   2008
  Planarity :  0.007   0.049   2080
  Dihedral  : 11.204  76.836   4464
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.23 (0.14), residues: 1528
  helix: -3.33 (0.09), residues: 1188
  sheet:  None (None), residues: 0
  loop : -2.93 (0.27), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 323 
 TYR   0.028   0.003   TYR A 415 
 PHE   0.022   0.004   PHE D  25 
 TRP   0.031   0.005   TRP D 329 
 HIS   0.008   0.002   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.01050 (12668)
  covalent geometry    : angle       1.09276 (17172)
  hydrogen bonds       : bond        0.29477 (  860)
  hydrogen bonds       : angle      10.30171 ( 2544)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  392 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 392
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.8905 (ttm) cc_final: 0.7858 (ttm)
REVERT: A  106 ASN cc_start: 0.8940 (t0) cc_final: 0.8648 (t0)
REVERT: A  134 CYS cc_start: 0.9196 (m) cc_final: 0.8970 (m)
REVERT: A  345 ASP cc_start: 0.8813 (t70) cc_final: 0.8596 (t70)
REVERT: A  424 GLU cc_start: 0.8789 (tp30) cc_final: 0.8494 (tp30)
REVERT: A  474 LYS cc_start: 0.7247 (tmtm) cc_final: 0.7013 (tttm)
REVERT: B   13 LEU cc_start: 0.8930 (mt) cc_final: 0.8681 (mt)
REVERT: B   19 MET cc_start: 0.8932 (ttm) cc_final: 0.8566 (ttm)
REVERT: B   22 VAL cc_start: 0.9703 (p) cc_final: 0.9487 (p)
REVERT: B  106 ASN cc_start: 0.8955 (t0) cc_final: 0.8648 (t0)
REVERT: B  134 CYS cc_start: 0.9135 (m) cc_final: 0.8857 (m)
REVERT: B  239 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8595 (mm-30)
REVERT: B  331 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8256 (mm-30)
REVERT: B  345 ASP cc_start: 0.8764 (t70) cc_final: 0.8554 (t70)
REVERT: B  363 THR cc_start: 0.9029 (p) cc_final: 0.8812 (t)
REVERT: B  424 GLU cc_start: 0.8758 (tp30) cc_final: 0.8433 (tp30)
REVERT: B  474 LYS cc_start: 0.7295 (tmtm) cc_final: 0.7076 (tttm)
REVERT: C   19 MET cc_start: 0.8885 (ttm) cc_final: 0.8105 (ttm)
REVERT: C  134 CYS cc_start: 0.9168 (m) cc_final: 0.8804 (m)
REVERT: C  345 ASP cc_start: 0.8758 (t70) cc_final: 0.8536 (t70)
REVERT: C  424 GLU cc_start: 0.8686 (tp30) cc_final: 0.8475 (tp30)
REVERT: C  437 CYS cc_start: 0.8670 (m) cc_final: 0.8349 (m)
REVERT: C  474 LYS cc_start: 0.7492 (tmtm) cc_final: 0.7183 (tttm)
REVERT: D   19 MET cc_start: 0.8936 (ttm) cc_final: 0.7992 (ttm)
REVERT: D  106 ASN cc_start: 0.8896 (t0) cc_final: 0.8627 (t0)
REVERT: D  134 CYS cc_start: 0.9239 (m) cc_final: 0.8874 (m)
REVERT: D  331 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8400 (mm-30)
REVERT: D  437 CYS cc_start: 0.8623 (m) cc_final: 0.8373 (m)
REVERT: D  474 LYS cc_start: 0.7578 (tmtm) cc_final: 0.7263 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 392
  average time/residue: 0.0969
  time to fit residues: 57.4357
Evaluate side-chains
  251 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.3980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0370
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
** A  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 GLN
A 401 ASN
A 431 GLN
B   5 HIS
B 401 ASN
** C  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 401 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.071037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.063008 restraints weight = 41915.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.064867 restraints weight = 19521.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.066092 restraints weight = 11074.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.066865 restraints weight = 7226.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.067398 restraints weight = 5153.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  12668  Z= 0.146
  Angle     :  0.639   8.356  17172  Z= 0.336
  Chirality :  0.040   0.137   2008
  Planarity :  0.004   0.028   2080
  Dihedral  :  5.087  18.700   1668
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.20 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.99 (0.19), residues: 1528
  helix: -0.80 (0.13), residues: 1212
  sheet:  None (None), residues: 0
  loop : -2.84 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 332 
 TYR   0.010   0.001   TYR C  89 
 PHE   0.016   0.002   PHE D 394 
 TRP   0.021   0.002   TRP D 104 
 HIS   0.004   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (12668)
  covalent geometry    : angle       0.63855 (17172)
  hydrogen bonds       : bond        0.04498 (  860)
  hydrogen bonds       : angle       4.46544 ( 2544)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  369 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 350
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.8363 (ttp) cc_final: 0.8000 (ttm)
REVERT: A  128 MET cc_start: 0.9032 (mtp) cc_final: 0.8827 (mtp)
REVERT: A  141 PHE cc_start: 0.9029 (t80) cc_final: 0.8746 (t80)
REVERT: A  327 LYS cc_start: 0.9485 (ttmt) cc_final: 0.9098 (tttm)
REVERT: A  345 ASP cc_start: 0.8686 (t70) cc_final: 0.8475 (t70)
REVERT: A  406 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8434 (mm-30)
REVERT: A  424 GLU cc_start: 0.8726 (tp30) cc_final: 0.8371 (tp30)
REVERT: A  437 CYS cc_start: 0.8595 (m) cc_final: 0.8318 (m)
REVERT: A  474 LYS cc_start: 0.8707 (tmtm) cc_final: 0.8047 (tttm)
REVERT: B   13 LEU cc_start: 0.8999 (mt) cc_final: 0.8755 (mt)
REVERT: B   77 MET cc_start: 0.8843 (tpp) cc_final: 0.8593 (tpp)
REVERT: B  134 CYS cc_start: 0.9163 (m) cc_final: 0.8948 (m)
REVERT: B  141 PHE cc_start: 0.8939 (t80) cc_final: 0.8645 (t80)
REVERT: B  239 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8434 (mm-30)
REVERT: B  345 ASP cc_start: 0.8689 (t70) cc_final: 0.8473 (t70)
REVERT: B  355 MET cc_start: 0.8904 (mmm) cc_final: 0.8633 (mmm)
REVERT: B  406 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8396 (mm-30)
REVERT: B  424 GLU cc_start: 0.8661 (tp30) cc_final: 0.8273 (tp30)
REVERT: B  437 CYS cc_start: 0.8651 (m) cc_final: 0.8296 (m)
REVERT: B  474 LYS cc_start: 0.8630 (tmtm) cc_final: 0.8023 (tttm)
REVERT: C   29 TYR cc_start: 0.8641 (m-80) cc_final: 0.8299 (m-80)
REVERT: C  131 LEU cc_start: 0.9593 (tp) cc_final: 0.9339 (tp)
REVERT: C  134 CYS cc_start: 0.9326 (m) cc_final: 0.8979 (m)
REVERT: C  201 TYR cc_start: 0.9114 (t80) cc_final: 0.8734 (t80)
REVERT: C  239 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8417 (mm-30)
REVERT: C  345 ASP cc_start: 0.8608 (t70) cc_final: 0.8370 (t70)
REVERT: C  355 MET cc_start: 0.9159 (mmm) cc_final: 0.8946 (mmm)
REVERT: C  406 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8225 (mm-30)
REVERT: C  408 SER cc_start: 0.9467 (m) cc_final: 0.9074 (p)
REVERT: C  424 GLU cc_start: 0.8742 (tp30) cc_final: 0.8395 (tp30)
REVERT: C  437 CYS cc_start: 0.8779 (m) cc_final: 0.8488 (m)
REVERT: C  474 LYS cc_start: 0.8657 (tmtm) cc_final: 0.8043 (tttm)
REVERT: D  131 LEU cc_start: 0.9576 (tp) cc_final: 0.9366 (tp)
REVERT: D  134 CYS cc_start: 0.9286 (m) cc_final: 0.8987 (m)
REVERT: D  141 PHE cc_start: 0.9014 (t80) cc_final: 0.8760 (t80)
REVERT: D  149 ILE cc_start: 0.9235 (mm) cc_final: 0.8993 (pt)
REVERT: D  215 LEU cc_start: 0.9467 (tp) cc_final: 0.9211 (tt)
REVERT: D  239 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8480 (mm-30)
REVERT: D  355 MET cc_start: 0.9148 (mmm) cc_final: 0.8922 (mmm)
REVERT: D  406 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8302 (mm-30)
REVERT: D  437 CYS cc_start: 0.8641 (m) cc_final: 0.8302 (m)
REVERT: D  474 LYS cc_start: 0.8740 (tmtm) cc_final: 0.8073 (tttm)
  outliers start: 19
  outliers final: 12
  residues processed: 360
  average time/residue: 0.0834
  time to fit residues: 48.1719
Evaluate side-chains
  306 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 294
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   65 ASP
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  351 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 147 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 100 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 75 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 HIS
** C  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 401 ASN
** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   5 HIS
** D  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.071038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.062966 restraints weight = 42563.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.064773 restraints weight = 19591.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.065827 restraints weight = 11137.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.066656 restraints weight = 7617.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.067225 restraints weight = 5471.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12668  Z= 0.142
  Angle     :  0.582   6.529  17172  Z= 0.306
  Chirality :  0.040   0.166   2008
  Planarity :  0.003   0.021   2080
  Dihedral  :  4.578  17.024   1668
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 12.61 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.21), residues: 1528
  helix:  0.54 (0.15), residues: 1196
  sheet:  None (None), residues: 0
  loop : -2.29 (0.30), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 338 
 TYR   0.012   0.001   TYR C  53 
 PHE   0.021   0.001   PHE C 141 
 TRP   0.013   0.002   TRP D 104 
 HIS   0.004   0.001   HIS C 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (12668)
  covalent geometry    : angle       0.58162 (17172)
  hydrogen bonds       : bond        0.03780 (  860)
  hydrogen bonds       : angle       3.92154 ( 2544)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 319
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 TYR cc_start: 0.9063 (t80) cc_final: 0.8850 (t80)
REVERT: A   77 MET cc_start: 0.8238 (ttp) cc_final: 0.7892 (ttp)
REVERT: A  141 PHE cc_start: 0.8971 (t80) cc_final: 0.8686 (t80)
REVERT: A  206 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8687 (ttp)
REVERT: A  215 LEU cc_start: 0.9490 (tp) cc_final: 0.9268 (tt)
REVERT: A  225 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8645 (mm-30)
REVERT: A  327 LYS cc_start: 0.9431 (ttmt) cc_final: 0.9148 (tttm)
REVERT: A  345 ASP cc_start: 0.8629 (t70) cc_final: 0.8389 (t70)
REVERT: A  424 GLU cc_start: 0.8674 (tp30) cc_final: 0.8286 (tp30)
REVERT: A  437 CYS cc_start: 0.8776 (m) cc_final: 0.8573 (m)
REVERT: A  474 LYS cc_start: 0.8667 (tmtm) cc_final: 0.8012 (tttm)
REVERT: B   16 ILE cc_start: 0.9703 (mt) cc_final: 0.9500 (pt)
REVERT: B   53 TYR cc_start: 0.9093 (t80) cc_final: 0.8663 (t80)
REVERT: B  134 CYS cc_start: 0.9194 (m) cc_final: 0.8966 (m)
REVERT: B  141 PHE cc_start: 0.8914 (t80) cc_final: 0.8684 (t80)
REVERT: B  149 ILE cc_start: 0.9088 (mm) cc_final: 0.8851 (tp)
REVERT: B  201 TYR cc_start: 0.9188 (t80) cc_final: 0.8747 (t80)
REVERT: B  206 MET cc_start: 0.9054 (mtp) cc_final: 0.8746 (ttp)
REVERT: B  239 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8505 (mm-30)
REVERT: B  345 ASP cc_start: 0.8677 (t70) cc_final: 0.8434 (t70)
REVERT: B  437 CYS cc_start: 0.8831 (m) cc_final: 0.8608 (m)
REVERT: B  474 LYS cc_start: 0.8602 (tmtm) cc_final: 0.8006 (tttm)
REVERT: C   53 TYR cc_start: 0.9001 (t80) cc_final: 0.7828 (t80)
REVERT: C   77 MET cc_start: 0.8930 (tpp) cc_final: 0.8071 (mmm)
REVERT: C  131 LEU cc_start: 0.9591 (tp) cc_final: 0.9357 (tp)
REVERT: C  134 CYS cc_start: 0.9307 (m) cc_final: 0.9016 (m)
REVERT: C  239 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8446 (mm-30)
REVERT: C  345 ASP cc_start: 0.8629 (t70) cc_final: 0.8364 (t70)
REVERT: C  408 SER cc_start: 0.9420 (m) cc_final: 0.9081 (p)
REVERT: C  415 TYR cc_start: 0.9057 (t80) cc_final: 0.8560 (t80)
REVERT: C  474 LYS cc_start: 0.8676 (tmtm) cc_final: 0.8042 (tttm)
REVERT: D   13 LEU cc_start: 0.9186 (mm) cc_final: 0.8878 (mm)
REVERT: D  134 CYS cc_start: 0.9280 (m) cc_final: 0.9031 (m)
REVERT: D  141 PHE cc_start: 0.9000 (t80) cc_final: 0.8755 (t80)
REVERT: D  149 ILE cc_start: 0.9218 (mm) cc_final: 0.8986 (mt)
REVERT: D  225 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8501 (mm-30)
REVERT: D  408 SER cc_start: 0.9440 (m) cc_final: 0.9118 (p)
REVERT: D  474 LYS cc_start: 0.8607 (tmtm) cc_final: 0.8017 (tttm)
  outliers start: 36
  outliers final: 21
  residues processed: 340
  average time/residue: 0.0848
  time to fit residues: 45.6113
Evaluate side-chains
  305 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 283
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain C residue   26 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  224 CYS
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  351 LEU
Chi-restraints excluded: chain D residue  442 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 105 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 110 optimal weight:    2.9990
   chunk 133 optimal weight:    0.6980
   chunk 138 optimal weight:    2.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 191 HIS
** D  15 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 = 0.3297 r_free = 0.3297 target = 0.070588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.062074 restraints weight = 42913.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.063898 restraints weight = 20422.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.065128 restraints weight = 11954.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.065923 restraints weight = 8055.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.066460 restraints weight = 5919.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.3986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12668  Z= 0.183
  Angle     :  0.594   7.467  17172  Z= 0.313
  Chirality :  0.041   0.180   2008
  Planarity :  0.003   0.022   2080
  Dihedral  :  4.391  16.876   1668
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.21 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.21), residues: 1528
  helix:  1.13 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -2.21 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 338 
 TYR   0.008   0.001   TYR A  29 
 PHE   0.016   0.001   PHE A 394 
 TRP   0.013   0.002   TRP B 219 
 HIS   0.004   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (12668)
  covalent geometry    : angle       0.59425 (17172)
  hydrogen bonds       : bond        0.03685 (  860)
  hydrogen bonds       : angle       3.78296 ( 2544)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 299
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 MET cc_start: 0.9016 (mtm) cc_final: 0.8649 (mpp)
REVERT: A  141 PHE cc_start: 0.8975 (t80) cc_final: 0.8664 (t80)
REVERT: A  179 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8432 (t)
REVERT: A  204 ILE cc_start: 0.9660 (tp) cc_final: 0.9392 (tp)
REVERT: A  206 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8818 (ttp)
REVERT: A  215 LEU cc_start: 0.9525 (tp) cc_final: 0.9217 (tt)
REVERT: A  327 LYS cc_start: 0.9439 (ttmt) cc_final: 0.9099 (tttm)
REVERT: A  345 ASP cc_start: 0.8649 (t70) cc_final: 0.8411 (t70)
REVERT: A  474 LYS cc_start: 0.8737 (tmtm) cc_final: 0.8065 (tttm)
REVERT: B   53 TYR cc_start: 0.9056 (t80) cc_final: 0.8514 (t80)
REVERT: B   77 MET cc_start: 0.8816 (tpp) cc_final: 0.8542 (tpp)
REVERT: B  134 CYS cc_start: 0.9270 (m) cc_final: 0.9008 (m)
REVERT: B  141 PHE cc_start: 0.8890 (t80) cc_final: 0.8637 (t80)
REVERT: B  179 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8123 (t)
REVERT: B  224 CYS cc_start: 0.9148 (m) cc_final: 0.8470 (t)
REVERT: B  225 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8443 (mm-30)
REVERT: B  239 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8578 (mm-30)
REVERT: B  345 ASP cc_start: 0.8672 (t70) cc_final: 0.8451 (t70)
REVERT: B  406 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8395 (mm-30)
REVERT: B  408 SER cc_start: 0.9557 (m) cc_final: 0.9051 (p)
REVERT: B  474 LYS cc_start: 0.8652 (tmtm) cc_final: 0.8022 (tttm)
REVERT: C   53 TYR cc_start: 0.8987 (t80) cc_final: 0.7774 (t80)
REVERT: C   77 MET cc_start: 0.8936 (tpp) cc_final: 0.8153 (mmm)
REVERT: C  134 CYS cc_start: 0.9339 (m) cc_final: 0.9043 (m)
REVERT: C  149 ILE cc_start: 0.9246 (mm) cc_final: 0.8760 (mt)
REVERT: C  239 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8463 (mm-30)
REVERT: C  345 ASP cc_start: 0.8615 (t70) cc_final: 0.8331 (t70)
REVERT: C  355 MET cc_start: 0.9306 (mmm) cc_final: 0.8866 (mmm)
REVERT: C  401 ASN cc_start: 0.9310 (t0) cc_final: 0.9094 (t0)
REVERT: C  408 SER cc_start: 0.9444 (m) cc_final: 0.9093 (p)
REVERT: C  415 TYR cc_start: 0.9032 (t80) cc_final: 0.8626 (t80)
REVERT: C  424 GLU cc_start: 0.8756 (tp30) cc_final: 0.8404 (tp30)
REVERT: C  474 LYS cc_start: 0.8729 (tmtm) cc_final: 0.8103 (tttm)
REVERT: D   13 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8858 (mm)
REVERT: D   56 MET cc_start: 0.8921 (mtm) cc_final: 0.8500 (mpp)
REVERT: D  134 CYS cc_start: 0.9354 (m) cc_final: 0.9063 (m)
REVERT: D  141 PHE cc_start: 0.8984 (t80) cc_final: 0.8687 (t80)
REVERT: D  215 LEU cc_start: 0.9450 (tp) cc_final: 0.9199 (tt)
REVERT: D  225 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8634 (mm-30)
REVERT: D  408 SER cc_start: 0.9422 (m) cc_final: 0.9110 (p)
REVERT: D  474 LYS cc_start: 0.8699 (tmtm) cc_final: 0.8123 (tttm)
  outliers start: 38
  outliers final: 28
  residues processed: 318
  average time/residue: 0.0828
  time to fit residues: 42.1112
Evaluate side-chains
  305 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 273
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  381 THR
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  217 CYS
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  351 LEU
Chi-restraints excluded: chain D residue  381 THR
Chi-restraints excluded: chain D residue  398 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 132 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 145 optimal weight:    1.9990
   chunk 114 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 55 optimal weight:    0.3980
   chunk 76 optimal weight:    7.9990
   chunk 133 optimal weight:    0.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   5 HIS
** B  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 191 HIS
** C  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  15 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.069604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.061636 restraints weight = 42838.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.063432 restraints weight = 19468.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.064448 restraints weight = 11000.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.065276 restraints weight = 7565.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.065801 restraints weight = 5427.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12668  Z= 0.192
  Angle     :  0.594   6.075  17172  Z= 0.313
  Chirality :  0.042   0.172   2008
  Planarity :  0.003   0.022   2080
  Dihedral  :  4.298  17.589   1668
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 16.47 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.21), residues: 1528
  helix:  1.43 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -2.32 (0.30), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 338 
 TYR   0.009   0.001   TYR A  29 
 PHE   0.020   0.001   PHE C 141 
 TRP   0.014   0.002   TRP B 219 
 HIS   0.004   0.001   HIS B   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (12668)
  covalent geometry    : angle       0.59360 (17172)
  hydrogen bonds       : bond        0.03655 (  860)
  hydrogen bonds       : angle       3.69929 ( 2544)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 285
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  141 PHE cc_start: 0.8959 (t80) cc_final: 0.8655 (t80)
REVERT: A  204 ILE cc_start: 0.9653 (tp) cc_final: 0.9395 (tp)
REVERT: A  206 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8779 (ttp)
REVERT: A  215 LEU cc_start: 0.9494 (tp) cc_final: 0.9276 (tt)
REVERT: A  327 LYS cc_start: 0.9384 (ttmt) cc_final: 0.9015 (tttm)
REVERT: A  345 ASP cc_start: 0.8705 (t70) cc_final: 0.8472 (t70)
REVERT: A  355 MET cc_start: 0.9115 (mmm) cc_final: 0.8771 (mmm)
REVERT: A  408 SER cc_start: 0.9555 (m) cc_final: 0.9119 (p)
REVERT: A  415 TYR cc_start: 0.8920 (t80) cc_final: 0.8495 (t80)
REVERT: A  474 LYS cc_start: 0.8691 (tmtm) cc_final: 0.8054 (tttm)
REVERT: B   53 TYR cc_start: 0.8983 (t80) cc_final: 0.8455 (t80)
REVERT: B   77 MET cc_start: 0.8775 (tpp) cc_final: 0.8442 (tpp)
REVERT: B  134 CYS cc_start: 0.9264 (m) cc_final: 0.8994 (m)
REVERT: B  141 PHE cc_start: 0.8879 (t80) cc_final: 0.8594 (t80)
REVERT: B  239 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8584 (mm-30)
REVERT: B  345 ASP cc_start: 0.8634 (t70) cc_final: 0.8412 (t70)
REVERT: B  408 SER cc_start: 0.9551 (m) cc_final: 0.9065 (p)
REVERT: B  474 LYS cc_start: 0.8665 (tmtm) cc_final: 0.8039 (tttm)
REVERT: C   53 TYR cc_start: 0.8970 (t80) cc_final: 0.8038 (t80)
REVERT: C   56 MET cc_start: 0.8819 (mtm) cc_final: 0.8462 (mtm)
REVERT: C   77 MET cc_start: 0.8950 (tpp) cc_final: 0.8118 (tmm)
REVERT: C  134 CYS cc_start: 0.9336 (m) cc_final: 0.9051 (m)
REVERT: C  149 ILE cc_start: 0.9226 (mm) cc_final: 0.8960 (mt)
REVERT: C  176 MET cc_start: 0.8555 (tpp) cc_final: 0.8348 (tpp)
REVERT: C  345 ASP cc_start: 0.8595 (t70) cc_final: 0.8317 (t70)
REVERT: C  355 MET cc_start: 0.9270 (mmm) cc_final: 0.9015 (mmm)
REVERT: C  398 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9174 (mm)
REVERT: C  401 ASN cc_start: 0.9299 (t0) cc_final: 0.9082 (t0)
REVERT: C  408 SER cc_start: 0.9438 (m) cc_final: 0.9095 (p)
REVERT: C  474 LYS cc_start: 0.8737 (tmtm) cc_final: 0.8107 (tttm)
REVERT: D   13 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8869 (mm)
REVERT: D   53 TYR cc_start: 0.8877 (t80) cc_final: 0.8664 (t80)
REVERT: D   62 MET cc_start: 0.8001 (mmm) cc_final: 0.7733 (mmm)
REVERT: D  134 CYS cc_start: 0.9331 (m) cc_final: 0.9049 (m)
REVERT: D  141 PHE cc_start: 0.8973 (t80) cc_final: 0.8644 (t80)
REVERT: D  206 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8783 (ttp)
REVERT: D  215 LEU cc_start: 0.9479 (tp) cc_final: 0.9219 (tt)
REVERT: D  225 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8693 (mm-30)
REVERT: D  355 MET cc_start: 0.9126 (mmm) cc_final: 0.8922 (mmm)
REVERT: D  398 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9146 (mm)
REVERT: D  408 SER cc_start: 0.9432 (m) cc_final: 0.9118 (p)
REVERT: D  474 LYS cc_start: 0.8684 (tmtm) cc_final: 0.8098 (tttm)
  outliers start: 41
  outliers final: 26
  residues processed: 304
  average time/residue: 0.0809
  time to fit residues: 39.3702
Evaluate side-chains
  290 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 259
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  398 ILE
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  217 CYS
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  351 LEU
Chi-restraints excluded: chain D residue  398 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 105 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 150 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 131 optimal weight:    6.9990
   chunk 133 optimal weight:    0.9980
   chunk 47 optimal weight:    0.4980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
A 333 HIS
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  15 ASN
D  15 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.071619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.063654 restraints weight = 42713.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.065518 restraints weight = 19479.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.066706 restraints weight = 10893.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.067459 restraints weight = 7029.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.067984 restraints weight = 5045.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.4506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12668  Z= 0.131
  Angle     :  0.573   6.900  17172  Z= 0.299
  Chirality :  0.041   0.178   2008
  Planarity :  0.002   0.023   2080
  Dihedral  :  4.175  16.756   1668
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 17.73 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.22), residues: 1528
  helix:  1.64 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -2.27 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 178 
 TYR   0.007   0.001   TYR D  53 
 PHE   0.015   0.001   PHE A 394 
 TRP   0.014   0.002   TRP A 219 
 HIS   0.002   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (12668)
  covalent geometry    : angle       0.57327 (17172)
  hydrogen bonds       : bond        0.03483 (  860)
  hydrogen bonds       : angle       3.56350 ( 2544)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  343 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 306
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 MET cc_start: 0.8943 (mtm) cc_final: 0.8644 (mtm)
REVERT: A  141 PHE cc_start: 0.8935 (t80) cc_final: 0.8663 (t80)
REVERT: A  204 ILE cc_start: 0.9625 (tp) cc_final: 0.9367 (tp)
REVERT: A  206 MET cc_start: 0.9120 (mtp) cc_final: 0.8768 (ttp)
REVERT: A  215 LEU cc_start: 0.9494 (tp) cc_final: 0.9253 (tt)
REVERT: A  327 LYS cc_start: 0.9381 (ttmt) cc_final: 0.9021 (tttm)
REVERT: A  345 ASP cc_start: 0.8640 (t70) cc_final: 0.8406 (t70)
REVERT: A  406 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8448 (mm-30)
REVERT: A  408 SER cc_start: 0.9549 (m) cc_final: 0.9081 (p)
REVERT: A  474 LYS cc_start: 0.8650 (tmtm) cc_final: 0.8013 (tttm)
REVERT: B   53 TYR cc_start: 0.8935 (t80) cc_final: 0.8516 (t80)
REVERT: B   56 MET cc_start: 0.8860 (mtt) cc_final: 0.8585 (mtt)
REVERT: B   69 ASP cc_start: 0.8833 (m-30) cc_final: 0.8601 (p0)
REVERT: B  134 CYS cc_start: 0.9189 (m) cc_final: 0.8974 (m)
REVERT: B  141 PHE cc_start: 0.8832 (t80) cc_final: 0.8582 (t80)
REVERT: B  201 TYR cc_start: 0.9255 (t80) cc_final: 0.8825 (t80)
REVERT: B  224 CYS cc_start: 0.9162 (m) cc_final: 0.8508 (t)
REVERT: B  225 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8697 (mm-30)
REVERT: B  239 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8552 (mm-30)
REVERT: B  345 ASP cc_start: 0.8630 (t70) cc_final: 0.8385 (t70)
REVERT: B  408 SER cc_start: 0.9505 (m) cc_final: 0.8999 (p)
REVERT: B  474 LYS cc_start: 0.8634 (tmtm) cc_final: 0.8006 (tttm)
REVERT: C   53 TYR cc_start: 0.8884 (t80) cc_final: 0.7753 (t80)
REVERT: C   77 MET cc_start: 0.8950 (tpp) cc_final: 0.8071 (tmm)
REVERT: C  134 CYS cc_start: 0.9290 (m) cc_final: 0.9036 (m)
REVERT: C  149 ILE cc_start: 0.9267 (mm) cc_final: 0.9030 (mt)
REVERT: C  239 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8515 (mm-30)
REVERT: C  345 ASP cc_start: 0.8621 (t70) cc_final: 0.8332 (t70)
REVERT: C  355 MET cc_start: 0.9307 (mmm) cc_final: 0.9011 (mmm)
REVERT: C  401 ASN cc_start: 0.9217 (t0) cc_final: 0.8983 (t0)
REVERT: C  408 SER cc_start: 0.9450 (m) cc_final: 0.9079 (p)
REVERT: C  415 TYR cc_start: 0.8675 (t80) cc_final: 0.8407 (t80)
REVERT: C  424 GLU cc_start: 0.8753 (tp30) cc_final: 0.8415 (tp30)
REVERT: C  474 LYS cc_start: 0.8601 (tmtm) cc_final: 0.8051 (tttm)
REVERT: D   13 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8686 (tp)
REVERT: D   53 TYR cc_start: 0.8867 (t80) cc_final: 0.8503 (t80)
REVERT: D   62 MET cc_start: 0.7919 (mmm) cc_final: 0.7682 (mmm)
REVERT: D  134 CYS cc_start: 0.9284 (m) cc_final: 0.9045 (m)
REVERT: D  141 PHE cc_start: 0.8918 (t80) cc_final: 0.8660 (t80)
REVERT: D  176 MET cc_start: 0.8202 (tpp) cc_final: 0.7911 (tpt)
REVERT: D  201 TYR cc_start: 0.9201 (t80) cc_final: 0.8782 (t80)
REVERT: D  206 MET cc_start: 0.9094 (mtp) cc_final: 0.8745 (ttp)
REVERT: D  225 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8732 (mm-30)
REVERT: D  239 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8553 (mm-30)
REVERT: D  408 SER cc_start: 0.9386 (m) cc_final: 0.9047 (p)
REVERT: D  424 GLU cc_start: 0.8697 (tp30) cc_final: 0.8467 (tp30)
REVERT: D  474 LYS cc_start: 0.8589 (tmtm) cc_final: 0.8014 (tttm)
  outliers start: 37
  outliers final: 24
  residues processed: 325
  average time/residue: 0.0796
  time to fit residues: 41.6531
Evaluate side-chains
  306 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 281
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  202 LEU
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  217 CYS
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  351 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 132 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 139 optimal weight:    1.9990
   chunk 116 optimal weight:    5.9990
   chunk 103 optimal weight:    0.8980
   chunk 141 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 121 optimal weight:    0.8980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  15 ASN
D  15 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.071478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.063341 restraints weight = 42582.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.065219 restraints weight = 19709.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.066415 restraints weight = 11140.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.067181 restraints weight = 7264.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.067725 restraints weight = 5226.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.4626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12668  Z= 0.147
  Angle     :  0.607  11.626  17172  Z= 0.312
  Chirality :  0.042   0.207   2008
  Planarity :  0.003   0.024   2080
  Dihedral  :  4.096  17.082   1668
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.77 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.22), residues: 1528
  helix:  1.79 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -2.28 (0.30), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 129 
 TYR   0.010   0.001   TYR C 385 
 PHE   0.016   0.001   PHE B 394 
 TRP   0.015   0.002   TRP D 219 
 HIS   0.003   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (12668)
  covalent geometry    : angle       0.60717 (17172)
  hydrogen bonds       : bond        0.03469 (  860)
  hydrogen bonds       : angle       3.55646 ( 2544)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 290
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 MET cc_start: 0.8956 (mtm) cc_final: 0.8669 (mtt)
REVERT: A  141 PHE cc_start: 0.8907 (t80) cc_final: 0.8667 (t80)
REVERT: A  186 MET cc_start: 0.5013 (mmm) cc_final: 0.4743 (mmt)
REVERT: A  204 ILE cc_start: 0.9625 (tp) cc_final: 0.9366 (tp)
REVERT: A  215 LEU cc_start: 0.9509 (tp) cc_final: 0.9257 (tt)
REVERT: A  327 LYS cc_start: 0.9382 (ttmt) cc_final: 0.9039 (tttm)
REVERT: A  345 ASP cc_start: 0.8590 (t70) cc_final: 0.8357 (t0)
REVERT: A  406 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8445 (mm-30)
REVERT: A  408 SER cc_start: 0.9540 (m) cc_final: 0.9095 (p)
REVERT: A  415 TYR cc_start: 0.8799 (t80) cc_final: 0.8558 (t80)
REVERT: A  474 LYS cc_start: 0.8652 (tmtm) cc_final: 0.8019 (tttm)
REVERT: B   53 TYR cc_start: 0.8934 (t80) cc_final: 0.8539 (t80)
REVERT: B   56 MET cc_start: 0.8900 (mtt) cc_final: 0.8694 (mtt)
REVERT: B   77 MET cc_start: 0.8760 (tpp) cc_final: 0.8487 (tpp)
REVERT: B  134 CYS cc_start: 0.9219 (m) cc_final: 0.8986 (m)
REVERT: B  141 PHE cc_start: 0.8819 (t80) cc_final: 0.8563 (t80)
REVERT: B  176 MET cc_start: 0.8279 (tpp) cc_final: 0.7883 (tpt)
REVERT: B  239 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8568 (mm-30)
REVERT: B  345 ASP cc_start: 0.8597 (t70) cc_final: 0.8378 (t70)
REVERT: B  408 SER cc_start: 0.9522 (m) cc_final: 0.9010 (p)
REVERT: B  474 LYS cc_start: 0.8641 (tmtm) cc_final: 0.8018 (tttm)
REVERT: C   53 TYR cc_start: 0.8892 (t80) cc_final: 0.8018 (t80)
REVERT: C   77 MET cc_start: 0.8941 (tpp) cc_final: 0.8047 (mmm)
REVERT: C  134 CYS cc_start: 0.9289 (m) cc_final: 0.9038 (m)
REVERT: C  149 ILE cc_start: 0.9279 (mm) cc_final: 0.9059 (mt)
REVERT: C  201 TYR cc_start: 0.9233 (t80) cc_final: 0.8798 (t80)
REVERT: C  206 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8763 (ttp)
REVERT: C  239 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8519 (mm-30)
REVERT: C  345 ASP cc_start: 0.8619 (t70) cc_final: 0.8349 (t70)
REVERT: C  355 MET cc_start: 0.9324 (mmm) cc_final: 0.9013 (mmm)
REVERT: C  401 ASN cc_start: 0.9236 (t0) cc_final: 0.9006 (t0)
REVERT: C  406 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8169 (mm-30)
REVERT: C  408 SER cc_start: 0.9425 (m) cc_final: 0.9065 (p)
REVERT: C  474 LYS cc_start: 0.8612 (tmtm) cc_final: 0.8055 (tttm)
REVERT: D   13 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8807 (mm)
REVERT: D  134 CYS cc_start: 0.9281 (m) cc_final: 0.9043 (m)
REVERT: D  141 PHE cc_start: 0.8898 (t80) cc_final: 0.8649 (t80)
REVERT: D  225 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8744 (mm-30)
REVERT: D  239 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8577 (mm-30)
REVERT: D  406 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8259 (mm-30)
REVERT: D  408 SER cc_start: 0.9389 (m) cc_final: 0.9036 (p)
REVERT: D  424 GLU cc_start: 0.8700 (tp30) cc_final: 0.8469 (tp30)
REVERT: D  474 LYS cc_start: 0.8592 (tmtm) cc_final: 0.8018 (tttm)
  outliers start: 35
  outliers final: 25
  residues processed: 309
  average time/residue: 0.0804
  time to fit residues: 39.9666
Evaluate side-chains
  297 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 270
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  202 LEU
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain C residue   26 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain C residue  206 MET
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  217 CYS
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  321 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 137 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 103 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   chunk 147 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9980
   chunk 116 optimal weight:    7.9990
   chunk 132 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
B   5 HIS
C  15 ASN
D  15 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.072154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.063910 restraints weight = 42755.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.065802 restraints weight = 19903.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.066979 restraints weight = 11312.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.067767 restraints weight = 7461.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.068295 restraints weight = 5355.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.4791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12668  Z= 0.137
  Angle     :  0.614   9.465  17172  Z= 0.316
  Chirality :  0.042   0.239   2008
  Planarity :  0.003   0.027   2080
  Dihedral  :  4.046  15.892   1668
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 19.51 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.22), residues: 1528
  helix:  1.87 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -2.36 (0.30), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 338 
 TYR   0.012   0.001   TYR D  53 
 PHE   0.016   0.001   PHE A 394 
 TRP   0.015   0.002   TRP B 219 
 HIS   0.004   0.001   HIS B   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (12668)
  covalent geometry    : angle       0.61417 (17172)
  hydrogen bonds       : bond        0.03488 (  860)
  hydrogen bonds       : angle       3.55482 ( 2544)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 285
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A   53 TYR cc_start: 0.8856 (t80) cc_final: 0.8576 (t80)
REVERT: A   56 MET cc_start: 0.8936 (mtm) cc_final: 0.8650 (mtt)
REVERT: A   78 LEU cc_start: 0.9525 (mt) cc_final: 0.9316 (mp)
REVERT: A  141 PHE cc_start: 0.8876 (t80) cc_final: 0.8642 (t80)
REVERT: A  204 ILE cc_start: 0.9619 (tp) cc_final: 0.9364 (tp)
REVERT: A  215 LEU cc_start: 0.9531 (tp) cc_final: 0.9294 (tt)
REVERT: A  327 LYS cc_start: 0.9372 (ttmt) cc_final: 0.9035 (tttm)
REVERT: A  345 ASP cc_start: 0.8592 (t70) cc_final: 0.8359 (t0)
REVERT: A  406 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8391 (mm-30)
REVERT: A  408 SER cc_start: 0.9538 (m) cc_final: 0.9078 (p)
REVERT: A  474 LYS cc_start: 0.8640 (tmtm) cc_final: 0.8014 (tttm)
REVERT: B   53 TYR cc_start: 0.8905 (t80) cc_final: 0.8522 (t80)
REVERT: B   56 MET cc_start: 0.8887 (mtt) cc_final: 0.8583 (mtt)
REVERT: B   77 MET cc_start: 0.8742 (tpp) cc_final: 0.8376 (tpp)
REVERT: B  128 MET cc_start: 0.8861 (mtp) cc_final: 0.8656 (mtp)
REVERT: B  134 CYS cc_start: 0.9214 (m) cc_final: 0.8980 (m)
REVERT: B  141 PHE cc_start: 0.8832 (t80) cc_final: 0.8591 (t80)
REVERT: B  176 MET cc_start: 0.8376 (tpp) cc_final: 0.7923 (tpt)
REVERT: B  239 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8636 (mm-30)
REVERT: B  345 ASP cc_start: 0.8564 (t70) cc_final: 0.8351 (t0)
REVERT: B  408 SER cc_start: 0.9503 (m) cc_final: 0.8994 (p)
REVERT: B  415 TYR cc_start: 0.8823 (t80) cc_final: 0.8620 (t80)
REVERT: B  474 LYS cc_start: 0.8627 (tmtm) cc_final: 0.8016 (tttm)
REVERT: C   53 TYR cc_start: 0.8719 (t80) cc_final: 0.8185 (t80)
REVERT: C   77 MET cc_start: 0.8967 (tpp) cc_final: 0.8142 (tmm)
REVERT: C  134 CYS cc_start: 0.9281 (m) cc_final: 0.9030 (m)
REVERT: C  239 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8543 (mm-30)
REVERT: C  345 ASP cc_start: 0.8616 (t70) cc_final: 0.8387 (t70)
REVERT: C  355 MET cc_start: 0.9333 (mmm) cc_final: 0.9006 (mmm)
REVERT: C  401 ASN cc_start: 0.9209 (t0) cc_final: 0.8973 (t0)
REVERT: C  406 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8181 (mm-30)
REVERT: C  408 SER cc_start: 0.9428 (m) cc_final: 0.9057 (p)
REVERT: C  474 LYS cc_start: 0.8607 (tmtm) cc_final: 0.8045 (tttm)
REVERT: D   13 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8804 (mm)
REVERT: D   55 MET cc_start: 0.8665 (tpp) cc_final: 0.8463 (tpt)
REVERT: D  134 CYS cc_start: 0.9297 (m) cc_final: 0.9047 (m)
REVERT: D  141 PHE cc_start: 0.8839 (t80) cc_final: 0.8589 (t80)
REVERT: D  206 MET cc_start: 0.9092 (mtp) cc_final: 0.8748 (ttp)
REVERT: D  406 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8241 (mm-30)
REVERT: D  408 SER cc_start: 0.9385 (m) cc_final: 0.9035 (p)
REVERT: D  474 LYS cc_start: 0.8583 (tmtm) cc_final: 0.8013 (tttm)
  outliers start: 32
  outliers final: 26
  residues processed: 303
  average time/residue: 0.0787
  time to fit residues: 37.9846
Evaluate side-chains
  297 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 270
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  202 LEU
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain C residue   26 MET
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  217 CYS
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  321 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 145 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 2 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 119 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0870
   chunk 0 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0770
   chunk 27 optimal weight:    0.0470
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6016

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
C  15 ASN
C  59 ASN
D  15 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.073597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.065363 restraints weight = 42391.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.067283 restraints weight = 19812.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.068459 restraints weight = 11286.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.069255 restraints weight = 7392.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.069807 restraints weight = 5335.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.4956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12668  Z= 0.127
  Angle     :  0.639  10.680  17172  Z= 0.322
  Chirality :  0.042   0.262   2008
  Planarity :  0.003   0.025   2080
  Dihedral  :  4.001  15.229   1668
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 19.81 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.22), residues: 1528
  helix:  1.95 (0.15), residues: 1196
  sheet:  None (None), residues: 0
  loop : -2.31 (0.30), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 178 
 TYR   0.014   0.001   TYR C  53 
 PHE   0.022   0.001   PHE C 141 
 TRP   0.015   0.002   TRP D 219 
 HIS   0.002   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (12668)
  covalent geometry    : angle       0.63887 (17172)
  hydrogen bonds       : bond        0.03447 (  860)
  hydrogen bonds       : angle       3.57868 ( 2544)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 305
  time to evaluate  : 0.493 
Fit side-chains
REVERT: A  141 PHE cc_start: 0.8819 (t80) cc_final: 0.8613 (t80)
REVERT: A  201 TYR cc_start: 0.9170 (t80) cc_final: 0.8802 (t80)
REVERT: A  204 ILE cc_start: 0.9606 (tp) cc_final: 0.9378 (tp)
REVERT: A  215 LEU cc_start: 0.9509 (tp) cc_final: 0.9261 (tt)
REVERT: A  327 LYS cc_start: 0.9356 (ttmt) cc_final: 0.9023 (tttm)
REVERT: A  406 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8356 (mm-30)
REVERT: A  408 SER cc_start: 0.9519 (m) cc_final: 0.9062 (p)
REVERT: A  474 LYS cc_start: 0.8631 (tmtm) cc_final: 0.8001 (tttm)
REVERT: B   53 TYR cc_start: 0.8853 (t80) cc_final: 0.8471 (t80)
REVERT: B   56 MET cc_start: 0.8905 (mtt) cc_final: 0.8581 (mtt)
REVERT: B   69 ASP cc_start: 0.8854 (m-30) cc_final: 0.8637 (p0)
REVERT: B   77 MET cc_start: 0.8747 (tpp) cc_final: 0.8376 (tpp)
REVERT: B  134 CYS cc_start: 0.9208 (m) cc_final: 0.8982 (m)
REVERT: B  141 PHE cc_start: 0.8792 (t80) cc_final: 0.8548 (t80)
REVERT: B  176 MET cc_start: 0.8402 (tpp) cc_final: 0.7958 (tpt)
REVERT: B  201 TYR cc_start: 0.9226 (t80) cc_final: 0.8846 (t80)
REVERT: B  239 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8591 (mm-30)
REVERT: B  345 ASP cc_start: 0.8568 (t70) cc_final: 0.8363 (t0)
REVERT: B  408 SER cc_start: 0.9500 (m) cc_final: 0.8982 (p)
REVERT: B  415 TYR cc_start: 0.8674 (t80) cc_final: 0.8244 (t80)
REVERT: B  474 LYS cc_start: 0.8576 (tmtm) cc_final: 0.7975 (tttm)
REVERT: C   53 TYR cc_start: 0.8975 (t80) cc_final: 0.7960 (t80)
REVERT: C   77 MET cc_start: 0.8905 (tpp) cc_final: 0.7999 (tmm)
REVERT: C  134 CYS cc_start: 0.9264 (m) cc_final: 0.9019 (m)
REVERT: C  239 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8531 (mm-30)
REVERT: C  345 ASP cc_start: 0.8572 (t70) cc_final: 0.8364 (t70)
REVERT: C  355 MET cc_start: 0.9328 (mmm) cc_final: 0.8830 (mmm)
REVERT: C  401 ASN cc_start: 0.9146 (t0) cc_final: 0.8908 (t0)
REVERT: C  406 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8172 (mm-30)
REVERT: C  408 SER cc_start: 0.9414 (m) cc_final: 0.9035 (p)
REVERT: C  474 LYS cc_start: 0.8558 (tmtm) cc_final: 0.8001 (tttm)
REVERT: D   13 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8623 (tp)
REVERT: D   53 TYR cc_start: 0.8965 (t80) cc_final: 0.8656 (t80)
REVERT: D   55 MET cc_start: 0.8664 (tpp) cc_final: 0.8460 (tpt)
REVERT: D  134 CYS cc_start: 0.9276 (m) cc_final: 0.9042 (m)
REVERT: D  141 PHE cc_start: 0.8821 (t80) cc_final: 0.8606 (t80)
REVERT: D  237 LEU cc_start: 0.9505 (tt) cc_final: 0.9294 (tp)
REVERT: D  239 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8550 (mm-30)
REVERT: D  401 ASN cc_start: 0.9178 (t0) cc_final: 0.8924 (t0)
REVERT: D  406 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8163 (mm-30)
REVERT: D  408 SER cc_start: 0.9359 (m) cc_final: 0.8964 (p)
REVERT: D  415 TYR cc_start: 0.8453 (t80) cc_final: 0.8251 (t80)
REVERT: D  424 GLU cc_start: 0.8735 (tp30) cc_final: 0.8494 (tp30)
REVERT: D  474 LYS cc_start: 0.8563 (tmtm) cc_final: 0.7993 (tttm)
  outliers start: 32
  outliers final: 24
  residues processed: 322
  average time/residue: 0.0807
  time to fit residues: 41.7460
Evaluate side-chains
  301 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 276
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  202 LEU
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain C residue   26 MET
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  217 CYS
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  321 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 135 optimal weight:    3.9990
   chunk 101 optimal weight:    0.6980
   chunk 134 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 124 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 141 optimal weight:    0.7980
   chunk 112 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
B  59 ASN
C  15 ASN
D  15 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.073872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.065462 restraints weight = 42882.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.067352 restraints weight = 20274.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.068548 restraints weight = 11669.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.069358 restraints weight = 7759.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.069895 restraints weight = 5605.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.5093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12668  Z= 0.142
  Angle     :  0.684  11.000  17172  Z= 0.345
  Chirality :  0.043   0.236   2008
  Planarity :  0.003   0.025   2080
  Dihedral  :  3.996  14.932   1668
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 20.99 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.21), residues: 1528
  helix:  1.92 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -2.38 (0.30), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 178 
 TYR   0.014   0.001   TYR C 415 
 PHE   0.025   0.001   PHE C 180 
 TRP   0.018   0.002   TRP D 219 
 HIS   0.003   0.001   HIS D 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (12668)
  covalent geometry    : angle       0.68430 (17172)
  hydrogen bonds       : bond        0.03586 (  860)
  hydrogen bonds       : angle       3.66095 ( 2544)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 283
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A   77 MET cc_start: 0.8163 (ttp) cc_final: 0.7944 (ttm)
REVERT: A  141 PHE cc_start: 0.8802 (t80) cc_final: 0.8578 (t80)
REVERT: A  204 ILE cc_start: 0.9631 (tp) cc_final: 0.9379 (tp)
REVERT: A  215 LEU cc_start: 0.9511 (tp) cc_final: 0.9242 (tt)
REVERT: A  327 LYS cc_start: 0.9359 (ttmt) cc_final: 0.9016 (tttm)
REVERT: A  408 SER cc_start: 0.9532 (m) cc_final: 0.9066 (p)
REVERT: A  474 LYS cc_start: 0.8626 (tmtm) cc_final: 0.7997 (tttm)
REVERT: B   53 TYR cc_start: 0.8717 (t80) cc_final: 0.8446 (t80)
REVERT: B   56 MET cc_start: 0.8823 (mtt) cc_final: 0.8622 (mtt)
REVERT: B   77 MET cc_start: 0.8734 (tpp) cc_final: 0.8365 (tpp)
REVERT: B  134 CYS cc_start: 0.9227 (m) cc_final: 0.8988 (m)
REVERT: B  141 PHE cc_start: 0.8792 (t80) cc_final: 0.8552 (t80)
REVERT: B  176 MET cc_start: 0.8383 (tpp) cc_final: 0.7949 (tpt)
REVERT: B  224 CYS cc_start: 0.9136 (m) cc_final: 0.8548 (t)
REVERT: B  239 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8631 (mm-30)
REVERT: B  345 ASP cc_start: 0.8549 (t70) cc_final: 0.8344 (t0)
REVERT: B  408 SER cc_start: 0.9509 (m) cc_final: 0.9001 (p)
REVERT: B  474 LYS cc_start: 0.8566 (tmtm) cc_final: 0.7959 (tttm)
REVERT: C   53 TYR cc_start: 0.9016 (t80) cc_final: 0.7884 (t80)
REVERT: C   61 MET cc_start: 0.8000 (mmp) cc_final: 0.7501 (mtm)
REVERT: C   77 MET cc_start: 0.8889 (tpp) cc_final: 0.8008 (tmm)
REVERT: C  134 CYS cc_start: 0.9282 (m) cc_final: 0.9027 (m)
REVERT: C  201 TYR cc_start: 0.9059 (t80) cc_final: 0.8717 (t80)
REVERT: C  206 MET cc_start: 0.9090 (mtp) cc_final: 0.8831 (ttp)
REVERT: C  239 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8550 (mm-30)
REVERT: C  331 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8893 (mm-30)
REVERT: C  345 ASP cc_start: 0.8568 (t70) cc_final: 0.8359 (t70)
REVERT: C  355 MET cc_start: 0.9326 (mmm) cc_final: 0.8825 (mmm)
REVERT: C  401 ASN cc_start: 0.9174 (t0) cc_final: 0.8921 (t0)
REVERT: C  406 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8171 (mm-30)
REVERT: C  408 SER cc_start: 0.9416 (m) cc_final: 0.9040 (p)
REVERT: C  474 LYS cc_start: 0.8572 (tmtm) cc_final: 0.8013 (tttm)
REVERT: D   13 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8636 (tp)
REVERT: D   53 TYR cc_start: 0.8991 (t80) cc_final: 0.8638 (t80)
REVERT: D  134 CYS cc_start: 0.9292 (m) cc_final: 0.9051 (m)
REVERT: D  141 PHE cc_start: 0.8821 (t80) cc_final: 0.8602 (t80)
REVERT: D  237 LEU cc_start: 0.9512 (tt) cc_final: 0.9267 (tp)
REVERT: D  408 SER cc_start: 0.9354 (m) cc_final: 0.8896 (p)
REVERT: D  474 LYS cc_start: 0.8568 (tmtm) cc_final: 0.8001 (tttm)
  outliers start: 28
  outliers final: 24
  residues processed: 298
  average time/residue: 0.0869
  time to fit residues: 41.2939
Evaluate side-chains
  295 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 270
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  202 LEU
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain C residue   26 MET
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  217 CYS
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  321 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 116 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 148 optimal weight:    0.7980
   chunk 85 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 122 optimal weight:    0.4980
   chunk 133 optimal weight:    0.7980
   chunk 102 optimal weight:    0.7980
   chunk 143 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  15 ASN
D  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.074822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.066495 restraints weight = 42459.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.068387 restraints weight = 19907.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.069548 restraints weight = 11424.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.070362 restraints weight = 7590.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.070911 restraints weight = 5479.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.5201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12668  Z= 0.137
  Angle     :  0.703  10.296  17172  Z= 0.349
  Chirality :  0.042   0.232   2008
  Planarity :  0.003   0.024   2080
  Dihedral  :  3.963  14.526   1668
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 20.92 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.21), residues: 1528
  helix:  1.94 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -2.34 (0.30), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 174 
 TYR   0.011   0.001   TYR A  53 
 PHE   0.024   0.001   PHE C 141 
 TRP   0.017   0.002   TRP D 219 
 HIS   0.002   0.001   HIS C 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (12668)
  covalent geometry    : angle       0.70256 (17172)
  hydrogen bonds       : bond        0.03500 (  860)
  hydrogen bonds       : angle       3.63714 ( 2544)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1976.67 seconds
wall clock time: 35 minutes 27.31 seconds (2127.31 seconds total)