Starting phenix.real_space_refine
on Wed Jul 30 13:45:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6c70_7352/07_2025/6c70_7352_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6c70_7352/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6c70_7352/07_2025/6c70_7352.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6c70_7352/07_2025/6c70_7352.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6c70_7352/07_2025/6c70_7352_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6c70_7352/07_2025/6c70_7352_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.159 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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:
    C, B, D
  Time building chain proxies: 7.02, per 1000 atoms: 0.57
  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: 3.22
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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: 1.06
  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: 3.65

  Time building geometry restraints manager: 3.71 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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:             3.780
  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:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     29.470
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.320
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.031   0.005   TRP D 329 
 HIS   0.008   0.002   HIS A 110 
 PHE   0.022   0.004   PHE D  25 
 TYR   0.028   0.003   TYR A 415 
 ARG   0.008   0.001   ARG B 323 

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

*********************** 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  : 1.365 
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: 0.8971 (m)
REVERT: A  345 ASP cc_start: 0.8813 (t70) cc_final: 0.8598 (t70)
REVERT: A  424 GLU cc_start: 0.8789 (tp30) cc_final: 0.8496 (tp30)
REVERT: A  474 LYS cc_start: 0.7247 (tmtm) cc_final: 0.7012 (tttm)
REVERT: B   13 LEU cc_start: 0.8930 (mt) cc_final: 0.8684 (mt)
REVERT: B   19 MET cc_start: 0.8932 (ttm) cc_final: 0.8569 (ttm)
REVERT: B   22 VAL cc_start: 0.9703 (p) cc_final: 0.9490 (p)
REVERT: B  106 ASN cc_start: 0.8955 (t0) cc_final: 0.8649 (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: 0.8596 (mm-30)
REVERT: B  331 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8254 (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: 0.8808 (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: 0.7072 (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: 0.8803 (m)
REVERT: C  345 ASP cc_start: 0.8758 (t70) cc_final: 0.8537 (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: 0.8352 (m)
REVERT: C  474 LYS cc_start: 0.7492 (tmtm) cc_final: 0.7180 (tttm)
REVERT: D   19 MET cc_start: 0.8936 (ttm) cc_final: 0.7990 (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: 0.8873 (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: 0.8372 (m)
REVERT: D  474 LYS cc_start: 0.7578 (tmtm) cc_final: 0.7262 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 392
  average time/residue: 0.2071
  time to fit residues: 120.3963
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  : 1.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    0.8980
   chunk 115 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 72 optimal weight:    0.6980
   chunk 88 optimal weight:    3.9990
   chunk 138 optimal weight:    0.7980
   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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 GLN
A 401 ASN
A 431 GLN
B   5 HIS
** B  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3308 r_free = 0.3308 target = 0.070636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.062694 restraints weight = 41594.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.064488 restraints weight = 19304.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.065680 restraints weight = 10979.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3063

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= 0.154
  Angle     :  0.639   8.227  17172  Z= 0.337
  Chirality :  0.040   0.137   2008
  Planarity :  0.004   0.027   2080
  Dihedral  :  5.070  18.987   1668
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.13 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.19), residues: 1528
  helix: -0.78 (0.13), residues: 1212
  sheet:  None (None), residues: 0
  loop : -2.81 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 104 
 HIS   0.004   0.001   HIS B   5 
 PHE   0.017   0.002   PHE D 394 
 TYR   0.011   0.001   TYR C  89 
 ARG   0.002   0.000   ARG C 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04431 (  860)
  hydrogen bonds       : angle       4.43595 ( 2544)
  covalent geometry    : bond        0.00328 (12668)
  covalent geometry    : angle       0.63855 (17172)

*********************** 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
  368 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 348
  time to evaluate  : 1.348 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.8366 (ttp) cc_final: 0.8001 (ttm)
REVERT: A  141 PHE cc_start: 0.9039 (t80) cc_final: 0.8767 (t80)
REVERT: A  327 LYS cc_start: 0.9460 (ttmt) cc_final: 0.9096 (tttm)
REVERT: A  345 ASP cc_start: 0.8675 (t70) cc_final: 0.8465 (t70)
REVERT: A  406 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8418 (mm-30)
REVERT: A  424 GLU cc_start: 0.8747 (tp30) cc_final: 0.8405 (tp30)
REVERT: A  437 CYS cc_start: 0.8655 (m) cc_final: 0.8379 (m)
REVERT: A  474 LYS cc_start: 0.8745 (tmtm) cc_final: 0.8072 (tttm)
REVERT: B   13 LEU cc_start: 0.9022 (mt) cc_final: 0.8790 (mt)
REVERT: B   77 MET cc_start: 0.8812 (tpp) cc_final: 0.8562 (tpp)
REVERT: B  134 CYS cc_start: 0.9230 (m) cc_final: 0.9005 (m)
REVERT: B  141 PHE cc_start: 0.8943 (t80) cc_final: 0.8661 (t80)
REVERT: B  239 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8514 (mm-30)
REVERT: B  345 ASP cc_start: 0.8700 (t70) cc_final: 0.8489 (t70)
REVERT: B  355 MET cc_start: 0.8901 (mmm) cc_final: 0.8637 (mmm)
REVERT: B  406 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8390 (mm-30)
REVERT: B  424 GLU cc_start: 0.8676 (tp30) cc_final: 0.8304 (tp30)
REVERT: B  437 CYS cc_start: 0.8731 (m) cc_final: 0.8377 (m)
REVERT: B  474 LYS cc_start: 0.8700 (tmtm) cc_final: 0.8092 (tttm)
REVERT: C   29 TYR cc_start: 0.8653 (m-80) cc_final: 0.8219 (m-80)
REVERT: C  131 LEU cc_start: 0.9583 (tp) cc_final: 0.9335 (tp)
REVERT: C  134 CYS cc_start: 0.9379 (m) cc_final: 0.9035 (m)
REVERT: C  201 TYR cc_start: 0.9135 (t80) cc_final: 0.8757 (t80)
REVERT: C  239 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8486 (mm-30)
REVERT: C  345 ASP cc_start: 0.8655 (t70) cc_final: 0.8419 (t70)
REVERT: C  355 MET cc_start: 0.9135 (mmm) cc_final: 0.8928 (mmm)
REVERT: C  406 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8232 (mm-30)
REVERT: C  408 SER cc_start: 0.9472 (m) cc_final: 0.9085 (p)
REVERT: C  424 GLU cc_start: 0.8761 (tp30) cc_final: 0.8412 (tp30)
REVERT: C  437 CYS cc_start: 0.8805 (m) cc_final: 0.8518 (m)
REVERT: C  474 LYS cc_start: 0.8729 (tmtm) cc_final: 0.8111 (tttm)
REVERT: D  131 LEU cc_start: 0.9568 (tp) cc_final: 0.9361 (tp)
REVERT: D  134 CYS cc_start: 0.9338 (m) cc_final: 0.9051 (m)
REVERT: D  141 PHE cc_start: 0.9017 (t80) cc_final: 0.8776 (t80)
REVERT: D  149 ILE cc_start: 0.9250 (mm) cc_final: 0.9009 (pt)
REVERT: D  215 LEU cc_start: 0.9477 (tp) cc_final: 0.9224 (tt)
REVERT: D  239 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8550 (mm-30)
REVERT: D  355 MET cc_start: 0.9133 (mmm) cc_final: 0.8910 (mmm)
REVERT: D  406 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8312 (mm-30)
REVERT: D  437 CYS cc_start: 0.8732 (m) cc_final: 0.8383 (m)
REVERT: D  474 LYS cc_start: 0.8741 (tmtm) cc_final: 0.8135 (tttm)
  outliers start: 20
  outliers final: 13
  residues processed: 359
  average time/residue: 0.1825
  time to fit residues: 102.7181
Evaluate side-chains
  304 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 291
  time to evaluate  : 1.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   58 VAL
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 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   65 ASP
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 61 optimal weight:    0.8980
   chunk 85 optimal weight:    0.8980
   chunk 138 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 140 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 128 optimal weight:    0.0270
   chunk 121 optimal weight:    0.7980
   chunk 133 optimal weight:    0.9990
   overall best weight:    0.7038

-------------------------------------------------------------------------------
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**
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.071665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.063785 restraints weight = 42625.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.065609 restraints weight = 19445.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.066791 restraints weight = 10913.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.3735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12668  Z= 0.134
  Angle     :  0.579   6.594  17172  Z= 0.304
  Chirality :  0.040   0.179   2008
  Planarity :  0.003   0.021   2080
  Dihedral  :  4.576  16.460   1668
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 12.76 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.21), residues: 1528
  helix:  0.52 (0.15), residues: 1196
  sheet:  None (None), residues: 0
  loop : -2.32 (0.30), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 104 
 HIS   0.004   0.001   HIS B 229 
 PHE   0.020   0.001   PHE C 141 
 TYR   0.012   0.001   TYR C  53 
 ARG   0.001   0.000   ARG A 178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03795 (  860)
  hydrogen bonds       : angle       3.94232 ( 2544)
  covalent geometry    : bond        0.00295 (12668)
  covalent geometry    : angle       0.57902 (17172)

*********************** 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
  364 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 331
  time to evaluate  : 1.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 TYR cc_start: 0.9088 (t80) cc_final: 0.8874 (t80)
REVERT: A   77 MET cc_start: 0.8288 (ttp) cc_final: 0.7966 (ttp)
REVERT: A  141 PHE cc_start: 0.8966 (t80) cc_final: 0.8686 (t80)
REVERT: A  206 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8687 (ttp)
REVERT: A  215 LEU cc_start: 0.9479 (tp) cc_final: 0.9269 (tt)
REVERT: A  224 CYS cc_start: 0.9046 (m) cc_final: 0.8570 (t)
REVERT: A  225 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8484 (mm-30)
REVERT: A  239 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8453 (mm-30)
REVERT: A  327 LYS cc_start: 0.9428 (ttmt) cc_final: 0.9159 (tttm)
REVERT: A  345 ASP cc_start: 0.8670 (t70) cc_final: 0.8425 (t70)
REVERT: A  424 GLU cc_start: 0.8649 (tp30) cc_final: 0.8267 (tp30)
REVERT: A  437 CYS cc_start: 0.8807 (m) cc_final: 0.8583 (m)
REVERT: A  474 LYS cc_start: 0.8724 (tmtm) cc_final: 0.8078 (tttm)
REVERT: B   16 ILE cc_start: 0.9707 (mt) cc_final: 0.9501 (pt)
REVERT: B   53 TYR cc_start: 0.9142 (t80) cc_final: 0.8685 (t80)
REVERT: B  134 CYS cc_start: 0.9215 (m) cc_final: 0.8994 (m)
REVERT: B  141 PHE cc_start: 0.8912 (t80) cc_final: 0.8692 (t80)
REVERT: B  149 ILE cc_start: 0.9107 (mm) cc_final: 0.8857 (tp)
REVERT: B  201 TYR cc_start: 0.9211 (t80) cc_final: 0.8766 (t80)
REVERT: B  206 MET cc_start: 0.9062 (mtp) cc_final: 0.8741 (ttp)
REVERT: B  239 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8525 (mm-30)
REVERT: B  345 ASP cc_start: 0.8701 (t70) cc_final: 0.8465 (t70)
REVERT: B  406 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8362 (mm-30)
REVERT: B  437 CYS cc_start: 0.8879 (m) cc_final: 0.8644 (m)
REVERT: B  474 LYS cc_start: 0.8641 (tmtm) cc_final: 0.8008 (tttm)
REVERT: C   29 TYR cc_start: 0.8602 (m-80) cc_final: 0.8128 (m-80)
REVERT: C   53 TYR cc_start: 0.9025 (t80) cc_final: 0.7855 (t80)
REVERT: C   77 MET cc_start: 0.8930 (tpp) cc_final: 0.8103 (mmm)
REVERT: C  131 LEU cc_start: 0.9580 (tp) cc_final: 0.9350 (tp)
REVERT: C  134 CYS cc_start: 0.9326 (m) cc_final: 0.9033 (m)
REVERT: C  149 ILE cc_start: 0.9173 (mm) cc_final: 0.8905 (mt)
REVERT: C  239 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8483 (mm-30)
REVERT: C  345 ASP cc_start: 0.8697 (t70) cc_final: 0.8422 (t70)
REVERT: C  408 SER cc_start: 0.9433 (m) cc_final: 0.9097 (p)
REVERT: C  415 TYR cc_start: 0.9082 (t80) cc_final: 0.8636 (t80)
REVERT: C  424 GLU cc_start: 0.8738 (tp30) cc_final: 0.8359 (tp30)
REVERT: C  474 LYS cc_start: 0.8708 (tmtm) cc_final: 0.8078 (tttm)
REVERT: D   13 LEU cc_start: 0.9201 (mm) cc_final: 0.8885 (mm)
REVERT: D  131 LEU cc_start: 0.9586 (tp) cc_final: 0.9376 (tp)
REVERT: D  134 CYS cc_start: 0.9310 (m) cc_final: 0.9060 (m)
REVERT: D  141 PHE cc_start: 0.9015 (t80) cc_final: 0.8800 (t80)
REVERT: D  149 ILE cc_start: 0.9212 (mm) cc_final: 0.8982 (mt)
REVERT: D  355 MET cc_start: 0.9190 (mmm) cc_final: 0.8939 (mmm)
REVERT: D  408 SER cc_start: 0.9442 (m) cc_final: 0.9115 (p)
REVERT: D  436 GLN cc_start: 0.8320 (tm-30) cc_final: 0.8021 (tm-30)
REVERT: D  474 LYS cc_start: 0.8636 (tmtm) cc_final: 0.8046 (tttm)
  outliers start: 33
  outliers final: 18
  residues processed: 351
  average time/residue: 0.1860
  time to fit residues: 101.5855
Evaluate side-chains
  305 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 286
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  125 ILE
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   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    4 LYS
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   81 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 82 optimal weight:    0.0870
   chunk 102 optimal weight:    1.9990
   chunk 135 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9990
   chunk 127 optimal weight:    0.7980
   chunk 105 optimal weight:    0.0570
   chunk 56 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 122 optimal weight:    0.7980
   overall best weight:    0.4476

-------------------------------------------------------------------------------
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**
** C  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.073498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.065462 restraints weight = 41848.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.067316 restraints weight = 19420.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.068486 restraints weight = 10991.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.4216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12668  Z= 0.118
  Angle     :  0.566   8.011  17172  Z= 0.294
  Chirality :  0.040   0.174   2008
  Planarity :  0.003   0.021   2080
  Dihedral  :  4.326  17.312   1668
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.65 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.21), residues: 1528
  helix:  1.12 (0.15), residues: 1196
  sheet:  None (None), residues: 0
  loop : -2.23 (0.30), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 219 
 HIS   0.003   0.001   HIS B 229 
 PHE   0.015   0.001   PHE A 394 
 TYR   0.007   0.001   TYR D  53 
 ARG   0.002   0.000   ARG B 178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03481 (  860)
  hydrogen bonds       : angle       3.66713 ( 2544)
  covalent geometry    : bond        0.00263 (12668)
  covalent geometry    : angle       0.56563 (17172)

*********************** 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
  365 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 331
  time to evaluate  : 1.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 MET cc_start: 0.9018 (mtm) cc_final: 0.8745 (mpp)
REVERT: A   77 MET cc_start: 0.8239 (ttp) cc_final: 0.7870 (ttp)
REVERT: A  141 PHE cc_start: 0.8916 (t80) cc_final: 0.8684 (t80)
REVERT: A  206 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8686 (ttp)
REVERT: A  239 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8551 (mm-30)
REVERT: A  327 LYS cc_start: 0.9421 (ttmt) cc_final: 0.9123 (tttm)
REVERT: A  345 ASP cc_start: 0.8640 (t70) cc_final: 0.8436 (t70)
REVERT: A  474 LYS cc_start: 0.8699 (tmtm) cc_final: 0.8070 (tttm)
REVERT: B   53 TYR cc_start: 0.9064 (t80) cc_final: 0.8556 (t80)
REVERT: B   77 MET cc_start: 0.8774 (tpp) cc_final: 0.8483 (tpp)
REVERT: B  134 CYS cc_start: 0.9187 (m) cc_final: 0.8983 (m)
REVERT: B  149 ILE cc_start: 0.9124 (mm) cc_final: 0.8893 (tp)
REVERT: B  186 MET cc_start: 0.5415 (mmm) cc_final: 0.5110 (tpt)
REVERT: B  201 TYR cc_start: 0.9224 (t80) cc_final: 0.8796 (t80)
REVERT: B  239 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8579 (mm-30)
REVERT: B  412 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8558 (tm-30)
REVERT: B  474 LYS cc_start: 0.8659 (tmtm) cc_final: 0.8008 (tttm)
REVERT: C   29 TYR cc_start: 0.8451 (m-80) cc_final: 0.8154 (m-80)
REVERT: C   53 TYR cc_start: 0.8968 (t80) cc_final: 0.7877 (t80)
REVERT: C   69 ASP cc_start: 0.8969 (m-30) cc_final: 0.8724 (m-30)
REVERT: C   77 MET cc_start: 0.8899 (tpp) cc_final: 0.8065 (mmm)
REVERT: C  131 LEU cc_start: 0.9575 (tp) cc_final: 0.9361 (tp)
REVERT: C  134 CYS cc_start: 0.9309 (m) cc_final: 0.9047 (m)
REVERT: C  149 ILE cc_start: 0.9175 (mm) cc_final: 0.8931 (mt)
REVERT: C  176 MET cc_start: 0.8564 (tpp) cc_final: 0.8239 (tpt)
REVERT: C  201 TYR cc_start: 0.9161 (t80) cc_final: 0.8775 (t80)
REVERT: C  239 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8490 (mm-30)
REVERT: C  345 ASP cc_start: 0.8657 (t70) cc_final: 0.8400 (t70)
REVERT: C  401 ASN cc_start: 0.9222 (t0) cc_final: 0.8999 (t0)
REVERT: C  408 SER cc_start: 0.9447 (m) cc_final: 0.9077 (p)
REVERT: C  415 TYR cc_start: 0.8986 (t80) cc_final: 0.8518 (t80)
REVERT: C  474 LYS cc_start: 0.8644 (tmtm) cc_final: 0.8019 (tttm)
REVERT: D   13 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8737 (tp)
REVERT: D   62 MET cc_start: 0.7943 (mmm) cc_final: 0.7681 (mmm)
REVERT: D  134 CYS cc_start: 0.9280 (m) cc_final: 0.9053 (m)
REVERT: D  141 PHE cc_start: 0.8958 (t80) cc_final: 0.8755 (t80)
REVERT: D  149 ILE cc_start: 0.9282 (mm) cc_final: 0.8931 (mt)
REVERT: D  176 MET cc_start: 0.8436 (tpp) cc_final: 0.8166 (tpt)
REVERT: D  239 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8532 (mm-30)
REVERT: D  355 MET cc_start: 0.9197 (mmm) cc_final: 0.8934 (mmm)
REVERT: D  408 SER cc_start: 0.9391 (m) cc_final: 0.9042 (p)
REVERT: D  415 TYR cc_start: 0.8876 (t80) cc_final: 0.8441 (t80)
REVERT: D  436 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7887 (tm-30)
REVERT: D  474 LYS cc_start: 0.8594 (tmtm) cc_final: 0.8038 (tttm)
  outliers start: 34
  outliers final: 21
  residues processed: 347
  average time/residue: 0.1865
  time to fit residues: 100.6000
Evaluate side-chains
  311 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 288
  time to evaluate  : 1.416 
-------------------------------------------------------------------------------
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  206 MET
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  125 ILE
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   47 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  224 CYS
Chi-restraints excluded: chain C residue  381 THR
Chi-restraints excluded: chain D residue    4 LYS
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   26 MET
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  381 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 138 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 131 optimal weight:    4.9990
   chunk 145 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   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   5 HIS
** A  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  15 ASN
** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.072575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.064520 restraints weight = 42241.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.066393 restraints weight = 19538.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.067600 restraints weight = 11046.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.4422

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= 0.134
  Angle     :  0.601  16.987  17172  Z= 0.304
  Chirality :  0.040   0.178   2008
  Planarity :  0.003   0.026   2080
  Dihedral  :  4.167  16.737   1668
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 16.77 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.22), residues: 1528
  helix:  1.46 (0.15), residues: 1196
  sheet:  None (None), residues: 0
  loop : -2.32 (0.30), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 219 
 HIS   0.002   0.001   HIS D 121 
 PHE   0.024   0.001   PHE B 141 
 TYR   0.007   0.001   TYR A  53 
 ARG   0.002   0.000   ARG D 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03415 (  860)
  hydrogen bonds       : angle       3.57463 ( 2544)
  covalent geometry    : bond        0.00303 (12668)
  covalent geometry    : angle       0.60114 (17172)

*********************** 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
  344 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 303
  time to evaluate  : 1.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 MET cc_start: 0.9012 (mtm) cc_final: 0.8778 (mtm)
REVERT: A  141 PHE cc_start: 0.8937 (t80) cc_final: 0.8718 (t80)
REVERT: A  327 LYS cc_start: 0.9404 (ttmt) cc_final: 0.9062 (tttm)
REVERT: A  474 LYS cc_start: 0.8711 (tmtm) cc_final: 0.8076 (tttm)
REVERT: B   53 TYR cc_start: 0.9061 (t80) cc_final: 0.8549 (t80)
REVERT: B   77 MET cc_start: 0.8794 (tpp) cc_final: 0.8407 (tpp)
REVERT: B  134 CYS cc_start: 0.9205 (m) cc_final: 0.8979 (m)
REVERT: B  186 MET cc_start: 0.5434 (mmm) cc_final: 0.5095 (tpt)
REVERT: B  204 ILE cc_start: 0.9613 (tp) cc_final: 0.9349 (tp)
REVERT: B  239 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8605 (mm-30)
REVERT: B  408 SER cc_start: 0.9554 (m) cc_final: 0.9040 (p)
REVERT: B  474 LYS cc_start: 0.8680 (tmtm) cc_final: 0.8056 (tttm)
REVERT: C   53 TYR cc_start: 0.8919 (t80) cc_final: 0.7786 (t80)
REVERT: C   77 MET cc_start: 0.8892 (tpp) cc_final: 0.8040 (tmm)
REVERT: C  134 CYS cc_start: 0.9312 (m) cc_final: 0.9051 (m)
REVERT: C  149 ILE cc_start: 0.9252 (mm) cc_final: 0.8771 (mt)
REVERT: C  225 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8596 (mm-30)
REVERT: C  239 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8514 (mm-30)
REVERT: C  345 ASP cc_start: 0.8663 (t70) cc_final: 0.8426 (t70)
REVERT: C  401 ASN cc_start: 0.9230 (t0) cc_final: 0.9007 (t0)
REVERT: C  408 SER cc_start: 0.9466 (m) cc_final: 0.9086 (p)
REVERT: C  415 TYR cc_start: 0.8956 (t80) cc_final: 0.8533 (t80)
REVERT: C  474 LYS cc_start: 0.8655 (tmtm) cc_final: 0.8042 (tttm)
REVERT: D   13 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8709 (tp)
REVERT: D   62 MET cc_start: 0.7948 (mmm) cc_final: 0.7667 (mmm)
REVERT: D  134 CYS cc_start: 0.9325 (m) cc_final: 0.9063 (m)
REVERT: D  141 PHE cc_start: 0.8936 (t80) cc_final: 0.8716 (t80)
REVERT: D  239 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8577 (mm-30)
REVERT: D  355 MET cc_start: 0.9232 (mmm) cc_final: 0.8977 (mmm)
REVERT: D  408 SER cc_start: 0.9380 (m) cc_final: 0.9048 (p)
REVERT: D  436 GLN cc_start: 0.8273 (tm-30) cc_final: 0.8036 (tm-30)
REVERT: D  474 LYS cc_start: 0.8609 (tmtm) cc_final: 0.8047 (tttm)
  outliers start: 41
  outliers final: 30
  residues processed: 326
  average time/residue: 0.1806
  time to fit residues: 91.9758
Evaluate side-chains
  306 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 275
  time to evaluate  : 1.518 
-------------------------------------------------------------------------------
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  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  125 ILE
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   26 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  224 CYS
Chi-restraints excluded: chain D residue    4 LYS
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  195 LEU
Chi-restraints excluded: chain D residue  217 CYS
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  442 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 127 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 126 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 142 optimal weight:    0.2980
   chunk 49 optimal weight:    3.9990
   chunk 141 optimal weight:    0.7980
   chunk 150 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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
D  15 ASN
** D 435 GLN ** 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 = 0.3346 r_free = 0.3346 target = 0.073154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.064991 restraints weight = 42713.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.066862 restraints weight = 19816.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.068016 restraints weight = 11224.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.4641

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= 0.132
  Angle     :  0.611  11.179  17172  Z= 0.310
  Chirality :  0.041   0.178   2008
  Planarity :  0.003   0.022   2080
  Dihedral  :  4.089  17.487   1668
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.73 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.22), residues: 1528
  helix:  1.66 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -2.34 (0.30), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 219 
 HIS   0.003   0.001   HIS D 121 
 PHE   0.017   0.001   PHE A 394 
 TYR   0.014   0.001   TYR C  29 
 ARG   0.001   0.000   ARG C 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03414 (  860)
  hydrogen bonds       : angle       3.54250 ( 2544)
  covalent geometry    : bond        0.00298 (12668)
  covalent geometry    : angle       0.61138 (17172)

*********************** 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
  336 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 296
  time to evaluate  : 1.462 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 ASP cc_start: 0.8891 (m-30) cc_final: 0.8685 (p0)
REVERT: A  141 PHE cc_start: 0.8898 (t80) cc_final: 0.8685 (t80)
REVERT: A  327 LYS cc_start: 0.9384 (ttmt) cc_final: 0.9041 (tttm)
REVERT: A  415 TYR cc_start: 0.8779 (t80) cc_final: 0.8331 (t80)
REVERT: A  474 LYS cc_start: 0.8706 (tmtm) cc_final: 0.8070 (tttm)
REVERT: B   53 TYR cc_start: 0.9033 (t80) cc_final: 0.8578 (t80)
REVERT: B  134 CYS cc_start: 0.9186 (m) cc_final: 0.8963 (m)
REVERT: B  186 MET cc_start: 0.5397 (mmm) cc_final: 0.5122 (tpt)
REVERT: B  201 TYR cc_start: 0.9226 (t80) cc_final: 0.8929 (t80)
REVERT: B  204 ILE cc_start: 0.9606 (tp) cc_final: 0.9332 (tp)
REVERT: B  239 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8587 (mm-30)
REVERT: B  408 SER cc_start: 0.9551 (m) cc_final: 0.9035 (p)
REVERT: B  474 LYS cc_start: 0.8641 (tmtm) cc_final: 0.8020 (tttm)
REVERT: C   53 TYR cc_start: 0.8852 (t80) cc_final: 0.8086 (t80)
REVERT: C   77 MET cc_start: 0.8879 (tpp) cc_final: 0.7948 (tmm)
REVERT: C  134 CYS cc_start: 0.9306 (m) cc_final: 0.9054 (m)
REVERT: C  149 ILE cc_start: 0.9177 (mm) cc_final: 0.8897 (tp)
REVERT: C  206 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8877 (ttp)
REVERT: C  345 ASP cc_start: 0.8654 (t70) cc_final: 0.8432 (t70)
REVERT: C  401 ASN cc_start: 0.9196 (t0) cc_final: 0.8977 (t0)
REVERT: C  406 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8162 (mm-30)
REVERT: C  408 SER cc_start: 0.9462 (m) cc_final: 0.9080 (p)
REVERT: C  415 TYR cc_start: 0.8926 (t80) cc_final: 0.8462 (t80)
REVERT: C  474 LYS cc_start: 0.8655 (tmtm) cc_final: 0.8041 (tttm)
REVERT: D   13 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8684 (tp)
REVERT: D   69 ASP cc_start: 0.8825 (m-30) cc_final: 0.8370 (m-30)
REVERT: D  134 CYS cc_start: 0.9335 (m) cc_final: 0.9086 (m)
REVERT: D  141 PHE cc_start: 0.8866 (t80) cc_final: 0.8602 (t80)
REVERT: D  206 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8784 (ttp)
REVERT: D  355 MET cc_start: 0.9235 (mmm) cc_final: 0.8977 (mmm)
REVERT: D  408 SER cc_start: 0.9400 (m) cc_final: 0.9052 (p)
REVERT: D  474 LYS cc_start: 0.8607 (tmtm) cc_final: 0.8050 (tttm)
  outliers start: 40
  outliers final: 26
  residues processed: 316
  average time/residue: 0.2039
  time to fit residues: 101.1986
Evaluate side-chains
  302 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 273
  time to evaluate  : 1.357 
-------------------------------------------------------------------------------
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   47 LEU
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  206 MET
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  224 CYS
Chi-restraints excluded: chain D residue    4 LYS
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  206 MET
Chi-restraints excluded: chain D residue  321 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 140 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 128 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   chunk 131 optimal weight:    0.1980
   chunk 150 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 116 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A   5 HIS
A  15 ASN
B 354 HIS
C  15 ASN
** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   6 GLN
D  15 ASN
** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.072365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.064017 restraints weight = 42179.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.065841 restraints weight = 19844.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.067000 restraints weight = 11462.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.4706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12668  Z= 0.155
  Angle     :  0.634  11.775  17172  Z= 0.324
  Chirality :  0.042   0.205   2008
  Planarity :  0.003   0.025   2080
  Dihedral  :  4.046  15.571   1668
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 18.40 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.22), residues: 1528
  helix:  1.80 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -2.31 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 219 
 HIS   0.002   0.001   HIS B 110 
 PHE   0.017   0.001   PHE B 394 
 TYR   0.012   0.001   TYR C  29 
 ARG   0.001   0.000   ARG D 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03423 (  860)
  hydrogen bonds       : angle       3.63580 ( 2544)
  covalent geometry    : bond        0.00347 (12668)
  covalent geometry    : angle       0.63439 (17172)

*********************** 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
  337 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 293
  time to evaluate  : 1.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 MET cc_start: 0.8750 (tpp) cc_final: 0.8527 (tpt)
REVERT: A  141 PHE cc_start: 0.8899 (t80) cc_final: 0.8685 (t80)
REVERT: A  327 LYS cc_start: 0.9397 (ttmt) cc_final: 0.9048 (tttm)
REVERT: A  474 LYS cc_start: 0.8713 (tmtm) cc_final: 0.8077 (tttm)
REVERT: B   53 TYR cc_start: 0.8981 (t80) cc_final: 0.8531 (t80)
REVERT: B   56 MET cc_start: 0.8943 (mtt) cc_final: 0.8687 (mtt)
REVERT: B   77 MET cc_start: 0.8864 (tpp) cc_final: 0.8572 (tpp)
REVERT: B  128 MET cc_start: 0.8965 (mtm) cc_final: 0.8756 (mtp)
REVERT: B  134 CYS cc_start: 0.9220 (m) cc_final: 0.8985 (m)
REVERT: B  186 MET cc_start: 0.5469 (mmm) cc_final: 0.5207 (tpt)
REVERT: B  204 ILE cc_start: 0.9584 (tp) cc_final: 0.9356 (tp)
REVERT: B  239 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8617 (mm-30)
REVERT: B  408 SER cc_start: 0.9549 (m) cc_final: 0.9045 (p)
REVERT: B  415 TYR cc_start: 0.8797 (t80) cc_final: 0.8343 (t80)
REVERT: B  474 LYS cc_start: 0.8672 (tmtm) cc_final: 0.8046 (tttm)
REVERT: C   53 TYR cc_start: 0.8710 (t80) cc_final: 0.8310 (t80)
REVERT: C   56 MET cc_start: 0.8922 (mtm) cc_final: 0.8579 (pmm)
REVERT: C   77 MET cc_start: 0.8948 (tpp) cc_final: 0.8143 (tmm)
REVERT: C  134 CYS cc_start: 0.9330 (m) cc_final: 0.9068 (m)
REVERT: C  186 MET cc_start: 0.4782 (mmm) cc_final: 0.4375 (mmt)
REVERT: C  206 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8853 (ttp)
REVERT: C  239 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8571 (mm-30)
REVERT: C  345 ASP cc_start: 0.8633 (t70) cc_final: 0.8423 (t70)
REVERT: C  401 ASN cc_start: 0.9265 (t0) cc_final: 0.9047 (t0)
REVERT: C  406 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8208 (mm-30)
REVERT: C  408 SER cc_start: 0.9466 (m) cc_final: 0.9104 (p)
REVERT: C  415 TYR cc_start: 0.8962 (t80) cc_final: 0.8562 (t80)
REVERT: C  474 LYS cc_start: 0.8696 (tmtm) cc_final: 0.8081 (tttm)
REVERT: D   13 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8678 (tp)
REVERT: D   53 TYR cc_start: 0.9035 (t80) cc_final: 0.8706 (t80)
REVERT: D   77 MET cc_start: 0.8153 (ttp) cc_final: 0.7872 (ttt)
REVERT: D  134 CYS cc_start: 0.9362 (m) cc_final: 0.9085 (m)
REVERT: D  141 PHE cc_start: 0.8815 (t80) cc_final: 0.8591 (t80)
REVERT: D  186 MET cc_start: 0.4801 (mmm) cc_final: 0.4333 (mmt)
REVERT: D  206 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8889 (ttp)
REVERT: D  355 MET cc_start: 0.9218 (mmm) cc_final: 0.8955 (mmm)
REVERT: D  408 SER cc_start: 0.9399 (m) cc_final: 0.9068 (p)
REVERT: D  415 TYR cc_start: 0.8850 (t80) cc_final: 0.8585 (t80)
REVERT: D  474 LYS cc_start: 0.8640 (tmtm) cc_final: 0.8076 (tttm)
  outliers start: 44
  outliers final: 31
  residues processed: 316
  average time/residue: 0.1823
  time to fit residues: 90.7831
Evaluate side-chains
  309 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 275
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
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  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   47 LEU
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 C residue  224 CYS
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  398 ILE
Chi-restraints excluded: chain D residue    4 LYS
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  206 MET
Chi-restraints excluded: chain D residue  217 CYS
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  351 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 131 optimal weight:    0.9980
   chunk 114 optimal weight:    7.9990
   chunk 140 optimal weight:    0.8980
   chunk 118 optimal weight:    3.9990
   chunk 121 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0870
   chunk 107 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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
D  15 ASN
** D 435 GLN ** 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 = 0.3364 r_free = 0.3364 target = 0.074109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.065723 restraints weight = 42689.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.067590 restraints weight = 20053.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.068847 restraints weight = 11469.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.4884

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= 0.133
  Angle     :  0.654  12.220  17172  Z= 0.327
  Chirality :  0.042   0.248   2008
  Planarity :  0.003   0.026   2080
  Dihedral  :  4.005  16.069   1668
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 19.66 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.22), residues: 1528
  helix:  1.84 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -2.38 (0.30), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 219 
 HIS   0.003   0.001   HIS D 121 
 PHE   0.017   0.001   PHE B 394 
 TYR   0.012   0.001   TYR C  53 
 ARG   0.002   0.000   ARG D 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03422 (  860)
  hydrogen bonds       : angle       3.61523 ( 2544)
  covalent geometry    : bond        0.00300 (12668)
  covalent geometry    : angle       0.65411 (17172)

*********************** 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
  331 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 293
  time to evaluate  : 1.493 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 MET cc_start: 0.8796 (tpp) cc_final: 0.8491 (tpt)
REVERT: A  327 LYS cc_start: 0.9374 (ttmt) cc_final: 0.9037 (tttm)
REVERT: A  474 LYS cc_start: 0.8677 (tmtm) cc_final: 0.8048 (tttm)
REVERT: B   53 TYR cc_start: 0.8907 (t80) cc_final: 0.8436 (t80)
REVERT: B   56 MET cc_start: 0.8935 (mtt) cc_final: 0.8558 (mtt)
REVERT: B   77 MET cc_start: 0.8791 (tpp) cc_final: 0.8389 (tpp)
REVERT: B  134 CYS cc_start: 0.9203 (m) cc_final: 0.8981 (m)
REVERT: B  186 MET cc_start: 0.5318 (mmm) cc_final: 0.5066 (tpt)
REVERT: B  204 ILE cc_start: 0.9566 (tp) cc_final: 0.9333 (tp)
REVERT: B  239 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8601 (mm-30)
REVERT: B  408 SER cc_start: 0.9543 (m) cc_final: 0.9055 (p)
REVERT: B  474 LYS cc_start: 0.8678 (tmtm) cc_final: 0.8060 (tttm)
REVERT: C   53 TYR cc_start: 0.8622 (t80) cc_final: 0.7922 (t80)
REVERT: C   77 MET cc_start: 0.8948 (tpp) cc_final: 0.8081 (tmm)
REVERT: C  134 CYS cc_start: 0.9311 (m) cc_final: 0.9058 (m)
REVERT: C  186 MET cc_start: 0.4418 (mmm) cc_final: 0.4117 (mmt)
REVERT: C  239 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8532 (mm-30)
REVERT: C  401 ASN cc_start: 0.9180 (t0) cc_final: 0.8951 (t0)
REVERT: C  406 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8160 (mm-30)
REVERT: C  408 SER cc_start: 0.9465 (m) cc_final: 0.9084 (p)
REVERT: C  474 LYS cc_start: 0.8608 (tmtm) cc_final: 0.8060 (tttm)
REVERT: D   13 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8691 (tp)
REVERT: D   53 TYR cc_start: 0.9009 (t80) cc_final: 0.8065 (t80)
REVERT: D   55 MET cc_start: 0.8778 (tpp) cc_final: 0.8493 (tpt)
REVERT: D  134 CYS cc_start: 0.9368 (m) cc_final: 0.9090 (m)
REVERT: D  186 MET cc_start: 0.4573 (mmm) cc_final: 0.4146 (mmt)
REVERT: D  206 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8878 (ttp)
REVERT: D  239 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8601 (mm-30)
REVERT: D  355 MET cc_start: 0.9239 (mmm) cc_final: 0.8987 (mmm)
REVERT: D  408 SER cc_start: 0.9396 (m) cc_final: 0.9039 (p)
REVERT: D  474 LYS cc_start: 0.8602 (tmtm) cc_final: 0.8037 (tttm)
  outliers start: 38
  outliers final: 29
  residues processed: 313
  average time/residue: 0.2004
  time to fit residues: 98.6431
Evaluate side-chains
  306 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 275
  time to evaluate  : 1.952 
-------------------------------------------------------------------------------
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  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   47 LEU
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 C residue  321 LEU
Chi-restraints excluded: chain D residue    4 LYS
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  206 MET
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  351 LEU
Chi-restraints excluded: chain D residue  450 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0770
   chunk 28 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 81 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 108 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.8340

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

Flipped N/Q/H residues before XYZ refinement:
C  15 ASN
C  59 ASN
D  15 ASN
D 401 ASN
** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.073998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.065621 restraints weight = 42665.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.067487 restraints weight = 20053.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.068675 restraints weight = 11570.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.4986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12668  Z= 0.140
  Angle     :  0.675  12.178  17172  Z= 0.337
  Chirality :  0.042   0.257   2008
  Planarity :  0.003   0.024   2080
  Dihedral  :  3.986  15.413   1668
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 19.88 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.22), residues: 1528
  helix:  1.86 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -2.32 (0.30), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 219 
 HIS   0.002   0.001   HIS B  82 
 PHE   0.035   0.001   PHE A 141 
 TYR   0.011   0.001   TYR C  29 
 ARG   0.002   0.000   ARG C 178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03438 (  860)
  hydrogen bonds       : angle       3.60861 ( 2544)
  covalent geometry    : bond        0.00319 (12668)
  covalent geometry    : angle       0.67467 (17172)

*********************** 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
  318 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 284
  time to evaluate  : 3.128 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 TYR cc_start: 0.9058 (t80) cc_final: 0.8691 (t80)
REVERT: A   55 MET cc_start: 0.8842 (tpp) cc_final: 0.8538 (tpt)
REVERT: A   61 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7988 (mmp)
REVERT: A   78 LEU cc_start: 0.9559 (mt) cc_final: 0.9342 (mp)
REVERT: A  186 MET cc_start: 0.4775 (mmp) cc_final: 0.4468 (mmp)
REVERT: A  327 LYS cc_start: 0.9377 (ttmt) cc_final: 0.9034 (tttm)
REVERT: A  474 LYS cc_start: 0.8684 (tmtm) cc_final: 0.8059 (tttm)
REVERT: B   53 TYR cc_start: 0.8870 (t80) cc_final: 0.8492 (t80)
REVERT: B   56 MET cc_start: 0.8914 (mtt) cc_final: 0.8570 (mtt)
REVERT: B   77 MET cc_start: 0.8779 (tpp) cc_final: 0.8401 (tpp)
REVERT: B  134 CYS cc_start: 0.9225 (m) cc_final: 0.8991 (m)
REVERT: B  186 MET cc_start: 0.5295 (mmm) cc_final: 0.5047 (tpt)
REVERT: B  204 ILE cc_start: 0.9566 (tp) cc_final: 0.9328 (tp)
REVERT: B  239 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8634 (mm-30)
REVERT: B  408 SER cc_start: 0.9540 (m) cc_final: 0.9051 (p)
REVERT: B  474 LYS cc_start: 0.8652 (tmtm) cc_final: 0.8034 (tttm)
REVERT: C   53 TYR cc_start: 0.8764 (t80) cc_final: 0.7521 (t80)
REVERT: C   77 MET cc_start: 0.8893 (tpp) cc_final: 0.7950 (tmm)
REVERT: C  134 CYS cc_start: 0.9327 (m) cc_final: 0.9062 (m)
REVERT: C  201 TYR cc_start: 0.9240 (t80) cc_final: 0.8851 (t80)
REVERT: C  239 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8581 (mm-30)
REVERT: C  401 ASN cc_start: 0.9208 (t0) cc_final: 0.8959 (t0)
REVERT: C  408 SER cc_start: 0.9469 (m) cc_final: 0.9091 (p)
REVERT: C  474 LYS cc_start: 0.8624 (tmtm) cc_final: 0.8078 (tttm)
REVERT: D   13 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8652 (tp)
REVERT: D  134 CYS cc_start: 0.9373 (m) cc_final: 0.9092 (m)
REVERT: D  186 MET cc_start: 0.4424 (mmm) cc_final: 0.4135 (mmt)
REVERT: D  206 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8885 (ttp)
REVERT: D  355 MET cc_start: 0.9221 (mmm) cc_final: 0.8963 (mmm)
REVERT: D  408 SER cc_start: 0.9402 (m) cc_final: 0.9055 (p)
REVERT: D  474 LYS cc_start: 0.8625 (tmtm) cc_final: 0.8062 (tttm)
  outliers start: 34
  outliers final: 28
  residues processed: 303
  average time/residue: 0.2882
  time to fit residues: 140.0842
Evaluate side-chains
  301 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 270
  time to evaluate  : 1.586 
-------------------------------------------------------------------------------
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  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   47 LEU
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 C residue  321 LEU
Chi-restraints excluded: chain D residue    4 LYS
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  206 MET
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  351 LEU
Chi-restraints excluded: chain D residue  450 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 98 optimal weight:    0.6980
   chunk 23 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 114 optimal weight:    7.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
C  15 ASN
D  15 ASN
D 401 ASN
** D 435 GLN ** 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 = 0.3367 r_free = 0.3367 target = 0.074127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.065791 restraints weight = 42274.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.067679 restraints weight = 19938.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.068871 restraints weight = 11472.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.5061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12668  Z= 0.147
  Angle     :  0.691  12.801  17172  Z= 0.345
  Chirality :  0.043   0.274   2008
  Planarity :  0.003   0.025   2080
  Dihedral  :  4.003  15.567   1668
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 20.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.22), residues: 1528
  helix:  1.94 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -2.31 (0.30), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 146 
 HIS   0.002   0.001   HIS B  82 
 PHE   0.036   0.001   PHE D 141 
 TYR   0.014   0.001   TYR D 385 
 ARG   0.001   0.000   ARG D 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03465 (  860)
  hydrogen bonds       : angle       3.65684 ( 2544)
  covalent geometry    : bond        0.00334 (12668)
  covalent geometry    : angle       0.69053 (17172)

********************** 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
  312 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 279
  time to evaluate  : 1.533 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 TYR cc_start: 0.9043 (t80) cc_final: 0.8625 (t80)
REVERT: A   55 MET cc_start: 0.8827 (tpp) cc_final: 0.8542 (tpt)
REVERT: A   61 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7982 (mmp)
REVERT: A  186 MET cc_start: 0.4604 (mmp) cc_final: 0.4284 (mmp)
REVERT: A  327 LYS cc_start: 0.9377 (ttmt) cc_final: 0.9034 (tttm)
REVERT: A  408 SER cc_start: 0.9310 (m) cc_final: 0.9065 (p)
REVERT: A  415 TYR cc_start: 0.8684 (t80) cc_final: 0.8433 (t80)
REVERT: A  474 LYS cc_start: 0.8679 (tmtm) cc_final: 0.8057 (tttm)
REVERT: B   53 TYR cc_start: 0.8832 (t80) cc_final: 0.8558 (t80)
REVERT: B   56 MET cc_start: 0.8813 (mtt) cc_final: 0.8564 (mtt)
REVERT: B   77 MET cc_start: 0.8748 (tpp) cc_final: 0.8434 (tpp)
REVERT: B  134 CYS cc_start: 0.9240 (m) cc_final: 0.8998 (m)
REVERT: B  186 MET cc_start: 0.5286 (mmm) cc_final: 0.5046 (tpt)
REVERT: B  239 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8635 (mm-30)
REVERT: B  408 SER cc_start: 0.9538 (m) cc_final: 0.9057 (p)
REVERT: B  474 LYS cc_start: 0.8628 (tmtm) cc_final: 0.8009 (tttm)
REVERT: C   53 TYR cc_start: 0.8822 (t80) cc_final: 0.7437 (t80)
REVERT: C   61 MET cc_start: 0.8158 (mmp) cc_final: 0.7627 (mtm)
REVERT: C   77 MET cc_start: 0.8880 (tpp) cc_final: 0.7943 (tmm)
REVERT: C  134 CYS cc_start: 0.9331 (m) cc_final: 0.9062 (m)
REVERT: C  201 TYR cc_start: 0.9214 (t80) cc_final: 0.8849 (t80)
REVERT: C  239 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8622 (mm-30)
REVERT: C  401 ASN cc_start: 0.9185 (t0) cc_final: 0.8945 (t0)
REVERT: C  406 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8178 (mm-30)
REVERT: C  408 SER cc_start: 0.9464 (m) cc_final: 0.9089 (p)
REVERT: C  474 LYS cc_start: 0.8621 (tmtm) cc_final: 0.8071 (tttm)
REVERT: D   13 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8676 (tp)
REVERT: D   77 MET cc_start: 0.8808 (mmm) cc_final: 0.8352 (tmm)
REVERT: D  134 CYS cc_start: 0.9375 (m) cc_final: 0.9100 (m)
REVERT: D  206 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8883 (ttp)
REVERT: D  355 MET cc_start: 0.9208 (mmm) cc_final: 0.8946 (mmm)
REVERT: D  408 SER cc_start: 0.9416 (m) cc_final: 0.9073 (p)
REVERT: D  415 TYR cc_start: 0.8463 (t80) cc_final: 0.8103 (t80)
REVERT: D  474 LYS cc_start: 0.8628 (tmtm) cc_final: 0.8061 (tttm)
  outliers start: 33
  outliers final: 27
  residues processed: 298
  average time/residue: 0.1875
  time to fit residues: 87.6743
Evaluate side-chains
  301 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 271
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
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  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   47 LEU
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 C residue  321 LEU
Chi-restraints excluded: chain D residue    4 LYS
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  206 MET
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  450 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 48 optimal weight:    0.0050
   chunk 46 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 147 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   chunk 102 optimal weight:    6.9990
   chunk 136 optimal weight:    0.0570
   chunk 7 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.5712

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

Flipped N/Q/H residues before XYZ refinement:
B  15 ASN
C  15 ASN
D   6 GLN
** D 435 GLN ** 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 = 0.3388 r_free = 0.3388 target = 0.075174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.066743 restraints weight = 42565.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.068646 restraints weight = 20198.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.069857 restraints weight = 11662.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
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   0.047  12668  Z= 0.131
  Angle     :  0.698  13.255  17172  Z= 0.344
  Chirality :  0.042   0.230   2008
  Planarity :  0.003   0.029   2080
  Dihedral  :  3.965  18.113   1668
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.29 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.21), residues: 1528
  helix:  1.99 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -2.38 (0.30), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 219 
 HIS   0.003   0.001   HIS B  24 
 PHE   0.035   0.001   PHE D 141 
 TYR   0.012   0.001   TYR D 385 
 ARG   0.002   0.000   ARG B 178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03456 (  860)
  hydrogen bonds       : angle       3.63174 ( 2544)
  covalent geometry    : bond        0.00296 (12668)
  covalent geometry    : angle       0.69768 (17172)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4049.57 seconds
wall clock time: 72 minutes 50.27 seconds (4370.27 seconds total)