Starting phenix.real_space_refine
on Wed Jan 15 02:13:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v8b_43033/01_2025/8v8b_43033.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v8b_43033/01_2025/8v8b_43033.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v8b_43033/01_2025/8v8b_43033.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v8b_43033/01_2025/8v8b_43033.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v8b_43033/01_2025/8v8b_43033.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v8b_43033/01_2025/8v8b_43033.cif"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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     156      5.16       5
     C   31733      2.51       5
     N    8528      2.21       5
     O   10283      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 50700
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 476, 3900
          Classifications: {'peptide': 476}
          Link IDs: {'PTRANS': 10, 'TRANS': 465}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, M, L
  Time building chain proxies: 9.59, per 1000 atoms: 0.19
  Number of scatterers: 50700
  At special positions: 0
  Unit cell: (186.84, 186.84, 137.16, 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     156     16.00
     O   10283      8.00
     N    8528      7.00
     C   31733      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: 9.30
  Conformation dependent library (CDL) restraints added in 4.6 seconds
  

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  11752

  Finding SS restraints...
    Secondary structure from input PDB file:
      247 helices and 65 sheets defined
      51.1% alpha, 14.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 4.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 14
      removed outlier: 3.795A  pdb=" N   ARG A  14 " --> pdb=" O   THR A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 15 through 22
    Processing helix  chain 'A' and resid 34 through 41
      removed outlier: 3.615A  pdb=" N   GLN A  40 " --> pdb=" O   SER A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 68
      removed outlier: 3.692A  pdb=" N   SER A  46 " --> pdb=" O   VAL A  42 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS A  47 " --> pdb=" O   ASN A  43 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   ARG A  57 " --> pdb=" O   MET A  53 " (cutoff:3.500A)
      Proline residue:  A  58  - end of helix
    Processing helix  chain 'A' and resid 71 through 76
      removed outlier: 3.704A  pdb=" N   VAL A  75 " --> pdb=" O   THR A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 108
      removed outlier: 3.559A  pdb=" N   TYR A  97 " --> pdb=" O   ASP A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 132
    Processing helix  chain 'A' and resid 132 through 148
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'A' and resid 258 through 260
      No H-bonds generated for 'chain 'A' and resid 258 through 260'
    Processing helix  chain 'A' and resid 261 through 284
    Processing helix  chain 'A' and resid 296 through 307
    Processing helix  chain 'A' and resid 338 through 341
    Processing helix  chain 'A' and resid 342 through 358
    Processing helix  chain 'A' and resid 373 through 411
      removed outlier: 3.666A  pdb=" N   TYR A 378 " --> pdb=" O   GLU A 374 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG A 386 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 424
      removed outlier: 4.102A  pdb=" N   THR A 423 " --> pdb=" O   ASP A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 446
    Processing helix  chain 'A' and resid 451 through 459
      removed outlier: 3.634A  pdb=" N   PHE A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 475
      removed outlier: 3.905A  pdb=" N   GLU A 468 " --> pdb=" O   ASP A 464 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL A 469 " --> pdb=" O   PRO A 465 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LYS A 470 " --> pdb=" O   GLU A 466 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 14
      removed outlier: 3.795A  pdb=" N   ARG B  14 " --> pdb=" O   THR B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 22
    Processing helix  chain 'B' and resid 34 through 41
      removed outlier: 3.615A  pdb=" N   GLN B  40 " --> pdb=" O   SER B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 68
      removed outlier: 3.692A  pdb=" N   SER B  46 " --> pdb=" O   VAL B  42 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LYS B  47 " --> pdb=" O   ASN B  43 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   ARG B  57 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      Proline residue:  B  58  - end of helix
    Processing helix  chain 'B' and resid 71 through 76
      removed outlier: 3.704A  pdb=" N   VAL B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 108
      removed outlier: 3.559A  pdb=" N   TYR B  97 " --> pdb=" O   ASP B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 132
    Processing helix  chain 'B' and resid 132 through 148
    Processing helix  chain 'B' and resid 223 through 225
      No H-bonds generated for 'chain 'B' and resid 223 through 225'
    Processing helix  chain 'B' and resid 258 through 260
      No H-bonds generated for 'chain 'B' and resid 258 through 260'
    Processing helix  chain 'B' and resid 261 through 284
    Processing helix  chain 'B' and resid 296 through 307
    Processing helix  chain 'B' and resid 338 through 341
    Processing helix  chain 'B' and resid 342 through 358
    Processing helix  chain 'B' and resid 373 through 411
      removed outlier: 3.665A  pdb=" N   TYR B 378 " --> pdb=" O   GLU B 374 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ARG B 386 " --> pdb=" O   GLY B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 420 through 424
      removed outlier: 4.102A  pdb=" N   THR B 423 " --> pdb=" O   ASP B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 446
    Processing helix  chain 'B' and resid 451 through 459
      removed outlier: 3.634A  pdb=" N   PHE B 459 " --> pdb=" O   LEU B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 464 through 475
      removed outlier: 3.906A  pdb=" N   GLU B 468 " --> pdb=" O   ASP B 464 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL B 469 " --> pdb=" O   PRO B 465 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LYS B 470 " --> pdb=" O   GLU B 466 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 14
      removed outlier: 3.794A  pdb=" N   ARG C  14 " --> pdb=" O   THR C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 15 through 22
    Processing helix  chain 'C' and resid 34 through 41
      removed outlier: 3.615A  pdb=" N   GLN C  40 " --> pdb=" O   SER C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 68
      removed outlier: 3.693A  pdb=" N   SER C  46 " --> pdb=" O   VAL C  42 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LYS C  47 " --> pdb=" O   ASN C  43 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   ARG C  57 " --> pdb=" O   MET C  53 " (cutoff:3.500A)
      Proline residue:  C  58  - end of helix
    Processing helix  chain 'C' and resid 71 through 76
      removed outlier: 3.704A  pdb=" N   VAL C  75 " --> pdb=" O   THR C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 108
      removed outlier: 3.559A  pdb=" N   TYR C  97 " --> pdb=" O   ASP C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 132
    Processing helix  chain 'C' and resid 132 through 148
    Processing helix  chain 'C' and resid 223 through 225
      No H-bonds generated for 'chain 'C' and resid 223 through 225'
    Processing helix  chain 'C' and resid 258 through 260
      No H-bonds generated for 'chain 'C' and resid 258 through 260'
    Processing helix  chain 'C' and resid 261 through 284
    Processing helix  chain 'C' and resid 296 through 307
    Processing helix  chain 'C' and resid 338 through 341
    Processing helix  chain 'C' and resid 342 through 358
    Processing helix  chain 'C' and resid 373 through 411
      removed outlier: 3.665A  pdb=" N   TYR C 378 " --> pdb=" O   GLU C 374 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG C 386 " --> pdb=" O   GLY C 382 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 420 through 424
      removed outlier: 4.101A  pdb=" N   THR C 423 " --> pdb=" O   ASP C 420 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 435 through 446
    Processing helix  chain 'C' and resid 451 through 459
      removed outlier: 3.634A  pdb=" N   PHE C 459 " --> pdb=" O   LEU C 455 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 464 through 475
      removed outlier: 3.905A  pdb=" N   GLU C 468 " --> pdb=" O   ASP C 464 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL C 469 " --> pdb=" O   PRO C 465 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   LYS C 470 " --> pdb=" O   GLU C 466 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 14
      removed outlier: 3.794A  pdb=" N   ARG D  14 " --> pdb=" O   THR D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 15 through 22
    Processing helix  chain 'D' and resid 34 through 41
      removed outlier: 3.614A  pdb=" N   GLN D  40 " --> pdb=" O   SER D  36 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 42 through 68
      removed outlier: 3.693A  pdb=" N   SER D  46 " --> pdb=" O   VAL D  42 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS D  47 " --> pdb=" O   ASN D  43 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   ARG D  57 " --> pdb=" O   MET D  53 " (cutoff:3.500A)
      Proline residue:  D  58  - end of helix
    Processing helix  chain 'D' and resid 71 through 76
      removed outlier: 3.704A  pdb=" N   VAL D  75 " --> pdb=" O   THR D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 93 through 108
      removed outlier: 3.559A  pdb=" N   TYR D  97 " --> pdb=" O   ASP D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 117 through 132
    Processing helix  chain 'D' and resid 132 through 148
    Processing helix  chain 'D' and resid 223 through 225
      No H-bonds generated for 'chain 'D' and resid 223 through 225'
    Processing helix  chain 'D' and resid 258 through 260
      No H-bonds generated for 'chain 'D' and resid 258 through 260'
    Processing helix  chain 'D' and resid 261 through 284
    Processing helix  chain 'D' and resid 296 through 307
    Processing helix  chain 'D' and resid 338 through 341
    Processing helix  chain 'D' and resid 342 through 358
    Processing helix  chain 'D' and resid 373 through 411
      removed outlier: 3.665A  pdb=" N   TYR D 378 " --> pdb=" O   GLU D 374 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ARG D 386 " --> pdb=" O   GLY D 382 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 420 through 424
      removed outlier: 4.102A  pdb=" N   THR D 423 " --> pdb=" O   ASP D 420 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 435 through 446
    Processing helix  chain 'D' and resid 451 through 459
      removed outlier: 3.634A  pdb=" N   PHE D 459 " --> pdb=" O   LEU D 455 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 464 through 475
      removed outlier: 3.905A  pdb=" N   GLU D 468 " --> pdb=" O   ASP D 464 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL D 469 " --> pdb=" O   PRO D 465 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LYS D 470 " --> pdb=" O   GLU D 466 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 10 through 14
      removed outlier: 3.795A  pdb=" N   ARG E  14 " --> pdb=" O   THR E  11 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 15 through 22
    Processing helix  chain 'E' and resid 34 through 41
      removed outlier: 3.615A  pdb=" N   GLN E  40 " --> pdb=" O   SER E  36 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 42 through 68
      removed outlier: 3.692A  pdb=" N   SER E  46 " --> pdb=" O   VAL E  42 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS E  47 " --> pdb=" O   ASN E  43 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   ARG E  57 " --> pdb=" O   MET E  53 " (cutoff:3.500A)
      Proline residue:  E  58  - end of helix
    Processing helix  chain 'E' and resid 71 through 76
      removed outlier: 3.704A  pdb=" N   VAL E  75 " --> pdb=" O   THR E  71 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 93 through 108
      removed outlier: 3.559A  pdb=" N   TYR E  97 " --> pdb=" O   ASP E  93 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 117 through 132
    Processing helix  chain 'E' and resid 132 through 148
    Processing helix  chain 'E' and resid 223 through 225
      No H-bonds generated for 'chain 'E' and resid 223 through 225'
    Processing helix  chain 'E' and resid 258 through 260
      No H-bonds generated for 'chain 'E' and resid 258 through 260'
    Processing helix  chain 'E' and resid 261 through 284
    Processing helix  chain 'E' and resid 296 through 307
    Processing helix  chain 'E' and resid 338 through 341
    Processing helix  chain 'E' and resid 342 through 358
    Processing helix  chain 'E' and resid 373 through 411
      removed outlier: 3.665A  pdb=" N   TYR E 378 " --> pdb=" O   GLU E 374 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG E 386 " --> pdb=" O   GLY E 382 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 420 through 424
      removed outlier: 4.102A  pdb=" N   THR E 423 " --> pdb=" O   ASP E 420 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 435 through 446
    Processing helix  chain 'E' and resid 451 through 459
      removed outlier: 3.634A  pdb=" N   PHE E 459 " --> pdb=" O   LEU E 455 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 464 through 475
      removed outlier: 3.905A  pdb=" N   GLU E 468 " --> pdb=" O   ASP E 464 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL E 469 " --> pdb=" O   PRO E 465 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LYS E 470 " --> pdb=" O   GLU E 466 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 10 through 14
      removed outlier: 3.794A  pdb=" N   ARG F  14 " --> pdb=" O   THR F  11 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 15 through 22
    Processing helix  chain 'F' and resid 34 through 41
      removed outlier: 3.614A  pdb=" N   GLN F  40 " --> pdb=" O   SER F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 42 through 68
      removed outlier: 3.692A  pdb=" N   SER F  46 " --> pdb=" O   VAL F  42 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LYS F  47 " --> pdb=" O   ASN F  43 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   ARG F  57 " --> pdb=" O   MET F  53 " (cutoff:3.500A)
      Proline residue:  F  58  - end of helix
    Processing helix  chain 'F' and resid 71 through 76
      removed outlier: 3.704A  pdb=" N   VAL F  75 " --> pdb=" O   THR F  71 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 93 through 108
      removed outlier: 3.559A  pdb=" N   TYR F  97 " --> pdb=" O   ASP F  93 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 117 through 132
    Processing helix  chain 'F' and resid 132 through 148
    Processing helix  chain 'F' and resid 223 through 225
      No H-bonds generated for 'chain 'F' and resid 223 through 225'
    Processing helix  chain 'F' and resid 258 through 260
      No H-bonds generated for 'chain 'F' and resid 258 through 260'
    Processing helix  chain 'F' and resid 261 through 284
    Processing helix  chain 'F' and resid 296 through 307
    Processing helix  chain 'F' and resid 338 through 341
    Processing helix  chain 'F' and resid 342 through 358
    Processing helix  chain 'F' and resid 373 through 411
      removed outlier: 3.666A  pdb=" N   TYR F 378 " --> pdb=" O   GLU F 374 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG F 386 " --> pdb=" O   GLY F 382 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 420 through 424
      removed outlier: 4.101A  pdb=" N   THR F 423 " --> pdb=" O   ASP F 420 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 435 through 446
    Processing helix  chain 'F' and resid 451 through 459
      removed outlier: 3.634A  pdb=" N   PHE F 459 " --> pdb=" O   LEU F 455 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 464 through 475
      removed outlier: 3.905A  pdb=" N   GLU F 468 " --> pdb=" O   ASP F 464 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL F 469 " --> pdb=" O   PRO F 465 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   LYS F 470 " --> pdb=" O   GLU F 466 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 14
      removed outlier: 3.794A  pdb=" N   ARG G  14 " --> pdb=" O   THR G  11 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 15 through 22
    Processing helix  chain 'G' and resid 34 through 41
      removed outlier: 3.614A  pdb=" N   GLN G  40 " --> pdb=" O   SER G  36 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 42 through 68
      removed outlier: 3.693A  pdb=" N   SER G  46 " --> pdb=" O   VAL G  42 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS G  47 " --> pdb=" O   ASN G  43 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   ARG G  57 " --> pdb=" O   MET G  53 " (cutoff:3.500A)
      Proline residue:  G  58  - end of helix
    Processing helix  chain 'G' and resid 71 through 76
      removed outlier: 3.704A  pdb=" N   VAL G  75 " --> pdb=" O   THR G  71 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 93 through 108
      removed outlier: 3.559A  pdb=" N   TYR G  97 " --> pdb=" O   ASP G  93 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 117 through 132
    Processing helix  chain 'G' and resid 132 through 148
    Processing helix  chain 'G' and resid 223 through 225
      No H-bonds generated for 'chain 'G' and resid 223 through 225'
    Processing helix  chain 'G' and resid 258 through 260
      No H-bonds generated for 'chain 'G' and resid 258 through 260'
    Processing helix  chain 'G' and resid 261 through 284
    Processing helix  chain 'G' and resid 296 through 307
    Processing helix  chain 'G' and resid 338 through 341
    Processing helix  chain 'G' and resid 342 through 358
    Processing helix  chain 'G' and resid 373 through 411
      removed outlier: 3.666A  pdb=" N   TYR G 378 " --> pdb=" O   GLU G 374 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG G 386 " --> pdb=" O   GLY G 382 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 420 through 424
      removed outlier: 4.102A  pdb=" N   THR G 423 " --> pdb=" O   ASP G 420 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 435 through 446
    Processing helix  chain 'G' and resid 451 through 459
      removed outlier: 3.634A  pdb=" N   PHE G 459 " --> pdb=" O   LEU G 455 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 464 through 475
      removed outlier: 3.905A  pdb=" N   GLU G 468 " --> pdb=" O   ASP G 464 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL G 469 " --> pdb=" O   PRO G 465 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   LYS G 470 " --> pdb=" O   GLU G 466 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 10 through 14
      removed outlier: 3.794A  pdb=" N   ARG H  14 " --> pdb=" O   THR H  11 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 15 through 22
    Processing helix  chain 'H' and resid 34 through 41
      removed outlier: 3.615A  pdb=" N   GLN H  40 " --> pdb=" O   SER H  36 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 42 through 68
      removed outlier: 3.691A  pdb=" N   SER H  46 " --> pdb=" O   VAL H  42 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS H  47 " --> pdb=" O   ASN H  43 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   ARG H  57 " --> pdb=" O   MET H  53 " (cutoff:3.500A)
      Proline residue:  H  58  - end of helix
    Processing helix  chain 'H' and resid 71 through 76
      removed outlier: 3.705A  pdb=" N   VAL H  75 " --> pdb=" O   THR H  71 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 93 through 108
      removed outlier: 3.559A  pdb=" N   TYR H  97 " --> pdb=" O   ASP H  93 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 117 through 132
    Processing helix  chain 'H' and resid 132 through 148
    Processing helix  chain 'H' and resid 223 through 225
      No H-bonds generated for 'chain 'H' and resid 223 through 225'
    Processing helix  chain 'H' and resid 258 through 260
      No H-bonds generated for 'chain 'H' and resid 258 through 260'
    Processing helix  chain 'H' and resid 261 through 284
    Processing helix  chain 'H' and resid 296 through 307
    Processing helix  chain 'H' and resid 338 through 341
    Processing helix  chain 'H' and resid 342 through 358
    Processing helix  chain 'H' and resid 373 through 411
      removed outlier: 3.666A  pdb=" N   TYR H 378 " --> pdb=" O   GLU H 374 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ARG H 386 " --> pdb=" O   GLY H 382 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 420 through 424
      removed outlier: 4.102A  pdb=" N   THR H 423 " --> pdb=" O   ASP H 420 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 435 through 446
    Processing helix  chain 'H' and resid 451 through 459
      removed outlier: 3.634A  pdb=" N   PHE H 459 " --> pdb=" O   LEU H 455 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 464 through 475
      removed outlier: 3.905A  pdb=" N   GLU H 468 " --> pdb=" O   ASP H 464 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL H 469 " --> pdb=" O   PRO H 465 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LYS H 470 " --> pdb=" O   GLU H 466 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 10 through 14
      removed outlier: 3.794A  pdb=" N   ARG I  14 " --> pdb=" O   THR I  11 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 15 through 22
    Processing helix  chain 'I' and resid 34 through 41
      removed outlier: 3.615A  pdb=" N   GLN I  40 " --> pdb=" O   SER I  36 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 42 through 68
      removed outlier: 3.692A  pdb=" N   SER I  46 " --> pdb=" O   VAL I  42 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS I  47 " --> pdb=" O   ASN I  43 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   ARG I  57 " --> pdb=" O   MET I  53 " (cutoff:3.500A)
      Proline residue:  I  58  - end of helix
    Processing helix  chain 'I' and resid 71 through 76
      removed outlier: 3.705A  pdb=" N   VAL I  75 " --> pdb=" O   THR I  71 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 93 through 108
      removed outlier: 3.559A  pdb=" N   TYR I  97 " --> pdb=" O   ASP I  93 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 117 through 132
    Processing helix  chain 'I' and resid 132 through 148
    Processing helix  chain 'I' and resid 223 through 225
      No H-bonds generated for 'chain 'I' and resid 223 through 225'
    Processing helix  chain 'I' and resid 258 through 260
      No H-bonds generated for 'chain 'I' and resid 258 through 260'
    Processing helix  chain 'I' and resid 261 through 284
    Processing helix  chain 'I' and resid 296 through 307
    Processing helix  chain 'I' and resid 338 through 341
    Processing helix  chain 'I' and resid 342 through 358
    Processing helix  chain 'I' and resid 373 through 411
      removed outlier: 3.666A  pdb=" N   TYR I 378 " --> pdb=" O   GLU I 374 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG I 386 " --> pdb=" O   GLY I 382 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 420 through 424
      removed outlier: 4.102A  pdb=" N   THR I 423 " --> pdb=" O   ASP I 420 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 435 through 446
    Processing helix  chain 'I' and resid 451 through 459
      removed outlier: 3.634A  pdb=" N   PHE I 459 " --> pdb=" O   LEU I 455 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 464 through 475
      removed outlier: 3.905A  pdb=" N   GLU I 468 " --> pdb=" O   ASP I 464 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL I 469 " --> pdb=" O   PRO I 465 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LYS I 470 " --> pdb=" O   GLU I 466 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 10 through 14
      removed outlier: 3.794A  pdb=" N   ARG J  14 " --> pdb=" O   THR J  11 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 15 through 22
    Processing helix  chain 'J' and resid 34 through 41
      removed outlier: 3.614A  pdb=" N   GLN J  40 " --> pdb=" O   SER J  36 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 42 through 68
      removed outlier: 3.692A  pdb=" N   SER J  46 " --> pdb=" O   VAL J  42 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS J  47 " --> pdb=" O   ASN J  43 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   ARG J  57 " --> pdb=" O   MET J  53 " (cutoff:3.500A)
      Proline residue:  J  58  - end of helix
    Processing helix  chain 'J' and resid 71 through 76
      removed outlier: 3.704A  pdb=" N   VAL J  75 " --> pdb=" O   THR J  71 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 93 through 108
      removed outlier: 3.559A  pdb=" N   TYR J  97 " --> pdb=" O   ASP J  93 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 117 through 132
    Processing helix  chain 'J' and resid 132 through 148
    Processing helix  chain 'J' and resid 223 through 225
      No H-bonds generated for 'chain 'J' and resid 223 through 225'
    Processing helix  chain 'J' and resid 258 through 260
      No H-bonds generated for 'chain 'J' and resid 258 through 260'
    Processing helix  chain 'J' and resid 261 through 284
    Processing helix  chain 'J' and resid 296 through 307
    Processing helix  chain 'J' and resid 338 through 341
    Processing helix  chain 'J' and resid 342 through 358
    Processing helix  chain 'J' and resid 373 through 411
      removed outlier: 3.666A  pdb=" N   TYR J 378 " --> pdb=" O   GLU J 374 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG J 386 " --> pdb=" O   GLY J 382 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 420 through 424
      removed outlier: 4.102A  pdb=" N   THR J 423 " --> pdb=" O   ASP J 420 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 435 through 446
    Processing helix  chain 'J' and resid 451 through 459
      removed outlier: 3.634A  pdb=" N   PHE J 459 " --> pdb=" O   LEU J 455 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 464 through 475
      removed outlier: 3.906A  pdb=" N   GLU J 468 " --> pdb=" O   ASP J 464 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL J 469 " --> pdb=" O   PRO J 465 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LYS J 470 " --> pdb=" O   GLU J 466 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 10 through 14
      removed outlier: 3.794A  pdb=" N   ARG K  14 " --> pdb=" O   THR K  11 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 15 through 22
    Processing helix  chain 'K' and resid 34 through 41
      removed outlier: 3.615A  pdb=" N   GLN K  40 " --> pdb=" O   SER K  36 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 42 through 68
      removed outlier: 3.692A  pdb=" N   SER K  46 " --> pdb=" O   VAL K  42 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LYS K  47 " --> pdb=" O   ASN K  43 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   ARG K  57 " --> pdb=" O   MET K  53 " (cutoff:3.500A)
      Proline residue:  K  58  - end of helix
    Processing helix  chain 'K' and resid 71 through 76
      removed outlier: 3.705A  pdb=" N   VAL K  75 " --> pdb=" O   THR K  71 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 93 through 108
      removed outlier: 3.558A  pdb=" N   TYR K  97 " --> pdb=" O   ASP K  93 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 117 through 132
    Processing helix  chain 'K' and resid 132 through 148
    Processing helix  chain 'K' and resid 223 through 225
      No H-bonds generated for 'chain 'K' and resid 223 through 225'
    Processing helix  chain 'K' and resid 258 through 260
      No H-bonds generated for 'chain 'K' and resid 258 through 260'
    Processing helix  chain 'K' and resid 261 through 284
    Processing helix  chain 'K' and resid 296 through 307
    Processing helix  chain 'K' and resid 338 through 341
    Processing helix  chain 'K' and resid 342 through 358
    Processing helix  chain 'K' and resid 373 through 411
      removed outlier: 3.666A  pdb=" N   TYR K 378 " --> pdb=" O   GLU K 374 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG K 386 " --> pdb=" O   GLY K 382 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 420 through 424
      removed outlier: 4.102A  pdb=" N   THR K 423 " --> pdb=" O   ASP K 420 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 435 through 446
    Processing helix  chain 'K' and resid 451 through 459
      removed outlier: 3.634A  pdb=" N   PHE K 459 " --> pdb=" O   LEU K 455 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 464 through 475
      removed outlier: 3.905A  pdb=" N   GLU K 468 " --> pdb=" O   ASP K 464 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL K 469 " --> pdb=" O   PRO K 465 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   LYS K 470 " --> pdb=" O   GLU K 466 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 10 through 14
      removed outlier: 3.794A  pdb=" N   ARG L  14 " --> pdb=" O   THR L  11 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 15 through 22
    Processing helix  chain 'L' and resid 34 through 41
      removed outlier: 3.614A  pdb=" N   GLN L  40 " --> pdb=" O   SER L  36 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 42 through 68
      removed outlier: 3.691A  pdb=" N   SER L  46 " --> pdb=" O   VAL L  42 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS L  47 " --> pdb=" O   ASN L  43 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   ARG L  57 " --> pdb=" O   MET L  53 " (cutoff:3.500A)
      Proline residue:  L  58  - end of helix
    Processing helix  chain 'L' and resid 71 through 76
      removed outlier: 3.704A  pdb=" N   VAL L  75 " --> pdb=" O   THR L  71 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 93 through 108
      removed outlier: 3.559A  pdb=" N   TYR L  97 " --> pdb=" O   ASP L  93 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 117 through 132
    Processing helix  chain 'L' and resid 132 through 148
    Processing helix  chain 'L' and resid 223 through 225
      No H-bonds generated for 'chain 'L' and resid 223 through 225'
    Processing helix  chain 'L' and resid 258 through 260
      No H-bonds generated for 'chain 'L' and resid 258 through 260'
    Processing helix  chain 'L' and resid 261 through 284
    Processing helix  chain 'L' and resid 296 through 307
    Processing helix  chain 'L' and resid 338 through 341
    Processing helix  chain 'L' and resid 342 through 358
    Processing helix  chain 'L' and resid 373 through 411
      removed outlier: 3.666A  pdb=" N   TYR L 378 " --> pdb=" O   GLU L 374 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG L 386 " --> pdb=" O   GLY L 382 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 420 through 424
      removed outlier: 4.102A  pdb=" N   THR L 423 " --> pdb=" O   ASP L 420 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 435 through 446
    Processing helix  chain 'L' and resid 451 through 459
      removed outlier: 3.634A  pdb=" N   PHE L 459 " --> pdb=" O   LEU L 455 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 464 through 475
      removed outlier: 3.905A  pdb=" N   GLU L 468 " --> pdb=" O   ASP L 464 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL L 469 " --> pdb=" O   PRO L 465 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LYS L 470 " --> pdb=" O   GLU L 466 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 10 through 14
      removed outlier: 3.795A  pdb=" N   ARG M  14 " --> pdb=" O   THR M  11 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 15 through 22
    Processing helix  chain 'M' and resid 34 through 41
      removed outlier: 3.615A  pdb=" N   GLN M  40 " --> pdb=" O   SER M  36 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 42 through 68
      removed outlier: 3.692A  pdb=" N   SER M  46 " --> pdb=" O   VAL M  42 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS M  47 " --> pdb=" O   ASN M  43 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   ARG M  57 " --> pdb=" O   MET M  53 " (cutoff:3.500A)
      Proline residue:  M  58  - end of helix
    Processing helix  chain 'M' and resid 71 through 76
      removed outlier: 3.704A  pdb=" N   VAL M  75 " --> pdb=" O   THR M  71 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 93 through 108
      removed outlier: 3.559A  pdb=" N   TYR M  97 " --> pdb=" O   ASP M  93 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 117 through 132
    Processing helix  chain 'M' and resid 132 through 148
    Processing helix  chain 'M' and resid 223 through 225
      No H-bonds generated for 'chain 'M' and resid 223 through 225'
    Processing helix  chain 'M' and resid 258 through 260
      No H-bonds generated for 'chain 'M' and resid 258 through 260'
    Processing helix  chain 'M' and resid 261 through 284
    Processing helix  chain 'M' and resid 296 through 307
    Processing helix  chain 'M' and resid 338 through 341
    Processing helix  chain 'M' and resid 342 through 358
    Processing helix  chain 'M' and resid 373 through 411
      removed outlier: 3.666A  pdb=" N   TYR M 378 " --> pdb=" O   GLU M 374 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ARG M 386 " --> pdb=" O   GLY M 382 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 420 through 424
      removed outlier: 4.102A  pdb=" N   THR M 423 " --> pdb=" O   ASP M 420 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 435 through 446
    Processing helix  chain 'M' and resid 451 through 459
      removed outlier: 3.634A  pdb=" N   PHE M 459 " --> pdb=" O   LEU M 455 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 464 through 475
      removed outlier: 3.905A  pdb=" N   GLU M 468 " --> pdb=" O   ASP M 464 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL M 469 " --> pdb=" O   PRO M 465 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LYS M 470 " --> pdb=" O   GLU M 466 " (cutoff:3.500A)
    Processing sheet with id=1, first strand: chain 'A' and resid 30 through 31
      removed outlier: 6.146A  pdb=" N   ASP A 177 " --> pdb=" O   SER A 184 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   SER A 184 " --> pdb=" O   ASP A 177 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   VAL A 215 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
      removed outlier: 8.844A  pdb=" N   ASN A 233 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ARG A 217 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'A' and resid 112 through 114
    Processing sheet with id=3, first strand: chain 'A' and resid 162 through 167
      removed outlier: 4.195A  pdb=" N   TYR A 151 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
    Processing sheet with id=4, first strand: chain 'A' and resid 286 through 291
      removed outlier: 3.838A  pdb=" N   MET A 286 " --> pdb=" O   ILE A 333 " (cutoff:3.500A)
    Processing sheet with id=5, first strand: chain 'A' and resid 315 through 317
    Processing sheet with id=6, first strand: chain 'B' and resid 30 through 31
      removed outlier: 6.146A  pdb=" N   ASP B 177 " --> pdb=" O   SER B 184 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   SER B 184 " --> pdb=" O   ASP B 177 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   VAL B 215 " --> pdb=" O   ASN B 233 " (cutoff:3.500A)
      removed outlier: 8.844A  pdb=" N   ASN B 233 " --> pdb=" O   VAL B 215 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ARG B 217 " --> pdb=" O   ARG B 231 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'B' and resid 112 through 114
    Processing sheet with id=8, first strand: chain 'B' and resid 162 through 167
      removed outlier: 4.195A  pdb=" N   TYR B 151 " --> pdb=" O   SER B 167 " (cutoff:3.500A)
    Processing sheet with id=9, first strand: chain 'B' and resid 286 through 291
      removed outlier: 3.837A  pdb=" N   MET B 286 " --> pdb=" O   ILE B 333 " (cutoff:3.500A)
    Processing sheet with id=10, first strand: chain 'B' and resid 315 through 317
    Processing sheet with id=11, first strand: chain 'C' and resid 30 through 31
      removed outlier: 6.146A  pdb=" N   ASP C 177 " --> pdb=" O   SER C 184 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   SER C 184 " --> pdb=" O   ASP C 177 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   VAL C 215 " --> pdb=" O   ASN C 233 " (cutoff:3.500A)
      removed outlier: 8.844A  pdb=" N   ASN C 233 " --> pdb=" O   VAL C 215 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ARG C 217 " --> pdb=" O   ARG C 231 " (cutoff:3.500A)
    Processing sheet with id=12, first strand: chain 'C' and resid 112 through 114
    Processing sheet with id=13, first strand: chain 'C' and resid 162 through 167
      removed outlier: 4.195A  pdb=" N   TYR C 151 " --> pdb=" O   SER C 167 " (cutoff:3.500A)
    Processing sheet with id=14, first strand: chain 'C' and resid 286 through 291
      removed outlier: 3.838A  pdb=" N   MET C 286 " --> pdb=" O   ILE C 333 " (cutoff:3.500A)
    Processing sheet with id=15, first strand: chain 'C' and resid 315 through 317
    Processing sheet with id=16, first strand: chain 'D' and resid 30 through 31
      removed outlier: 6.146A  pdb=" N   ASP D 177 " --> pdb=" O   SER D 184 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   SER D 184 " --> pdb=" O   ASP D 177 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   VAL D 215 " --> pdb=" O   ASN D 233 " (cutoff:3.500A)
      removed outlier: 8.844A  pdb=" N   ASN D 233 " --> pdb=" O   VAL D 215 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   ARG D 217 " --> pdb=" O   ARG D 231 " (cutoff:3.500A)
    Processing sheet with id=17, first strand: chain 'D' and resid 112 through 114
    Processing sheet with id=18, first strand: chain 'D' and resid 162 through 167
      removed outlier: 4.195A  pdb=" N   TYR D 151 " --> pdb=" O   SER D 167 " (cutoff:3.500A)
    Processing sheet with id=19, first strand: chain 'D' and resid 286 through 291
      removed outlier: 3.837A  pdb=" N   MET D 286 " --> pdb=" O   ILE D 333 " (cutoff:3.500A)
    Processing sheet with id=20, first strand: chain 'D' and resid 315 through 317
    Processing sheet with id=21, first strand: chain 'E' and resid 30 through 31
      removed outlier: 6.146A  pdb=" N   ASP E 177 " --> pdb=" O   SER E 184 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   SER E 184 " --> pdb=" O   ASP E 177 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   VAL E 215 " --> pdb=" O   ASN E 233 " (cutoff:3.500A)
      removed outlier: 8.844A  pdb=" N   ASN E 233 " --> pdb=" O   VAL E 215 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ARG E 217 " --> pdb=" O   ARG E 231 " (cutoff:3.500A)
    Processing sheet with id=22, first strand: chain 'E' and resid 112 through 114
    Processing sheet with id=23, first strand: chain 'E' and resid 162 through 167
      removed outlier: 4.195A  pdb=" N   TYR E 151 " --> pdb=" O   SER E 167 " (cutoff:3.500A)
    Processing sheet with id=24, first strand: chain 'E' and resid 286 through 291
      removed outlier: 3.838A  pdb=" N   MET E 286 " --> pdb=" O   ILE E 333 " (cutoff:3.500A)
    Processing sheet with id=25, first strand: chain 'E' and resid 315 through 317
    Processing sheet with id=26, first strand: chain 'F' and resid 30 through 31
      removed outlier: 6.146A  pdb=" N   ASP F 177 " --> pdb=" O   SER F 184 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   SER F 184 " --> pdb=" O   ASP F 177 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   VAL F 215 " --> pdb=" O   ASN F 233 " (cutoff:3.500A)
      removed outlier: 8.844A  pdb=" N   ASN F 233 " --> pdb=" O   VAL F 215 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ARG F 217 " --> pdb=" O   ARG F 231 " (cutoff:3.500A)
    Processing sheet with id=27, first strand: chain 'F' and resid 112 through 114
    Processing sheet with id=28, first strand: chain 'F' and resid 162 through 167
      removed outlier: 4.195A  pdb=" N   TYR F 151 " --> pdb=" O   SER F 167 " (cutoff:3.500A)
    Processing sheet with id=29, first strand: chain 'F' and resid 286 through 291
      removed outlier: 3.838A  pdb=" N   MET F 286 " --> pdb=" O   ILE F 333 " (cutoff:3.500A)
    Processing sheet with id=30, first strand: chain 'F' and resid 315 through 317
    Processing sheet with id=31, first strand: chain 'G' and resid 30 through 31
      removed outlier: 6.146A  pdb=" N   ASP G 177 " --> pdb=" O   SER G 184 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   SER G 184 " --> pdb=" O   ASP G 177 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   VAL G 215 " --> pdb=" O   ASN G 233 " (cutoff:3.500A)
      removed outlier: 8.845A  pdb=" N   ASN G 233 " --> pdb=" O   VAL G 215 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ARG G 217 " --> pdb=" O   ARG G 231 " (cutoff:3.500A)
    Processing sheet with id=32, first strand: chain 'G' and resid 112 through 114
    Processing sheet with id=33, first strand: chain 'G' and resid 162 through 167
      removed outlier: 4.195A  pdb=" N   TYR G 151 " --> pdb=" O   SER G 167 " (cutoff:3.500A)
    Processing sheet with id=34, first strand: chain 'G' and resid 286 through 291
      removed outlier: 3.837A  pdb=" N   MET G 286 " --> pdb=" O   ILE G 333 " (cutoff:3.500A)
    Processing sheet with id=35, first strand: chain 'G' and resid 315 through 317
    Processing sheet with id=36, first strand: chain 'H' and resid 30 through 31
      removed outlier: 6.146A  pdb=" N   ASP H 177 " --> pdb=" O   SER H 184 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   SER H 184 " --> pdb=" O   ASP H 177 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   VAL H 215 " --> pdb=" O   ASN H 233 " (cutoff:3.500A)
      removed outlier: 8.845A  pdb=" N   ASN H 233 " --> pdb=" O   VAL H 215 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ARG H 217 " --> pdb=" O   ARG H 231 " (cutoff:3.500A)
    Processing sheet with id=37, first strand: chain 'H' and resid 112 through 114
    Processing sheet with id=38, first strand: chain 'H' and resid 162 through 167
      removed outlier: 4.196A  pdb=" N   TYR H 151 " --> pdb=" O   SER H 167 " (cutoff:3.500A)
    Processing sheet with id=39, first strand: chain 'H' and resid 286 through 291
      removed outlier: 3.837A  pdb=" N   MET H 286 " --> pdb=" O   ILE H 333 " (cutoff:3.500A)
    Processing sheet with id=40, first strand: chain 'H' and resid 315 through 317
    Processing sheet with id=41, first strand: chain 'I' and resid 30 through 31
      removed outlier: 6.145A  pdb=" N   ASP I 177 " --> pdb=" O   SER I 184 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   SER I 184 " --> pdb=" O   ASP I 177 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   VAL I 215 " --> pdb=" O   ASN I 233 " (cutoff:3.500A)
      removed outlier: 8.844A  pdb=" N   ASN I 233 " --> pdb=" O   VAL I 215 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ARG I 217 " --> pdb=" O   ARG I 231 " (cutoff:3.500A)
    Processing sheet with id=42, first strand: chain 'I' and resid 112 through 114
    Processing sheet with id=43, first strand: chain 'I' and resid 162 through 167
      removed outlier: 4.195A  pdb=" N   TYR I 151 " --> pdb=" O   SER I 167 " (cutoff:3.500A)
    Processing sheet with id=44, first strand: chain 'I' and resid 286 through 291
      removed outlier: 3.838A  pdb=" N   MET I 286 " --> pdb=" O   ILE I 333 " (cutoff:3.500A)
    Processing sheet with id=45, first strand: chain 'I' and resid 315 through 317
    Processing sheet with id=46, first strand: chain 'J' and resid 30 through 31
      removed outlier: 6.145A  pdb=" N   ASP J 177 " --> pdb=" O   SER J 184 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   SER J 184 " --> pdb=" O   ASP J 177 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   VAL J 215 " --> pdb=" O   ASN J 233 " (cutoff:3.500A)
      removed outlier: 8.844A  pdb=" N   ASN J 233 " --> pdb=" O   VAL J 215 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ARG J 217 " --> pdb=" O   ARG J 231 " (cutoff:3.500A)
    Processing sheet with id=47, first strand: chain 'J' and resid 112 through 114
    Processing sheet with id=48, first strand: chain 'J' and resid 162 through 167
      removed outlier: 4.195A  pdb=" N   TYR J 151 " --> pdb=" O   SER J 167 " (cutoff:3.500A)
    Processing sheet with id=49, first strand: chain 'J' and resid 286 through 291
      removed outlier: 3.838A  pdb=" N   MET J 286 " --> pdb=" O   ILE J 333 " (cutoff:3.500A)
    Processing sheet with id=50, first strand: chain 'J' and resid 315 through 317
    Processing sheet with id=51, first strand: chain 'K' and resid 30 through 31
      removed outlier: 6.146A  pdb=" N   ASP K 177 " --> pdb=" O   SER K 184 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   SER K 184 " --> pdb=" O   ASP K 177 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   VAL K 215 " --> pdb=" O   ASN K 233 " (cutoff:3.500A)
      removed outlier: 8.844A  pdb=" N   ASN K 233 " --> pdb=" O   VAL K 215 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   ARG K 217 " --> pdb=" O   ARG K 231 " (cutoff:3.500A)
    Processing sheet with id=52, first strand: chain 'K' and resid 112 through 114
    Processing sheet with id=53, first strand: chain 'K' and resid 162 through 167
      removed outlier: 4.195A  pdb=" N   TYR K 151 " --> pdb=" O   SER K 167 " (cutoff:3.500A)
    Processing sheet with id=54, first strand: chain 'K' and resid 286 through 291
      removed outlier: 3.838A  pdb=" N   MET K 286 " --> pdb=" O   ILE K 333 " (cutoff:3.500A)
    Processing sheet with id=55, first strand: chain 'K' and resid 315 through 317
    Processing sheet with id=56, first strand: chain 'L' and resid 30 through 31
      removed outlier: 6.146A  pdb=" N   ASP L 177 " --> pdb=" O   SER L 184 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   SER L 184 " --> pdb=" O   ASP L 177 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   VAL L 215 " --> pdb=" O   ASN L 233 " (cutoff:3.500A)
      removed outlier: 8.844A  pdb=" N   ASN L 233 " --> pdb=" O   VAL L 215 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ARG L 217 " --> pdb=" O   ARG L 231 " (cutoff:3.500A)
    Processing sheet with id=57, first strand: chain 'L' and resid 112 through 114
    Processing sheet with id=58, first strand: chain 'L' and resid 162 through 167
      removed outlier: 4.195A  pdb=" N   TYR L 151 " --> pdb=" O   SER L 167 " (cutoff:3.500A)
    Processing sheet with id=59, first strand: chain 'L' and resid 286 through 291
      removed outlier: 3.838A  pdb=" N   MET L 286 " --> pdb=" O   ILE L 333 " (cutoff:3.500A)
    Processing sheet with id=60, first strand: chain 'L' and resid 315 through 317
    Processing sheet with id=61, first strand: chain 'M' and resid 30 through 31
      removed outlier: 6.146A  pdb=" N   ASP M 177 " --> pdb=" O   SER M 184 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   SER M 184 " --> pdb=" O   ASP M 177 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   VAL M 215 " --> pdb=" O   ASN M 233 " (cutoff:3.500A)
      removed outlier: 8.844A  pdb=" N   ASN M 233 " --> pdb=" O   VAL M 215 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ARG M 217 " --> pdb=" O   ARG M 231 " (cutoff:3.500A)
    Processing sheet with id=62, first strand: chain 'M' and resid 112 through 114
    Processing sheet with id=63, first strand: chain 'M' and resid 162 through 167
      removed outlier: 4.196A  pdb=" N   TYR M 151 " --> pdb=" O   SER M 167 " (cutoff:3.500A)
    Processing sheet with id=64, first strand: chain 'M' and resid 286 through 291
      removed outlier: 3.837A  pdb=" N   MET M 286 " --> pdb=" O   ILE M 333 " (cutoff:3.500A)
    Processing sheet with id=65, first strand: chain 'M' and resid 315 through 317

    2535 hydrogen bonds defined for protein.
    7371 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: 15.67

  Time building geometry restraints manager: 11.01 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: 16768
        1.34 -     1.46: 7018
        1.46 -     1.58: 27473
        1.58 -     1.70: 0
        1.70 -     1.82: 312
  Bond restraints: 51571
  Sorted by residual:
  bond pdb=" N   MET J   1 "
       pdb=" CA  MET J   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.93e+00
  bond pdb=" N   MET I   1 "
       pdb=" CA  MET I   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.89e+00
  bond pdb=" N   MET L   1 "
       pdb=" CA  MET L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.88e+00
  bond pdb=" N   MET G   1 "
       pdb=" CA  MET G   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.87e+00
  bond pdb=" N   MET C   1 "
       pdb=" CA  MET C   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.86e+00
  ... (remaining 51566 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 61748
        1.32 -     2.65: 6519
        2.65 -     3.97: 1140
        3.97 -     5.29: 106
        5.29 -     6.62: 63
  Bond angle restraints: 69576
  Sorted by residual:
  angle pdb=" CA  GLN F 340 "
        pdb=" CB  GLN F 340 "
        pdb=" CG  GLN F 340 "
      ideal   model   delta    sigma   weight residual
     114.10  120.20   -6.10 2.00e+00 2.50e-01 9.30e+00
  angle pdb=" CA  GLN E 340 "
        pdb=" CB  GLN E 340 "
        pdb=" CG  GLN E 340 "
      ideal   model   delta    sigma   weight residual
     114.10  120.19   -6.09 2.00e+00 2.50e-01 9.28e+00
  angle pdb=" CA  GLN D 340 "
        pdb=" CB  GLN D 340 "
        pdb=" CG  GLN D 340 "
      ideal   model   delta    sigma   weight residual
     114.10  120.19   -6.09 2.00e+00 2.50e-01 9.26e+00
  angle pdb=" CA  GLN H 340 "
        pdb=" CB  GLN H 340 "
        pdb=" CG  GLN H 340 "
      ideal   model   delta    sigma   weight residual
     114.10  120.18   -6.08 2.00e+00 2.50e-01 9.25e+00
  angle pdb=" CA  GLN C 340 "
        pdb=" CB  GLN C 340 "
        pdb=" CG  GLN C 340 "
      ideal   model   delta    sigma   weight residual
     114.10  120.18   -6.08 2.00e+00 2.50e-01 9.25e+00
  ... (remaining 69571 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.17: 27426
       14.17 -    28.34: 2975
       28.34 -    42.51: 682
       42.51 -    56.68: 179
       56.68 -    70.85: 146
  Dihedral angle restraints: 31408
    sinusoidal: 13078
      harmonic: 18330
  Sorted by residual:
  dihedral pdb=" CA  LEU H  20 "
           pdb=" C   LEU H  20 "
           pdb=" N   PHE H  21 "
           pdb=" CA  PHE H  21 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.12  -20.88     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  LEU L  20 "
           pdb=" C   LEU L  20 "
           pdb=" N   PHE L  21 "
           pdb=" CA  PHE L  21 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.13  -20.87     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  LEU I  20 "
           pdb=" C   LEU I  20 "
           pdb=" N   PHE I  21 "
           pdb=" CA  PHE I  21 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.13  -20.87     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 31405 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 4884
       0.047 -    0.095: 1762
       0.095 -    0.142: 697
       0.142 -    0.190: 150
       0.190 -    0.237: 47
  Chirality restraints: 7540
  Sorted by residual:
  chirality pdb=" CA  LYS D 260 "
            pdb=" N   LYS D 260 "
            pdb=" C   LYS D 260 "
            pdb=" CB  LYS D 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CA  LYS M 260 "
            pdb=" N   LYS M 260 "
            pdb=" C   LYS M 260 "
            pdb=" CB  LYS M 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CA  LYS F 260 "
            pdb=" N   LYS F 260 "
            pdb=" C   LYS F 260 "
            pdb=" CB  LYS F 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  ... (remaining 7537 not shown)

  Planarity restraints: 9191
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  84 "   -0.020 2.00e-02 2.50e+03   2.58e-02 1.33e+01
        pdb=" CG  TYR D  84 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  84 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  84 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  84 "    0.013 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  84 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  84 "    0.039 2.00e-02 2.50e+03
        pdb=" OH  TYR D  84 "   -0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR G  84 "   -0.020 2.00e-02 2.50e+03   2.58e-02 1.33e+01
        pdb=" CG  TYR G  84 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR G  84 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR G  84 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR G  84 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR G  84 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR G  84 "    0.039 2.00e-02 2.50e+03
        pdb=" OH  TYR G  84 "   -0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR J  84 "   -0.019 2.00e-02 2.50e+03   2.58e-02 1.33e+01
        pdb=" CG  TYR J  84 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR J  84 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR J  84 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR J  84 "    0.013 2.00e-02 2.50e+03
        pdb=" CE2 TYR J  84 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR J  84 "    0.039 2.00e-02 2.50e+03
        pdb=" OH  TYR J  84 "   -0.038 2.00e-02 2.50e+03
  ... (remaining 9188 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 14685
        2.84 -     3.35: 47980
        3.35 -     3.87: 83996
        3.87 -     4.38: 100203
        4.38 -     4.90: 164026
  Nonbonded interactions: 410890
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN J 340 "
            pdb=" OE1 GLU J 343 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" NE2 GLN I 340 "
            pdb=" OE1 GLU I 343 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" NE2 GLN F 340 "
            pdb=" OE1 GLU F 343 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" NE2 GLN L 340 "
            pdb=" OE1 GLU L 343 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" NE2 GLN B 340 "
            pdb=" OE1 GLU B 343 "
     model   vdw
     2.320 3.120
  ... (remaining 410885 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: 0.31
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.040
  Extract box with map and model:          1.400
  Check model and map are aligned:         0.280
  Set scattering table:                    0.340
  Process input model:                     68.970
  Find NCS groups from input model:        0.880
  Set up NCS constraints:                  0.130
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   85.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  51571  Z= 0.326
  Angle     :  0.873   6.617  69576  Z= 0.536
  Chirality :  0.059   0.237   7540
  Planarity :  0.010   0.102   9191
  Dihedral  : 13.660  70.849  19656
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 1.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  4.62 %
    Favored  : 95.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.09), residues: 6162
  helix: -1.18 (0.08), residues: 2704
  sheet:  1.23 (0.14), residues: 1040
  loop : -0.28 (0.12), residues: 2418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS E 238 
 PHE   0.037   0.003   PHE C 101 
 TYR   0.044   0.005   TYR E  66 
 ARG   0.030   0.003   ARG F 348 

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

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

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1034 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 1021
  time to evaluate  : 4.340 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8650 (mtt) cc_final: 0.8429 (mtt)
REVERT: A  129 ASP cc_start: 0.6959 (t0) cc_final: 0.6610 (t0)
REVERT: A  213 HIS cc_start: 0.6497 (m-70) cc_final: 0.6273 (m170)
REVERT: A  286 MET cc_start: 0.8758 (ttm) cc_final: 0.8317 (mtp)
REVERT: A  376 MET cc_start: 0.8663 (mmm) cc_final: 0.8352 (tpt)
REVERT: A  425 ARG cc_start: 0.7369 (mtm-85) cc_final: 0.7087 (mtm-85)
REVERT: A  452 GLN cc_start: 0.6677 (mm-40) cc_final: 0.6351 (mp-120)
REVERT: A  456 MET cc_start: 0.7546 (mtt) cc_final: 0.7276 (mtt)
REVERT: B   53 MET cc_start: 0.8650 (mtt) cc_final: 0.8361 (mtm)
REVERT: B  163 ARG cc_start: 0.7913 (mmm-85) cc_final: 0.7637 (mmt180)
REVERT: B  211 THR cc_start: 0.8097 (m) cc_final: 0.7860 (p)
REVERT: B  221 ASN cc_start: 0.7799 (p0) cc_final: 0.7309 (p0)
REVERT: B  286 MET cc_start: 0.8812 (ttm) cc_final: 0.8439 (mtp)
REVERT: B  301 ARG cc_start: 0.8247 (mtp-110) cc_final: 0.7972 (mtm-85)
REVERT: B  365 ASP cc_start: 0.8058 (m-30) cc_final: 0.7638 (m-30)
REVERT: B  440 LEU cc_start: 0.8086 (tp) cc_final: 0.7608 (tt)
REVERT: B  452 GLN cc_start: 0.6977 (mm-40) cc_final: 0.6607 (mp10)
REVERT: B  456 MET cc_start: 0.7433 (mtt) cc_final: 0.7194 (mtt)
REVERT: C   53 MET cc_start: 0.8619 (mtt) cc_final: 0.8372 (mtm)
REVERT: C  185 ILE cc_start: 0.8349 (mt) cc_final: 0.7992 (mt)
REVERT: C  211 THR cc_start: 0.8319 (m) cc_final: 0.7994 (p)
REVERT: C  221 ASN cc_start: 0.7823 (p0) cc_final: 0.7607 (p0)
REVERT: C  279 MET cc_start: 0.9145 (mtp) cc_final: 0.8934 (mtp)
REVERT: C  301 ARG cc_start: 0.8335 (mtp-110) cc_final: 0.8090 (mtm-85)
REVERT: C  365 ASP cc_start: 0.7796 (m-30) cc_final: 0.7411 (m-30)
REVERT: C  452 GLN cc_start: 0.6984 (mm-40) cc_final: 0.6590 (mp-120)
REVERT: C  456 MET cc_start: 0.7556 (mtt) cc_final: 0.7284 (mtt)
REVERT: D  189 ARG cc_start: 0.8264 (mtp-110) cc_final: 0.8055 (mtp85)
REVERT: D  209 LEU cc_start: 0.8415 (tt) cc_final: 0.8207 (tp)
REVERT: D  211 THR cc_start: 0.8024 (m) cc_final: 0.7731 (p)
REVERT: D  221 ASN cc_start: 0.7810 (p0) cc_final: 0.7278 (p0)
REVERT: D  286 MET cc_start: 0.8772 (ttm) cc_final: 0.8366 (mtp)
REVERT: D  292 ASN cc_start: 0.8250 (t0) cc_final: 0.7978 (m-40)
REVERT: D  363 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7091 (mppt)
REVERT: E    1 MET cc_start: 0.5031 (mmm) cc_final: 0.4726 (mmt)
REVERT: E   85 MET cc_start: 0.9077 (mtt) cc_final: 0.8804 (mtt)
REVERT: E  163 ARG cc_start: 0.7853 (mmm-85) cc_final: 0.7626 (mmt180)
REVERT: E  182 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7759 (mtp180)
REVERT: E  211 THR cc_start: 0.8361 (m) cc_final: 0.8048 (p)
REVERT: E  229 THR cc_start: 0.7326 (p) cc_final: 0.7004 (t)
REVERT: E  286 MET cc_start: 0.8851 (ttm) cc_final: 0.8360 (mtp)
REVERT: E  301 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7926 (mtm110)
REVERT: E  363 LYS cc_start: 0.8114 (mmtp) cc_final: 0.6921 (mppt)
REVERT: E  425 ARG cc_start: 0.7301 (mtm-85) cc_final: 0.7033 (mtm-85)
REVERT: E  452 GLN cc_start: 0.6873 (mm-40) cc_final: 0.6557 (mp-120)
REVERT: F   53 MET cc_start: 0.8595 (mtt) cc_final: 0.8380 (mtt)
REVERT: F  134 GLU cc_start: 0.7810 (tt0) cc_final: 0.7548 (tt0)
REVERT: F  211 THR cc_start: 0.8198 (m) cc_final: 0.7954 (p)
REVERT: F  362 MET cc_start: 0.8411 (ptm) cc_final: 0.8108 (ptp)
REVERT: F  365 ASP cc_start: 0.7978 (m-30) cc_final: 0.7445 (m-30)
REVERT: F  376 MET cc_start: 0.8688 (mmm) cc_final: 0.8350 (tpt)
REVERT: G  129 ASP cc_start: 0.7036 (t0) cc_final: 0.6642 (t0)
REVERT: G  211 THR cc_start: 0.8185 (m) cc_final: 0.7885 (p)
REVERT: G  213 HIS cc_start: 0.6423 (m-70) cc_final: 0.6208 (m-70)
REVERT: G  221 ASN cc_start: 0.7975 (p0) cc_final: 0.7404 (p0)
REVERT: G  279 MET cc_start: 0.9172 (mtp) cc_final: 0.8834 (mtp)
REVERT: G  286 MET cc_start: 0.8815 (ttm) cc_final: 0.8338 (mtp)
REVERT: G  422 ASN cc_start: 0.7935 (t0) cc_final: 0.7693 (t0)
REVERT: G  452 GLN cc_start: 0.6986 (mm-40) cc_final: 0.6672 (mp10)
REVERT: H  163 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7748 (mmt180)
REVERT: H  191 LEU cc_start: 0.8512 (mt) cc_final: 0.8211 (mm)
REVERT: H  211 THR cc_start: 0.8182 (m) cc_final: 0.7912 (p)
REVERT: H  229 THR cc_start: 0.7131 (p) cc_final: 0.6881 (t)
REVERT: H  286 MET cc_start: 0.8757 (ttm) cc_final: 0.8494 (mtp)
REVERT: H  365 ASP cc_start: 0.7966 (m-30) cc_final: 0.7580 (m-30)
REVERT: H  371 GLN cc_start: 0.7446 (mt0) cc_final: 0.7243 (mt0)
REVERT: H  452 GLN cc_start: 0.6785 (mm-40) cc_final: 0.6402 (mp-120)
REVERT: I   53 MET cc_start: 0.8544 (mtt) cc_final: 0.8332 (mtt)
REVERT: I  129 ASP cc_start: 0.7099 (t0) cc_final: 0.6839 (t0)
REVERT: I  185 ILE cc_start: 0.8363 (mt) cc_final: 0.8161 (mt)
REVERT: I  211 THR cc_start: 0.8222 (m) cc_final: 0.7881 (p)
REVERT: I  221 ASN cc_start: 0.7769 (p0) cc_final: 0.7317 (p0)
REVERT: I  376 MET cc_start: 0.8546 (mmm) cc_final: 0.8344 (tpt)
REVERT: I  440 LEU cc_start: 0.8175 (tp) cc_final: 0.7729 (tt)
REVERT: J  163 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7616 (mmt180)
REVERT: J  191 LEU cc_start: 0.8639 (mt) cc_final: 0.8367 (mm)
REVERT: J  211 THR cc_start: 0.8248 (m) cc_final: 0.7915 (p)
REVERT: J  221 ASN cc_start: 0.8032 (p0) cc_final: 0.7550 (p0)
REVERT: J  229 THR cc_start: 0.7334 (p) cc_final: 0.7123 (m)
REVERT: J  301 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7897 (mmm-85)
REVERT: J  452 GLN cc_start: 0.6725 (mm-40) cc_final: 0.6524 (mm110)
REVERT: K  211 THR cc_start: 0.8134 (m) cc_final: 0.7860 (p)
REVERT: K  229 THR cc_start: 0.7322 (p) cc_final: 0.7042 (t)
REVERT: K  286 MET cc_start: 0.8667 (ttm) cc_final: 0.8278 (mtp)
REVERT: K  363 LYS cc_start: 0.8071 (mmtp) cc_final: 0.6995 (mppt)
REVERT: K  376 MET cc_start: 0.8623 (mmm) cc_final: 0.8231 (tpp)
REVERT: L   53 MET cc_start: 0.8590 (mtt) cc_final: 0.8325 (mtt)
REVERT: L  211 THR cc_start: 0.7946 (m) cc_final: 0.7720 (p)
REVERT: L  221 ASN cc_start: 0.7910 (p0) cc_final: 0.7351 (p0)
REVERT: L  286 MET cc_start: 0.8743 (ttm) cc_final: 0.8376 (mtp)
REVERT: L  362 MET cc_start: 0.8449 (ptm) cc_final: 0.8073 (ptp)
REVERT: L  452 GLN cc_start: 0.6847 (mm-40) cc_final: 0.6297 (mp-120)
REVERT: M   11 THR cc_start: 0.7476 (p) cc_final: 0.7209 (t)
REVERT: M  211 THR cc_start: 0.8141 (m) cc_final: 0.7852 (p)
REVERT: M  221 ASN cc_start: 0.7917 (p0) cc_final: 0.7355 (p0)
REVERT: M  286 MET cc_start: 0.8750 (ttm) cc_final: 0.8260 (mtp)
REVERT: M  362 MET cc_start: 0.8269 (ptm) cc_final: 0.7938 (ptp)
REVERT: M  422 ASN cc_start: 0.7724 (t0) cc_final: 0.7519 (t0)
REVERT: M  452 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6743 (mp-120)
  outliers start: 13
  outliers final: 3
  residues processed: 1034
  average time/residue: 1.4178
  time to fit residues: 1800.3845
Evaluate side-chains
  685 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 682
  time to evaluate  : 4.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain H residue   96 SER
Chi-restraints excluded: chain K residue   96 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 611
   random chunks:
   chunk 515 optimal weight:    0.0980
   chunk 463 optimal weight:    6.9990
   chunk 256 optimal weight:   10.0000
   chunk 158 optimal weight:    6.9990
   chunk 312 optimal weight:    0.8980
   chunk 247 optimal weight:   10.0000
   chunk 478 optimal weight:    4.9990
   chunk 185 optimal weight:    0.4980
   chunk 291 optimal weight:    0.6980
   chunk 356 optimal weight:    0.9980
   chunk 554 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 112 GLN
A 336 GLN
A 361 ASN
B  22 ASN
B 112 GLN
B 336 GLN
B 361 ASN
B 422 ASN
C  22 ASN
C 112 GLN
C 336 GLN
C 361 ASN
C 371 GLN
C 422 ASN
D  22 ASN
D 112 GLN
D 336 GLN
D 361 ASN
D 371 GLN
D 422 ASN
D 429 ASN
E  22 ASN
E 112 GLN
E 221 ASN
E 336 GLN
E 340 GLN
E 371 GLN
F  22 ASN
F 221 ASN
F 336 GLN
F 361 ASN
F 422 ASN
F 452 GLN
G  22 ASN
G 112 GLN
G 336 GLN
G 371 GLN
H  22 ASN
H 112 GLN
H 336 GLN
H 422 ASN
I  22 ASN
I 336 GLN
I 361 ASN
I 371 GLN
I 422 ASN
J  22 ASN
J 112 GLN
J 336 GLN
J 361 ASN
J 422 ASN
K  22 ASN
K 112 GLN
K 336 GLN
K 361 ASN
K 422 ASN
L  22 ASN
L 112 GLN
L 336 GLN
L 361 ASN
L 371 GLN
L 422 ASN
M  22 ASN
M 112 GLN
M 336 GLN
M 361 ASN
M 429 ASN

Total number of N/Q/H flips: 68

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.188434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.124000 restraints weight = 47890.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.06
r_work: 0.3111 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  51571  Z= 0.158
  Angle     :  0.542   5.293  69576  Z= 0.309
  Chirality :  0.040   0.147   7540
  Planarity :  0.003   0.038   9191
  Dihedral  :  4.798  17.065   6945
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 0.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  8.33 %
    Favored  : 89.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.10), residues: 6162
  helix:  1.29 (0.09), residues: 2678
  sheet:  1.47 (0.15), residues: 1040
  loop :  0.02 (0.12), residues: 2444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  92 
 PHE   0.026   0.002   PHE M 235 
 TYR   0.017   0.002   TYR J  66 
 ARG   0.008   0.000   ARG L 156 

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

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

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  909 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 142
    poor density    : 767
  time to evaluate  : 4.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.7240 (t80) cc_final: 0.6897 (t80)
REVERT: A   32 ASP cc_start: 0.6545 (p0) cc_final: 0.6215 (t70)
REVERT: A   53 MET cc_start: 0.8634 (mtt) cc_final: 0.8363 (mtt)
REVERT: A  125 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7437 (mp0)
REVERT: A  129 ASP cc_start: 0.7269 (t0) cc_final: 0.6880 (t0)
REVERT: A  168 ASP cc_start: 0.8648 (t0) cc_final: 0.8414 (t0)
REVERT: A  213 HIS cc_start: 0.6417 (m-70) cc_final: 0.6157 (m170)
REVERT: A  286 MET cc_start: 0.8945 (ttm) cc_final: 0.8348 (mtp)
REVERT: A  365 ASP cc_start: 0.7336 (m-30) cc_final: 0.6778 (m-30)
REVERT: A  376 MET cc_start: 0.8403 (mmm) cc_final: 0.8136 (mmp)
REVERT: A  403 LYS cc_start: 0.7657 (mttt) cc_final: 0.7289 (mtpt)
REVERT: A  452 GLN cc_start: 0.6309 (mm-40) cc_final: 0.5771 (mp-120)
REVERT: A  456 MET cc_start: 0.7302 (mtt) cc_final: 0.7035 (mtt)
REVERT: B   32 ASP cc_start: 0.6784 (p0) cc_final: 0.6468 (p0)
REVERT: B   47 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7383 (ttmt)
REVERT: B   53 MET cc_start: 0.8568 (mtt) cc_final: 0.8216 (mtm)
REVERT: B  125 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7719 (mp0)
REVERT: B  129 ASP cc_start: 0.7351 (t0) cc_final: 0.7051 (t0)
REVERT: B  163 ARG cc_start: 0.7946 (mmm-85) cc_final: 0.7452 (mmt180)
REVERT: B  206 THR cc_start: 0.7836 (t) cc_final: 0.7592 (t)
REVERT: B  211 THR cc_start: 0.7753 (m) cc_final: 0.7459 (p)
REVERT: B  221 ASN cc_start: 0.7418 (p0) cc_final: 0.7010 (p0)
REVERT: B  286 MET cc_start: 0.8984 (ttm) cc_final: 0.8767 (mtp)
REVERT: B  301 ARG cc_start: 0.8403 (mtp-110) cc_final: 0.8200 (mtm-85)
REVERT: B  365 ASP cc_start: 0.7693 (m-30) cc_final: 0.7119 (m-30)
REVERT: B  440 LEU cc_start: 0.7878 (tp) cc_final: 0.7337 (tt)
REVERT: B  452 GLN cc_start: 0.6571 (mm-40) cc_final: 0.6179 (mp10)
REVERT: C    1 MET cc_start: 0.4950 (mmt) cc_final: 0.4157 (mmt)
REVERT: C   47 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7521 (mtmt)
REVERT: C   53 MET cc_start: 0.8664 (mtt) cc_final: 0.8328 (mtm)
REVERT: C  185 ILE cc_start: 0.8110 (mt) cc_final: 0.7685 (mt)
REVERT: C  211 THR cc_start: 0.8052 (m) cc_final: 0.7638 (p)
REVERT: C  221 ASN cc_start: 0.7347 (p0) cc_final: 0.7118 (p0)
REVERT: C  279 MET cc_start: 0.9021 (mtp) cc_final: 0.8817 (mtp)
REVERT: C  286 MET cc_start: 0.8943 (ttm) cc_final: 0.8729 (ttp)
REVERT: C  362 MET cc_start: 0.8422 (ptp) cc_final: 0.8003 (ptp)
REVERT: C  365 ASP cc_start: 0.7498 (m-30) cc_final: 0.7013 (m-30)
REVERT: C  403 LYS cc_start: 0.7734 (mttt) cc_final: 0.7140 (mppt)
REVERT: C  429 ASN cc_start: 0.8668 (m110) cc_final: 0.8055 (t0)
REVERT: C  456 MET cc_start: 0.7510 (mtt) cc_final: 0.7291 (mtt)
REVERT: D  125 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7632 (mp0)
REVERT: D  156 ARG cc_start: 0.6940 (mmm160) cc_final: 0.6674 (mmm160)
REVERT: D  178 ASN cc_start: 0.7403 (p0) cc_final: 0.7153 (p0)
REVERT: D  209 LEU cc_start: 0.8037 (tt) cc_final: 0.7821 (tp)
REVERT: D  221 ASN cc_start: 0.7473 (p0) cc_final: 0.7090 (p0)
REVERT: D  286 MET cc_start: 0.8911 (ttm) cc_final: 0.8429 (mtp)
REVERT: D  363 LYS cc_start: 0.8046 (mmtp) cc_final: 0.6741 (mppt)
REVERT: D  422 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7481 (m-40)
REVERT: E  125 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7568 (mp0)
REVERT: E  156 ARG cc_start: 0.6846 (mtp180) cc_final: 0.6446 (mmm160)
REVERT: E  163 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7547 (mmm160)
REVERT: E  211 THR cc_start: 0.8102 (m) cc_final: 0.7742 (p)
REVERT: E  286 MET cc_start: 0.8788 (ttm) cc_final: 0.8285 (mtp)
REVERT: E  422 ASN cc_start: 0.7814 (t160) cc_final: 0.7567 (m110)
REVERT: F   32 ASP cc_start: 0.6686 (p0) cc_final: 0.6479 (p0)
REVERT: F   53 MET cc_start: 0.8650 (mtt) cc_final: 0.8413 (mtt)
REVERT: F   83 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7519 (mp0)
REVERT: F  211 THR cc_start: 0.7917 (m) cc_final: 0.7579 (p)
REVERT: F  362 MET cc_start: 0.8631 (ptm) cc_final: 0.8169 (ptp)
REVERT: F  365 ASP cc_start: 0.7554 (m-30) cc_final: 0.6923 (m-30)
REVERT: F  403 LYS cc_start: 0.7746 (mttt) cc_final: 0.7012 (mppt)
REVERT: G   11 THR cc_start: 0.6643 (p) cc_final: 0.6415 (t)
REVERT: G   32 ASP cc_start: 0.6725 (p0) cc_final: 0.6225 (t70)
REVERT: G   47 LYS cc_start: 0.7515 (tppp) cc_final: 0.7265 (ttmt)
REVERT: G  125 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7522 (mp0)
REVERT: G  129 ASP cc_start: 0.7357 (t0) cc_final: 0.6931 (t0)
REVERT: G  211 THR cc_start: 0.7826 (m) cc_final: 0.7443 (p)
REVERT: G  213 HIS cc_start: 0.6142 (m-70) cc_final: 0.5776 (m-70)
REVERT: G  217 ARG cc_start: 0.7513 (mtt-85) cc_final: 0.7233 (mtt90)
REVERT: G  221 ASN cc_start: 0.7373 (p0) cc_final: 0.6893 (p0)
REVERT: G  396 LYS cc_start: 0.8506 (mttp) cc_final: 0.8295 (ttmm)
REVERT: G  422 ASN cc_start: 0.7774 (t0) cc_final: 0.7518 (t0)
REVERT: G  452 GLN cc_start: 0.6710 (mm-40) cc_final: 0.6313 (mp10)
REVERT: H  163 ARG cc_start: 0.8029 (mmm-85) cc_final: 0.7546 (mmt180)
REVERT: H  211 THR cc_start: 0.7849 (m) cc_final: 0.7515 (p)
REVERT: H  217 ARG cc_start: 0.7731 (mtt90) cc_final: 0.7529 (mtt180)
REVERT: H  323 GLU cc_start: 0.6489 (mt-10) cc_final: 0.6271 (mt-10)
REVERT: H  365 ASP cc_start: 0.7552 (m-30) cc_final: 0.6910 (m-30)
REVERT: H  371 GLN cc_start: 0.6661 (mt0) cc_final: 0.6338 (mt0)
REVERT: H  425 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6885 (mtm-85)
REVERT: H  452 GLN cc_start: 0.6521 (mm-40) cc_final: 0.6189 (mp10)
REVERT: I   32 ASP cc_start: 0.6448 (p0) cc_final: 0.6232 (p0)
REVERT: I   47 LYS cc_start: 0.7521 (mtmt) cc_final: 0.7000 (tptp)
REVERT: I  125 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7573 (mp0)
REVERT: I  129 ASP cc_start: 0.7414 (t0) cc_final: 0.7139 (t0)
REVERT: I  170 MET cc_start: 0.9160 (mtm) cc_final: 0.8900 (mtp)
REVERT: I  178 ASN cc_start: 0.7605 (p0) cc_final: 0.7376 (p0)
REVERT: I  185 ILE cc_start: 0.8226 (mt) cc_final: 0.7968 (mt)
REVERT: I  211 THR cc_start: 0.7914 (m) cc_final: 0.7540 (p)
REVERT: I  403 LYS cc_start: 0.7843 (mttt) cc_final: 0.7168 (mppt)
REVERT: I  440 LEU cc_start: 0.8113 (tp) cc_final: 0.7674 (tt)
REVERT: I  441 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7978 (tttt)
REVERT: J  156 ARG cc_start: 0.6770 (mmm160) cc_final: 0.6457 (mmm160)
REVERT: J  163 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7457 (mmt180)
REVERT: J  211 THR cc_start: 0.7934 (m) cc_final: 0.7538 (p)
REVERT: J  221 ASN cc_start: 0.7647 (p0) cc_final: 0.7277 (p0)
REVERT: J  301 ARG cc_start: 0.8358 (mtp-110) cc_final: 0.8100 (mmm-85)
REVERT: J  309 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8585 (mp)
REVERT: J  323 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6472 (mt-10)
REVERT: J  403 LYS cc_start: 0.7761 (mttt) cc_final: 0.7078 (mppt)
REVERT: J  422 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7680 (m-40)
REVERT: J  452 GLN cc_start: 0.6215 (mm-40) cc_final: 0.6012 (mm110)
REVERT: K   53 MET cc_start: 0.8580 (mtt) cc_final: 0.8241 (mtm)
REVERT: K   54 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8301 (m-30)
REVERT: K  170 MET cc_start: 0.9103 (mtm) cc_final: 0.8894 (mtm)
REVERT: K  211 THR cc_start: 0.7997 (m) cc_final: 0.7612 (p)
REVERT: K  286 MET cc_start: 0.8787 (ttm) cc_final: 0.8491 (mtp)
REVERT: K  422 ASN cc_start: 0.7824 (t160) cc_final: 0.7616 (m-40)
REVERT: K  440 LEU cc_start: 0.8168 (tp) cc_final: 0.7737 (tt)
REVERT: K  446 SER cc_start: 0.6721 (m) cc_final: 0.6512 (p)
REVERT: L   32 ASP cc_start: 0.6792 (p0) cc_final: 0.6502 (p0)
REVERT: L   53 MET cc_start: 0.8717 (mtt) cc_final: 0.8472 (mtt)
REVERT: L   83 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7543 (mp0)
REVERT: L  125 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7502 (mp0)
REVERT: L  156 ARG cc_start: 0.6654 (mmm160) cc_final: 0.6403 (mmm160)
REVERT: L  211 THR cc_start: 0.7763 (m) cc_final: 0.7484 (p)
REVERT: L  221 ASN cc_start: 0.7479 (p0) cc_final: 0.6964 (p0)
REVERT: L  362 MET cc_start: 0.8535 (ptm) cc_final: 0.8121 (ptp)
REVERT: L  403 LYS cc_start: 0.7611 (mttt) cc_final: 0.6972 (mttp)
REVERT: L  422 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7159 (m110)
REVERT: M  134 GLU cc_start: 0.8037 (tt0) cc_final: 0.7829 (tt0)
REVERT: M  211 THR cc_start: 0.7814 (m) cc_final: 0.7477 (p)
REVERT: M  221 ASN cc_start: 0.7541 (p0) cc_final: 0.7272 (p0)
REVERT: M  286 MET cc_start: 0.8871 (ttm) cc_final: 0.8309 (mtp)
REVERT: M  422 ASN cc_start: 0.7816 (t0) cc_final: 0.7483 (t0)
  outliers start: 142
  outliers final: 28
  residues processed: 867
  average time/residue: 1.3670
  time to fit residues: 1473.5404
Evaluate side-chains
  724 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 680
  time to evaluate  : 4.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain B residue   47 LYS
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   47 LYS
Chi-restraints excluded: chain D residue  125 GLU
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  422 ASN
Chi-restraints excluded: chain E residue  125 GLU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  181 GLU
Chi-restraints excluded: chain F residue  298 VAL
Chi-restraints excluded: chain F residue  315 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue  125 GLU
Chi-restraints excluded: chain G residue  298 VAL
Chi-restraints excluded: chain G residue  315 VAL
Chi-restraints excluded: chain G residue  450 ILE
Chi-restraints excluded: chain H residue  396 LYS
Chi-restraints excluded: chain H residue  425 ARG
Chi-restraints excluded: chain H residue  450 ILE
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  125 GLU
Chi-restraints excluded: chain I residue  441 LYS
Chi-restraints excluded: chain J residue  125 GLU
Chi-restraints excluded: chain J residue  298 VAL
Chi-restraints excluded: chain J residue  309 LEU
Chi-restraints excluded: chain J residue  422 ASN
Chi-restraints excluded: chain K residue   23 ASP
Chi-restraints excluded: chain K residue   54 ASP
Chi-restraints excluded: chain L residue   96 SER
Chi-restraints excluded: chain L residue  125 GLU
Chi-restraints excluded: chain L residue  298 VAL
Chi-restraints excluded: chain L residue  422 ASN
Chi-restraints excluded: chain L residue  444 ILE
Chi-restraints excluded: chain M residue   23 ASP
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue  315 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 611
   random chunks:
   chunk 439 optimal weight:    1.9990
   chunk 267 optimal weight:   10.0000
   chunk 512 optimal weight:    8.9990
   chunk 271 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 202 optimal weight:    6.9990
   chunk 70 optimal weight:   20.0000
   chunk 203 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 213 optimal weight:    0.8980
   chunk 391 optimal weight:    8.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
A 221 ASN
B 112 GLN
B 422 ASN
C 350 ASN
C 371 GLN
C 422 ASN
D 371 GLN
D 422 ASN
E 221 ASN
E 340 GLN
E 350 ASN
E 361 ASN
F 221 ASN
F 422 ASN
F 452 GLN
G 340 GLN
H 112 GLN
H 350 ASN
H 361 ASN
H 422 ASN
I 112 GLN
I 336 GLN
I 350 ASN
I 371 GLN
I 422 ASN
J 422 ASN
L 371 GLN
M 336 GLN
M 350 ASN
M 429 ASN

Total number of N/Q/H flips: 31

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.181823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.116430 restraints weight = 47366.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.59
r_work: 0.3024 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  51571  Z= 0.406
  Angle     :  0.722   8.197  69576  Z= 0.402
  Chirality :  0.051   0.161   7540
  Planarity :  0.005   0.055   9191
  Dihedral  :  5.023  17.029   6942
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  :  9.36 %
    Favored  : 87.71 %
  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:  1.01 (0.10), residues: 6162
  helix:  1.38 (0.09), residues: 2717
  sheet:  1.07 (0.14), residues: 1144
  loop : -0.31 (0.12), residues: 2301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.003   HIS K 354 
 PHE   0.028   0.003   PHE M 235 
 TYR   0.025   0.003   TYR B  66 
 ARG   0.012   0.001   ARG J  89 

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

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

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  915 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 165
    poor density    : 750
  time to evaluate  : 4.388 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8820 (mtt) cc_final: 0.8592 (mtt)
REVERT: A  125 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7499 (mp0)
REVERT: A  206 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7753 (t)
REVERT: A  213 HIS cc_start: 0.6545 (m-70) cc_final: 0.6236 (m170)
REVERT: A  286 MET cc_start: 0.8982 (ttm) cc_final: 0.8471 (mtp)
REVERT: A  429 ASN cc_start: 0.8411 (m-40) cc_final: 0.8119 (t0)
REVERT: A  452 GLN cc_start: 0.6677 (mm-40) cc_final: 0.6106 (mp-120)
REVERT: A  456 MET cc_start: 0.7463 (mtt) cc_final: 0.7252 (mtt)
REVERT: B   47 LYS cc_start: 0.7721 (tptp) cc_final: 0.7439 (ttmt)
REVERT: B   53 MET cc_start: 0.8678 (mtt) cc_final: 0.8346 (mtm)
REVERT: B  125 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7677 (mp0)
REVERT: B  129 ASP cc_start: 0.7357 (t0) cc_final: 0.7021 (t0)
REVERT: B  159 ASP cc_start: 0.6594 (m-30) cc_final: 0.5826 (t0)
REVERT: B  163 ARG cc_start: 0.8012 (mmm-85) cc_final: 0.7565 (mmt180)
REVERT: B  221 ASN cc_start: 0.7291 (p0) cc_final: 0.6918 (p0)
REVERT: B  286 MET cc_start: 0.9052 (ttm) cc_final: 0.8628 (mtp)
REVERT: B  301 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.8147 (mtm-85)
REVERT: B  340 GLN cc_start: 0.8813 (tp40) cc_final: 0.8549 (tm130)
REVERT: B  365 ASP cc_start: 0.7251 (m-30) cc_final: 0.6682 (m-30)
REVERT: B  429 ASN cc_start: 0.8471 (m-40) cc_final: 0.7953 (t0)
REVERT: B  440 LEU cc_start: 0.7908 (tp) cc_final: 0.7356 (tt)
REVERT: C    1 MET cc_start: 0.4946 (mmt) cc_final: 0.4041 (mmt)
REVERT: C   47 LYS cc_start: 0.7688 (tptp) cc_final: 0.7405 (mtmt)
REVERT: C  185 ILE cc_start: 0.8168 (mt) cc_final: 0.7885 (mt)
REVERT: C  221 ASN cc_start: 0.7390 (p0) cc_final: 0.7094 (p0)
REVERT: C  279 MET cc_start: 0.9263 (mtp) cc_final: 0.8970 (mtp)
REVERT: C  362 MET cc_start: 0.8490 (ptp) cc_final: 0.8005 (ptp)
REVERT: C  365 ASP cc_start: 0.7580 (m-30) cc_final: 0.7088 (m-30)
REVERT: C  429 ASN cc_start: 0.8629 (m110) cc_final: 0.8187 (t0)
REVERT: D  125 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7707 (mp0)
REVERT: D  209 LEU cc_start: 0.8097 (tt) cc_final: 0.7804 (tp)
REVERT: D  221 ASN cc_start: 0.7218 (p0) cc_final: 0.6833 (p0)
REVERT: D  286 MET cc_start: 0.9008 (ttm) cc_final: 0.8528 (mtp)
REVERT: D  327 SER cc_start: 0.7652 (t) cc_final: 0.7364 (p)
REVERT: D  363 LYS cc_start: 0.8157 (mmtp) cc_final: 0.6862 (mppt)
REVERT: D  452 GLN cc_start: 0.6725 (mm-40) cc_final: 0.6353 (mp10)
REVERT: E  125 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7653 (mp0)
REVERT: E  159 ASP cc_start: 0.6213 (m-30) cc_final: 0.5655 (t0)
REVERT: E  211 THR cc_start: 0.7970 (m) cc_final: 0.7725 (p)
REVERT: E  255 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8881 (mptp)
REVERT: E  292 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7598 (t0)
REVERT: E  422 ASN cc_start: 0.7960 (OUTLIER) cc_final: 0.7727 (m110)
REVERT: F   53 MET cc_start: 0.8759 (mtt) cc_final: 0.8547 (mtt)
REVERT: F   83 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7857 (mp0)
REVERT: F  292 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.7815 (m110)
REVERT: F  365 ASP cc_start: 0.7700 (m-30) cc_final: 0.7028 (m-30)
REVERT: F  429 ASN cc_start: 0.8580 (m-40) cc_final: 0.8229 (t0)
REVERT: G   11 THR cc_start: 0.6977 (p) cc_final: 0.6773 (t)
REVERT: G   32 ASP cc_start: 0.6762 (p0) cc_final: 0.6307 (t70)
REVERT: G   47 LYS cc_start: 0.7508 (tppp) cc_final: 0.7192 (ttmt)
REVERT: G  125 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7787 (mm-30)
REVERT: G  129 ASP cc_start: 0.7415 (t0) cc_final: 0.6988 (t0)
REVERT: G  213 HIS cc_start: 0.6031 (m-70) cc_final: 0.5638 (m-70)
REVERT: G  217 ARG cc_start: 0.7620 (mtt-85) cc_final: 0.7366 (mtt90)
REVERT: G  221 ASN cc_start: 0.7539 (p0) cc_final: 0.7082 (p0)
REVERT: G  327 SER cc_start: 0.7559 (t) cc_final: 0.7307 (p)
REVERT: G  422 ASN cc_start: 0.7907 (t0) cc_final: 0.7631 (t0)
REVERT: G  429 ASN cc_start: 0.8316 (m-40) cc_final: 0.7987 (t0)
REVERT: G  452 GLN cc_start: 0.6989 (mm-40) cc_final: 0.6606 (mp10)
REVERT: H   54 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8415 (m-30)
REVERT: H  163 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7614 (mmt180)
REVERT: H  286 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8235 (tpp)
REVERT: H  309 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8756 (tp)
REVERT: H  327 SER cc_start: 0.7770 (t) cc_final: 0.7370 (p)
REVERT: H  365 ASP cc_start: 0.7920 (m-30) cc_final: 0.7459 (m-30)
REVERT: H  371 GLN cc_start: 0.6793 (mt0) cc_final: 0.6494 (mt0)
REVERT: H  425 ARG cc_start: 0.7304 (mtp180) cc_final: 0.7038 (mtm-85)
REVERT: H  429 ASN cc_start: 0.8272 (m-40) cc_final: 0.7983 (t0)
REVERT: H  452 GLN cc_start: 0.6855 (mm-40) cc_final: 0.6428 (mp10)
REVERT: I    8 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6803 (mt-10)
REVERT: I   47 LYS cc_start: 0.7487 (mtmt) cc_final: 0.6938 (tptp)
REVERT: I  129 ASP cc_start: 0.7380 (t0) cc_final: 0.7074 (t0)
REVERT: I  170 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8902 (mtp)
REVERT: I  211 THR cc_start: 0.7916 (m) cc_final: 0.7701 (p)
REVERT: I  213 HIS cc_start: 0.6297 (m90) cc_final: 0.6062 (m-70)
REVERT: I  327 SER cc_start: 0.7586 (t) cc_final: 0.7340 (p)
REVERT: I  340 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7979 (tp-100)
REVERT: I  365 ASP cc_start: 0.7747 (m-30) cc_final: 0.7223 (m-30)
REVERT: I  429 ASN cc_start: 0.8376 (m-40) cc_final: 0.8128 (t0)
REVERT: I  440 LEU cc_start: 0.8104 (tp) cc_final: 0.7639 (tt)
REVERT: J  156 ARG cc_start: 0.6943 (mmm160) cc_final: 0.6692 (mmm160)
REVERT: J  163 ARG cc_start: 0.7912 (mmm-85) cc_final: 0.7508 (mmt180)
REVERT: J  211 THR cc_start: 0.7939 (m) cc_final: 0.7695 (p)
REVERT: J  217 ARG cc_start: 0.7668 (mtt-85) cc_final: 0.7397 (mtt90)
REVERT: J  221 ASN cc_start: 0.7662 (p0) cc_final: 0.7307 (p0)
REVERT: J  301 ARG cc_start: 0.8531 (mtp-110) cc_final: 0.8291 (mtm-85)
REVERT: J  309 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8602 (mp)
REVERT: J  323 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6387 (mt-10)
REVERT: J  327 SER cc_start: 0.7627 (t) cc_final: 0.7270 (p)
REVERT: J  422 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7784 (m-40)
REVERT: J  440 LEU cc_start: 0.8258 (tp) cc_final: 0.7761 (tt)
REVERT: J  450 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.6264 (mp)
REVERT: J  452 GLN cc_start: 0.6624 (mm-40) cc_final: 0.6289 (mm110)
REVERT: K  125 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7757 (mp0)
REVERT: K  185 ILE cc_start: 0.8161 (mt) cc_final: 0.7901 (mt)
REVERT: K  211 THR cc_start: 0.7682 (m) cc_final: 0.7419 (p)
REVERT: K  286 MET cc_start: 0.8937 (ttm) cc_final: 0.8414 (mtp)
REVERT: K  327 SER cc_start: 0.7654 (t) cc_final: 0.7341 (p)
REVERT: K  363 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.6910 (mmmm)
REVERT: K  422 ASN cc_start: 0.8030 (OUTLIER) cc_final: 0.7742 (m-40)
REVERT: K  446 SER cc_start: 0.7118 (m) cc_final: 0.6798 (p)
REVERT: L   32 ASP cc_start: 0.6719 (p0) cc_final: 0.6343 (m-30)
REVERT: L   53 MET cc_start: 0.8705 (mtt) cc_final: 0.8496 (mtt)
REVERT: L   83 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7784 (mp0)
REVERT: L  125 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7461 (mp0)
REVERT: L  159 ASP cc_start: 0.6316 (m-30) cc_final: 0.5585 (OUTLIER)
REVERT: L  211 THR cc_start: 0.8000 (m) cc_final: 0.7780 (p)
REVERT: L  221 ASN cc_start: 0.7446 (p0) cc_final: 0.6966 (p0)
REVERT: L  286 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8394 (tpp)
REVERT: L  327 SER cc_start: 0.7812 (t) cc_final: 0.7480 (p)
REVERT: L  365 ASP cc_start: 0.7809 (m-30) cc_final: 0.7531 (m-30)
REVERT: L  422 ASN cc_start: 0.7977 (t0) cc_final: 0.7451 (m110)
REVERT: L  429 ASN cc_start: 0.8692 (m-40) cc_final: 0.8241 (t0)
REVERT: M   47 LYS cc_start: 0.7694 (tppp) cc_final: 0.7242 (tptp)
REVERT: M  211 THR cc_start: 0.7867 (m) cc_final: 0.7631 (p)
REVERT: M  221 ASN cc_start: 0.7489 (p0) cc_final: 0.7272 (p0)
REVERT: M  327 SER cc_start: 0.7739 (t) cc_final: 0.7386 (p)
REVERT: M  365 ASP cc_start: 0.7763 (m-30) cc_final: 0.7129 (m-30)
REVERT: M  422 ASN cc_start: 0.7867 (t0) cc_final: 0.7516 (t0)
REVERT: M  452 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.5583 (mp10)
  outliers start: 165
  outliers final: 70
  residues processed: 850
  average time/residue: 1.3530
  time to fit residues: 1428.1898
Evaluate side-chains
  806 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 93
    poor density    : 713
  time to evaluate  : 4.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  292 ASN
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  422 ASN
Chi-restraints excluded: chain B residue  444 ILE
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  292 ASN
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  444 ILE
Chi-restraints excluded: chain D residue   23 ASP
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue  125 GLU
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 GLU
Chi-restraints excluded: chain E residue  255 LYS
Chi-restraints excluded: chain E residue  292 ASN
Chi-restraints excluded: chain E residue  309 LEU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  422 ASN
Chi-restraints excluded: chain F residue   54 ASP
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  133 VAL
Chi-restraints excluded: chain F residue  229 THR
Chi-restraints excluded: chain F residue  286 MET
Chi-restraints excluded: chain F residue  292 ASN
Chi-restraints excluded: chain F residue  298 VAL
Chi-restraints excluded: chain F residue  315 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue  125 GLU
Chi-restraints excluded: chain G residue  181 GLU
Chi-restraints excluded: chain G residue  298 VAL
Chi-restraints excluded: chain G residue  315 VAL
Chi-restraints excluded: chain G residue  432 LEU
Chi-restraints excluded: chain G residue  450 ILE
Chi-restraints excluded: chain H residue   54 ASP
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  133 VAL
Chi-restraints excluded: chain H residue  206 THR
Chi-restraints excluded: chain H residue  286 MET
Chi-restraints excluded: chain H residue  309 LEU
Chi-restraints excluded: chain H residue  422 ASN
Chi-restraints excluded: chain H residue  436 LEU
Chi-restraints excluded: chain H residue  450 ILE
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   46 SER
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  170 MET
Chi-restraints excluded: chain I residue  181 GLU
Chi-restraints excluded: chain I residue  229 THR
Chi-restraints excluded: chain I residue  286 MET
Chi-restraints excluded: chain I residue  340 GLN
Chi-restraints excluded: chain I residue  362 MET
Chi-restraints excluded: chain I residue  422 ASN
Chi-restraints excluded: chain I residue  450 ILE
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue   78 THR
Chi-restraints excluded: chain J residue  292 ASN
Chi-restraints excluded: chain J residue  298 VAL
Chi-restraints excluded: chain J residue  309 LEU
Chi-restraints excluded: chain J residue  422 ASN
Chi-restraints excluded: chain J residue  450 ILE
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain K residue  206 THR
Chi-restraints excluded: chain K residue  292 ASN
Chi-restraints excluded: chain K residue  363 LYS
Chi-restraints excluded: chain K residue  422 ASN
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue   96 SER
Chi-restraints excluded: chain L residue  125 GLU
Chi-restraints excluded: chain L residue  286 MET
Chi-restraints excluded: chain L residue  292 ASN
Chi-restraints excluded: chain L residue  298 VAL
Chi-restraints excluded: chain L residue  444 ILE
Chi-restraints excluded: chain M residue   78 THR
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue  315 VAL
Chi-restraints excluded: chain M residue  376 MET
Chi-restraints excluded: chain M residue  452 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 611
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 610 optimal weight:    8.9990
   chunk 290 optimal weight:    2.9990
   chunk 132 optimal weight:    0.7980
   chunk 391 optimal weight:   10.0000
   chunk 329 optimal weight:   10.0000
   chunk 253 optimal weight:    9.9990
   chunk 331 optimal weight:    0.9990
   chunk 134 optimal weight:    8.9990
   chunk 131 optimal weight:    3.9990
   chunk 354 optimal weight:    0.7980
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
B 112 GLN
C 112 GLN
C 371 GLN
C 422 ASN
D 112 GLN
D 350 ASN
D 371 GLN
E 112 GLN
E 221 ASN
E 340 GLN
F 221 ASN
F 422 ASN
F 452 GLN
G 340 GLN
H 112 GLN
I 112 GLN
I 371 GLN
K 112 GLN
L 112 GLN
L 371 GLN

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.183826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.117817 restraints weight = 47363.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 2.14
r_work: 0.3040 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  51571  Z= 0.216
  Angle     :  0.557   5.726  69576  Z= 0.313
  Chirality :  0.042   0.148   7540
  Planarity :  0.004   0.037   9191
  Dihedral  :  4.675  16.753   6942
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 1.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 10.77 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.10), residues: 6162
  helix:  1.65 (0.10), residues: 2743
  sheet:  1.06 (0.14), residues: 1131
  loop : -0.50 (0.12), residues: 2288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS D  92 
 PHE   0.027   0.002   PHE G 235 
 TYR   0.018   0.002   TYR J  66 
 ARG   0.005   0.000   ARG F  79 

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

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

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  867 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 144
    poor density    : 723
  time to evaluate  : 4.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8719 (mtt) cc_final: 0.8479 (mtt)
REVERT: A   54 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8107 (m-30)
REVERT: A  125 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7490 (mp0)
REVERT: A  183 ASN cc_start: 0.8400 (m110) cc_final: 0.8170 (m110)
REVERT: A  213 HIS cc_start: 0.6569 (m-70) cc_final: 0.6237 (m170)
REVERT: A  255 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8902 (mmtp)
REVERT: A  286 MET cc_start: 0.8981 (ttm) cc_final: 0.8480 (mtp)
REVERT: A  403 LYS cc_start: 0.7812 (mttt) cc_final: 0.7441 (mtpt)
REVERT: A  429 ASN cc_start: 0.8433 (m-40) cc_final: 0.8078 (t0)
REVERT: A  444 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.7003 (mm)
REVERT: A  452 GLN cc_start: 0.6460 (mm-40) cc_final: 0.5876 (mp-120)
REVERT: A  456 MET cc_start: 0.7329 (mtt) cc_final: 0.7077 (mtt)
REVERT: B   47 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7405 (ttmt)
REVERT: B   53 MET cc_start: 0.8605 (mtt) cc_final: 0.8266 (mtm)
REVERT: B  125 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7648 (mp0)
REVERT: B  129 ASP cc_start: 0.7234 (t0) cc_final: 0.6891 (t0)
REVERT: B  159 ASP cc_start: 0.6518 (m-30) cc_final: 0.5729 (t0)
REVERT: B  163 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7442 (mmt180)
REVERT: B  221 ASN cc_start: 0.7226 (p0) cc_final: 0.6843 (p0)
REVERT: B  286 MET cc_start: 0.9061 (ttm) cc_final: 0.8625 (mtp)
REVERT: B  340 GLN cc_start: 0.8743 (tp40) cc_final: 0.8449 (tm130)
REVERT: B  365 ASP cc_start: 0.7184 (m-30) cc_final: 0.6592 (m-30)
REVERT: B  429 ASN cc_start: 0.8503 (m-40) cc_final: 0.7997 (t0)
REVERT: B  440 LEU cc_start: 0.7869 (tp) cc_final: 0.7276 (tt)
REVERT: C    1 MET cc_start: 0.5055 (mmt) cc_final: 0.4181 (mmt)
REVERT: C  185 ILE cc_start: 0.8192 (mt) cc_final: 0.7876 (mt)
REVERT: C  221 ASN cc_start: 0.7155 (p0) cc_final: 0.6861 (p0)
REVERT: C  279 MET cc_start: 0.9190 (mtp) cc_final: 0.8983 (mtp)
REVERT: C  362 MET cc_start: 0.8444 (ptp) cc_final: 0.7883 (ptp)
REVERT: C  365 ASP cc_start: 0.7548 (m-30) cc_final: 0.7054 (m-30)
REVERT: C  429 ASN cc_start: 0.8680 (m110) cc_final: 0.8165 (t0)
REVERT: D  125 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7615 (mp0)
REVERT: D  209 LEU cc_start: 0.8012 (tt) cc_final: 0.7686 (tp)
REVERT: D  221 ASN cc_start: 0.7418 (p0) cc_final: 0.7060 (p0)
REVERT: D  286 MET cc_start: 0.8986 (ttm) cc_final: 0.8456 (mtp)
REVERT: D  327 SER cc_start: 0.7737 (t) cc_final: 0.7401 (p)
REVERT: D  363 LYS cc_start: 0.8099 (mmtp) cc_final: 0.7566 (mttp)
REVERT: D  422 ASN cc_start: 0.7884 (t0) cc_final: 0.7389 (m110)
REVERT: D  452 GLN cc_start: 0.6583 (mm-40) cc_final: 0.6322 (mp10)
REVERT: E   54 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8324 (m-30)
REVERT: E   83 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7879 (mp0)
REVERT: E  125 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7486 (mp0)
REVERT: E  159 ASP cc_start: 0.6153 (m-30) cc_final: 0.5537 (t0)
REVERT: E  292 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.7827 (t0)
REVERT: E  422 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7733 (m110)
REVERT: F   53 MET cc_start: 0.8710 (mtt) cc_final: 0.8488 (mtt)
REVERT: F   83 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7793 (mp0)
REVERT: F  206 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7584 (t)
REVERT: F  365 ASP cc_start: 0.7600 (m-30) cc_final: 0.6913 (m-30)
REVERT: F  429 ASN cc_start: 0.8573 (m-40) cc_final: 0.8191 (t0)
REVERT: G   11 THR cc_start: 0.6855 (p) cc_final: 0.6631 (t)
REVERT: G   47 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7150 (ttmp)
REVERT: G   83 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7731 (mp0)
REVERT: G  125 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7816 (mm-30)
REVERT: G  129 ASP cc_start: 0.7383 (t0) cc_final: 0.6976 (t0)
REVERT: G  211 THR cc_start: 0.7894 (m) cc_final: 0.7451 (p)
REVERT: G  213 HIS cc_start: 0.5932 (m-70) cc_final: 0.5585 (m-70)
REVERT: G  221 ASN cc_start: 0.7614 (p0) cc_final: 0.7181 (p0)
REVERT: G  422 ASN cc_start: 0.7904 (t0) cc_final: 0.7627 (t0)
REVERT: G  429 ASN cc_start: 0.8310 (m-40) cc_final: 0.7968 (t0)
REVERT: G  452 GLN cc_start: 0.6830 (mm-40) cc_final: 0.6543 (mp10)
REVERT: H  163 ARG cc_start: 0.7899 (mmm-85) cc_final: 0.7568 (mmt180)
REVERT: H  211 THR cc_start: 0.7868 (m) cc_final: 0.7345 (p)
REVERT: H  309 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8747 (tp)
REVERT: H  327 SER cc_start: 0.7754 (t) cc_final: 0.7358 (p)
REVERT: H  365 ASP cc_start: 0.7892 (m-30) cc_final: 0.7325 (m-30)
REVERT: H  371 GLN cc_start: 0.6802 (mt0) cc_final: 0.6528 (mt0)
REVERT: H  425 ARG cc_start: 0.7245 (mtp180) cc_final: 0.6961 (mtm-85)
REVERT: H  429 ASN cc_start: 0.8253 (m-40) cc_final: 0.7854 (t0)
REVERT: H  452 GLN cc_start: 0.6813 (mm-40) cc_final: 0.6309 (mp10)
REVERT: I   83 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7735 (mp0)
REVERT: I  129 ASP cc_start: 0.7356 (t0) cc_final: 0.7089 (t0)
REVERT: I  170 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8847 (mtp)
REVERT: I  185 ILE cc_start: 0.8271 (mt) cc_final: 0.8001 (mt)
REVERT: I  211 THR cc_start: 0.7768 (m) cc_final: 0.7536 (p)
REVERT: I  221 ASN cc_start: 0.7096 (p0) cc_final: 0.6715 (p0)
REVERT: I  340 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.7930 (tp-100)
REVERT: I  365 ASP cc_start: 0.7454 (m-30) cc_final: 0.6920 (m-30)
REVERT: I  440 LEU cc_start: 0.8083 (tp) cc_final: 0.7575 (tt)
REVERT: I  453 THR cc_start: 0.7082 (m) cc_final: 0.6863 (t)
REVERT: J   11 THR cc_start: 0.6979 (t) cc_final: 0.6759 (m)
REVERT: J  163 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7410 (mmt180)
REVERT: J  217 ARG cc_start: 0.7623 (mtt-85) cc_final: 0.7155 (mtt90)
REVERT: J  221 ASN cc_start: 0.7509 (p0) cc_final: 0.7131 (p0)
REVERT: J  301 ARG cc_start: 0.8482 (mtp-110) cc_final: 0.8233 (mtm-85)
REVERT: J  309 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8623 (mp)
REVERT: J  323 GLU cc_start: 0.6470 (mt-10) cc_final: 0.6259 (mt-10)
REVERT: J  403 LYS cc_start: 0.7699 (mttt) cc_final: 0.7066 (mppt)
REVERT: J  440 LEU cc_start: 0.8195 (tp) cc_final: 0.7676 (tt)
REVERT: J  452 GLN cc_start: 0.6440 (mm-40) cc_final: 0.6140 (mm110)
REVERT: K  125 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7658 (mp0)
REVERT: K  185 ILE cc_start: 0.8196 (mt) cc_final: 0.7917 (mt)
REVERT: K  221 ASN cc_start: 0.7195 (p0) cc_final: 0.6648 (p0)
REVERT: K  286 MET cc_start: 0.8901 (ttm) cc_final: 0.8617 (mtp)
REVERT: K  327 SER cc_start: 0.7712 (t) cc_final: 0.7390 (p)
REVERT: K  363 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7472 (mttp)
REVERT: K  422 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7701 (m-40)
REVERT: K  446 SER cc_start: 0.7096 (m) cc_final: 0.6806 (p)
REVERT: L   53 MET cc_start: 0.8675 (mtt) cc_final: 0.8445 (mtt)
REVERT: L   83 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7780 (mp0)
REVERT: L  159 ASP cc_start: 0.6539 (m-30) cc_final: 0.5768 (OUTLIER)
REVERT: L  206 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7603 (t)
REVERT: L  211 THR cc_start: 0.7846 (m) cc_final: 0.7574 (p)
REVERT: L  221 ASN cc_start: 0.7317 (p0) cc_final: 0.6870 (p0)
REVERT: L  365 ASP cc_start: 0.7413 (m-30) cc_final: 0.7100 (m-30)
REVERT: L  422 ASN cc_start: 0.7996 (t0) cc_final: 0.7494 (m-40)
REVERT: L  429 ASN cc_start: 0.8655 (m-40) cc_final: 0.8166 (t0)
REVERT: L  452 GLN cc_start: 0.6470 (mm-40) cc_final: 0.5931 (mp10)
REVERT: M   47 LYS cc_start: 0.7727 (tppp) cc_final: 0.7302 (tptp)
REVERT: M  327 SER cc_start: 0.7745 (t) cc_final: 0.7396 (p)
REVERT: M  365 ASP cc_start: 0.7722 (m-30) cc_final: 0.7089 (m-30)
REVERT: M  422 ASN cc_start: 0.7810 (t0) cc_final: 0.7438 (t0)
REVERT: M  441 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8012 (tttt)
REVERT: M  452 GLN cc_start: 0.6802 (OUTLIER) cc_final: 0.5450 (mp10)
REVERT: M  456 MET cc_start: 0.7252 (mtt) cc_final: 0.7004 (mtt)
  outliers start: 144
  outliers final: 64
  residues processed: 820
  average time/residue: 1.4046
  time to fit residues: 1418.6340
Evaluate side-chains
  778 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 692
  time to evaluate  : 4.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  255 LYS
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain B residue   47 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  292 ASN
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue  125 GLU
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain E residue   54 ASP
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 GLU
Chi-restraints excluded: chain E residue  292 ASN
Chi-restraints excluded: chain E residue  309 LEU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  422 ASN
Chi-restraints excluded: chain F residue   54 ASP
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  181 GLU
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain F residue  315 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue  125 GLU
Chi-restraints excluded: chain G residue  181 GLU
Chi-restraints excluded: chain G residue  298 VAL
Chi-restraints excluded: chain G residue  315 VAL
Chi-restraints excluded: chain G residue  450 ILE
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  133 VAL
Chi-restraints excluded: chain H residue  309 LEU
Chi-restraints excluded: chain H residue  436 LEU
Chi-restraints excluded: chain H residue  450 ILE
Chi-restraints excluded: chain I residue   46 SER
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  125 GLU
Chi-restraints excluded: chain I residue  170 MET
Chi-restraints excluded: chain I residue  229 THR
Chi-restraints excluded: chain I residue  340 GLN
Chi-restraints excluded: chain I residue  362 MET
Chi-restraints excluded: chain I residue  450 ILE
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue   78 THR
Chi-restraints excluded: chain J residue  125 GLU
Chi-restraints excluded: chain J residue  292 ASN
Chi-restraints excluded: chain J residue  298 VAL
Chi-restraints excluded: chain J residue  309 LEU
Chi-restraints excluded: chain K residue   47 LYS
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain K residue  292 ASN
Chi-restraints excluded: chain K residue  363 LYS
Chi-restraints excluded: chain K residue  422 ASN
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue   96 SER
Chi-restraints excluded: chain L residue  125 GLU
Chi-restraints excluded: chain L residue  206 THR
Chi-restraints excluded: chain L residue  292 ASN
Chi-restraints excluded: chain L residue  298 VAL
Chi-restraints excluded: chain M residue   78 THR
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue  125 GLU
Chi-restraints excluded: chain M residue  206 THR
Chi-restraints excluded: chain M residue  315 VAL
Chi-restraints excluded: chain M residue  376 MET
Chi-restraints excluded: chain M residue  441 LYS
Chi-restraints excluded: chain M residue  452 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 611
   random chunks:
   chunk 202 optimal weight:    7.9990
   chunk 378 optimal weight:    0.6980
   chunk 404 optimal weight:    8.9990
   chunk 470 optimal weight:   10.0000
   chunk 529 optimal weight:    9.9990
   chunk 574 optimal weight:    0.9980
   chunk 452 optimal weight:    7.9990
   chunk 252 optimal weight:    4.9990
   chunk 543 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 168 optimal weight:    0.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
A 340 GLN
B 112 GLN
C 112 GLN
C 371 GLN
C 422 ASN
D 371 GLN
E 112 GLN
E 340 GLN
F 178 ASN
F 221 ASN
F 422 ASN
F 452 GLN
G 340 GLN
H 112 GLN
H 422 ASN
I 112 GLN
I 371 GLN
I 452 GLN
J 422 ASN
L 112 GLN
L 422 ASN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.183287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.116955 restraints weight = 47375.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.20
r_work: 0.3037 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  51571  Z= 0.248
  Angle     :  0.570   6.235  69576  Z= 0.318
  Chirality :  0.043   0.149   7540
  Planarity :  0.004   0.041   9191
  Dihedral  :  4.638  16.408   6942
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 1.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 11.64 %
    Favored  : 85.33 %
  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:  1.07 (0.10), residues: 6162
  helix:  1.68 (0.10), residues: 2743
  sheet:  0.98 (0.14), residues: 1144
  loop : -0.62 (0.12), residues: 2275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS K 354 
 PHE   0.029   0.002   PHE G 235 
 TYR   0.019   0.002   TYR I 218 
 ARG   0.008   0.001   ARG F 425 

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

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

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  900 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 171
    poor density    : 729
  time to evaluate  : 4.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8706 (mtt) cc_final: 0.8449 (mtt)
REVERT: A   54 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8061 (m-30)
REVERT: A   83 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7883 (mp0)
REVERT: A  125 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7498 (mp0)
REVERT: A  178 ASN cc_start: 0.7314 (p0) cc_final: 0.7077 (p0)
REVERT: A  183 ASN cc_start: 0.8399 (m110) cc_final: 0.8137 (m110)
REVERT: A  206 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7715 (t)
REVERT: A  213 HIS cc_start: 0.6499 (m-70) cc_final: 0.6152 (m170)
REVERT: A  217 ARG cc_start: 0.7555 (mtt90) cc_final: 0.7353 (mtt90)
REVERT: A  286 MET cc_start: 0.8970 (ttm) cc_final: 0.8415 (mtp)
REVERT: A  429 ASN cc_start: 0.8448 (m-40) cc_final: 0.8105 (t0)
REVERT: A  452 GLN cc_start: 0.6487 (mm-40) cc_final: 0.6076 (mm110)
REVERT: A  456 MET cc_start: 0.7371 (mtt) cc_final: 0.7133 (mtt)
REVERT: B   32 ASP cc_start: 0.6719 (p0) cc_final: 0.6497 (p0)
REVERT: B   47 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7402 (ttmt)
REVERT: B   53 MET cc_start: 0.8593 (mtt) cc_final: 0.8266 (mtm)
REVERT: B  125 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7720 (mp0)
REVERT: B  129 ASP cc_start: 0.7269 (t0) cc_final: 0.6923 (t0)
REVERT: B  159 ASP cc_start: 0.6362 (m-30) cc_final: 0.5718 (t0)
REVERT: B  163 ARG cc_start: 0.7802 (mmm-85) cc_final: 0.7503 (mmt180)
REVERT: B  206 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7474 (t)
REVERT: B  221 ASN cc_start: 0.7163 (p0) cc_final: 0.6813 (p0)
REVERT: B  286 MET cc_start: 0.9046 (ttm) cc_final: 0.8603 (mtp)
REVERT: B  340 GLN cc_start: 0.8725 (tp40) cc_final: 0.8448 (tm130)
REVERT: B  365 ASP cc_start: 0.7198 (m-30) cc_final: 0.6624 (m-30)
REVERT: B  429 ASN cc_start: 0.8468 (m-40) cc_final: 0.7949 (t0)
REVERT: B  440 LEU cc_start: 0.7916 (tp) cc_final: 0.7308 (tt)
REVERT: C    8 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6770 (mt-10)
REVERT: C  185 ILE cc_start: 0.8168 (mt) cc_final: 0.7839 (mt)
REVERT: C  221 ASN cc_start: 0.6997 (p0) cc_final: 0.6737 (p0)
REVERT: C  235 PHE cc_start: 0.7588 (t80) cc_final: 0.7388 (t80)
REVERT: C  279 MET cc_start: 0.9218 (mtp) cc_final: 0.8978 (mtp)
REVERT: C  362 MET cc_start: 0.8459 (ptp) cc_final: 0.7888 (ptp)
REVERT: C  363 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7338 (mmmm)
REVERT: C  365 ASP cc_start: 0.7525 (m-30) cc_final: 0.7043 (m-30)
REVERT: C  429 ASN cc_start: 0.8662 (m110) cc_final: 0.8164 (t0)
REVERT: D  125 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7615 (mp0)
REVERT: D  209 LEU cc_start: 0.7973 (tt) cc_final: 0.7631 (tp)
REVERT: D  221 ASN cc_start: 0.7256 (p0) cc_final: 0.6934 (p0)
REVERT: D  286 MET cc_start: 0.8956 (ttm) cc_final: 0.8462 (mtp)
REVERT: D  327 SER cc_start: 0.7797 (t) cc_final: 0.7482 (p)
REVERT: D  363 LYS cc_start: 0.8103 (mmtp) cc_final: 0.7611 (mttp)
REVERT: D  422 ASN cc_start: 0.8153 (t0) cc_final: 0.7680 (m110)
REVERT: D  452 GLN cc_start: 0.6702 (mm-40) cc_final: 0.6315 (mp10)
REVERT: E   54 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8329 (m-30)
REVERT: E  125 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7617 (mp0)
REVERT: E  143 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8418 (t0)
REVERT: E  159 ASP cc_start: 0.6312 (m-30) cc_final: 0.5721 (t0)
REVERT: E  292 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.7824 (t0)
REVERT: E  422 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7781 (m110)
REVERT: E  440 LEU cc_start: 0.8134 (tp) cc_final: 0.7644 (tt)
REVERT: F   47 LYS cc_start: 0.7619 (tppp) cc_final: 0.7217 (tptp)
REVERT: F   53 MET cc_start: 0.8713 (mtt) cc_final: 0.8501 (mtt)
REVERT: F   83 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7883 (mp0)
REVERT: F  206 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7589 (t)
REVERT: F  365 ASP cc_start: 0.7698 (m-30) cc_final: 0.7001 (m-30)
REVERT: F  429 ASN cc_start: 0.8567 (m-40) cc_final: 0.8189 (t0)
REVERT: G   47 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7131 (ttmp)
REVERT: G   83 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7700 (mp0)
REVERT: G  125 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7753 (mm-30)
REVERT: G  129 ASP cc_start: 0.7375 (t0) cc_final: 0.6952 (t0)
REVERT: G  213 HIS cc_start: 0.5958 (m-70) cc_final: 0.5619 (m-70)
REVERT: G  221 ASN cc_start: 0.7526 (p0) cc_final: 0.7133 (p0)
REVERT: G  327 SER cc_start: 0.7665 (t) cc_final: 0.7438 (p)
REVERT: G  422 ASN cc_start: 0.7897 (t0) cc_final: 0.7622 (t0)
REVERT: G  429 ASN cc_start: 0.8382 (m-40) cc_final: 0.7995 (t0)
REVERT: G  452 GLN cc_start: 0.6918 (mm-40) cc_final: 0.6549 (mp10)
REVERT: H   54 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8359 (m-30)
REVERT: H   83 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7907 (mp0)
REVERT: H  163 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7587 (mmt180)
REVERT: H  309 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8754 (tp)
REVERT: H  327 SER cc_start: 0.7763 (t) cc_final: 0.7395 (p)
REVERT: H  365 ASP cc_start: 0.7906 (m-30) cc_final: 0.7439 (m-30)
REVERT: H  371 GLN cc_start: 0.6762 (mt0) cc_final: 0.6353 (mt0)
REVERT: H  422 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7608 (m-40)
REVERT: H  425 ARG cc_start: 0.7269 (mtp180) cc_final: 0.6977 (mtm-85)
REVERT: H  429 ASN cc_start: 0.8259 (m-40) cc_final: 0.7858 (t0)
REVERT: H  452 GLN cc_start: 0.6906 (mm-40) cc_final: 0.6644 (mm110)
REVERT: I    8 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6778 (mt-10)
REVERT: I   83 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7810 (mp0)
REVERT: I  129 ASP cc_start: 0.7441 (t0) cc_final: 0.7182 (t0)
REVERT: I  170 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8908 (mtp)
REVERT: I  185 ILE cc_start: 0.8253 (mt) cc_final: 0.8033 (mt)
REVERT: I  206 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7632 (t)
REVERT: I  221 ASN cc_start: 0.7048 (p0) cc_final: 0.6722 (p0)
REVERT: I  327 SER cc_start: 0.7610 (t) cc_final: 0.7373 (p)
REVERT: I  440 LEU cc_start: 0.8105 (tp) cc_final: 0.7574 (tt)
REVERT: I  453 THR cc_start: 0.7142 (m) cc_final: 0.6931 (t)
REVERT: J   11 THR cc_start: 0.6960 (t) cc_final: 0.6759 (m)
REVERT: J  163 ARG cc_start: 0.7798 (mmm-85) cc_final: 0.7335 (mmt180)
REVERT: J  221 ASN cc_start: 0.7283 (p0) cc_final: 0.6934 (p0)
REVERT: J  309 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8581 (mp)
REVERT: J  323 GLU cc_start: 0.6477 (mt-10) cc_final: 0.6268 (mt-10)
REVERT: J  403 LYS cc_start: 0.7717 (mttt) cc_final: 0.7036 (mppt)
REVERT: J  423 THR cc_start: 0.7699 (p) cc_final: 0.7473 (p)
REVERT: J  440 LEU cc_start: 0.8178 (tp) cc_final: 0.7600 (tt)
REVERT: J  452 GLN cc_start: 0.6491 (mm-40) cc_final: 0.6179 (mm110)
REVERT: K  125 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7734 (mp0)
REVERT: K  221 ASN cc_start: 0.7027 (p0) cc_final: 0.6529 (p0)
REVERT: K  286 MET cc_start: 0.8925 (ttm) cc_final: 0.8649 (mtp)
REVERT: K  327 SER cc_start: 0.7779 (t) cc_final: 0.7505 (p)
REVERT: K  363 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7530 (mttp)
REVERT: K  422 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7715 (m-40)
REVERT: K  429 ASN cc_start: 0.8459 (m-40) cc_final: 0.7988 (t0)
REVERT: K  446 SER cc_start: 0.7156 (m) cc_final: 0.6867 (p)
REVERT: K  452 GLN cc_start: 0.6682 (mm-40) cc_final: 0.6317 (mp10)
REVERT: L   31 TYR cc_start: 0.7990 (t80) cc_final: 0.7769 (t80)
REVERT: L   53 MET cc_start: 0.8657 (mtt) cc_final: 0.8418 (mtt)
REVERT: L   83 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7817 (mp0)
REVERT: L  125 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7322 (mp0)
REVERT: L  143 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8550 (t0)
REVERT: L  156 ARG cc_start: 0.6576 (mmm160) cc_final: 0.6317 (mmm160)
REVERT: L  159 ASP cc_start: 0.6584 (m-30) cc_final: 0.5776 (OUTLIER)
REVERT: L  206 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7627 (t)
REVERT: L  211 THR cc_start: 0.7876 (OUTLIER) cc_final: 0.7660 (p)
REVERT: L  221 ASN cc_start: 0.7167 (p0) cc_final: 0.6765 (p0)
REVERT: L  327 SER cc_start: 0.7786 (t) cc_final: 0.7501 (p)
REVERT: L  365 ASP cc_start: 0.7556 (m-30) cc_final: 0.7240 (m-30)
REVERT: L  422 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7605 (m-40)
REVERT: L  429 ASN cc_start: 0.8634 (m-40) cc_final: 0.8180 (t0)
REVERT: L  452 GLN cc_start: 0.6575 (mm-40) cc_final: 0.6013 (mp10)
REVERT: M   47 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7245 (tptp)
REVERT: M  217 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7561 (mtt90)
REVERT: M  327 SER cc_start: 0.7720 (t) cc_final: 0.7379 (p)
REVERT: M  365 ASP cc_start: 0.7716 (m-30) cc_final: 0.7097 (m-30)
REVERT: M  422 ASN cc_start: 0.7904 (t0) cc_final: 0.7508 (t0)
REVERT: M  441 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8000 (tttt)
REVERT: M  446 SER cc_start: 0.7175 (m) cc_final: 0.6947 (p)
REVERT: M  450 ILE cc_start: 0.6788 (mp) cc_final: 0.6574 (mp)
REVERT: M  456 MET cc_start: 0.7283 (mtt) cc_final: 0.7038 (mtt)
  outliers start: 171
  outliers final: 75
  residues processed: 835
  average time/residue: 1.3701
  time to fit residues: 1416.2789
Evaluate side-chains
  821 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 107
    poor density    : 714
  time to evaluate  : 4.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain B residue   47 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  292 ASN
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  363 LYS
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue  125 GLU
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  192 ARG
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain E residue   54 ASP
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 GLU
Chi-restraints excluded: chain E residue  143 ASP
Chi-restraints excluded: chain E residue  262 ILE
Chi-restraints excluded: chain E residue  292 ASN
Chi-restraints excluded: chain E residue  309 LEU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  422 ASN
Chi-restraints excluded: chain F residue   54 ASP
Chi-restraints excluded: chain F residue   57 ARG
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  181 GLU
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain F residue  286 MET
Chi-restraints excluded: chain F residue  315 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue  125 GLU
Chi-restraints excluded: chain G residue  298 VAL
Chi-restraints excluded: chain G residue  309 LEU
Chi-restraints excluded: chain G residue  315 VAL
Chi-restraints excluded: chain G residue  432 LEU
Chi-restraints excluded: chain G residue  450 ILE
Chi-restraints excluded: chain H residue   54 ASP
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  133 VAL
Chi-restraints excluded: chain H residue  206 THR
Chi-restraints excluded: chain H residue  309 LEU
Chi-restraints excluded: chain H residue  422 ASN
Chi-restraints excluded: chain H residue  436 LEU
Chi-restraints excluded: chain H residue  450 ILE
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   46 SER
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  170 MET
Chi-restraints excluded: chain I residue  181 GLU
Chi-restraints excluded: chain I residue  206 THR
Chi-restraints excluded: chain I residue  229 THR
Chi-restraints excluded: chain I residue  286 MET
Chi-restraints excluded: chain I residue  362 MET
Chi-restraints excluded: chain I residue  450 ILE
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue   78 THR
Chi-restraints excluded: chain J residue  125 GLU
Chi-restraints excluded: chain J residue  292 ASN
Chi-restraints excluded: chain J residue  298 VAL
Chi-restraints excluded: chain J residue  309 LEU
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain K residue  192 ARG
Chi-restraints excluded: chain K residue  206 THR
Chi-restraints excluded: chain K residue  292 ASN
Chi-restraints excluded: chain K residue  363 LYS
Chi-restraints excluded: chain K residue  422 ASN
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue   96 SER
Chi-restraints excluded: chain L residue  125 GLU
Chi-restraints excluded: chain L residue  143 ASP
Chi-restraints excluded: chain L residue  206 THR
Chi-restraints excluded: chain L residue  211 THR
Chi-restraints excluded: chain L residue  292 ASN
Chi-restraints excluded: chain L residue  293 LEU
Chi-restraints excluded: chain L residue  298 VAL
Chi-restraints excluded: chain L residue  422 ASN
Chi-restraints excluded: chain L residue  441 LYS
Chi-restraints excluded: chain M residue   47 LYS
Chi-restraints excluded: chain M residue   78 THR
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue  125 GLU
Chi-restraints excluded: chain M residue  206 THR
Chi-restraints excluded: chain M residue  217 ARG
Chi-restraints excluded: chain M residue  237 SER
Chi-restraints excluded: chain M residue  315 VAL
Chi-restraints excluded: chain M residue  362 MET
Chi-restraints excluded: chain M residue  376 MET
Chi-restraints excluded: chain M residue  441 LYS
Chi-restraints excluded: chain M residue  452 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 611
   random chunks:
   chunk 233 optimal weight:   10.0000
   chunk 493 optimal weight:   20.0000
   chunk 59 optimal weight:    6.9990
   chunk 180 optimal weight:    2.9990
   chunk 152 optimal weight:    0.8980
   chunk 510 optimal weight:    8.9990
   chunk 432 optimal weight:    4.9990
   chunk 467 optimal weight:    1.9990
   chunk 577 optimal weight:    5.9990
   chunk 327 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
B 112 GLN
B 422 ASN
C 371 GLN
C 422 ASN
C 452 GLN
D 371 GLN
E 112 GLN
E 221 ASN
E 340 GLN
F 178 ASN
F 221 ASN
F 422 ASN
F 452 GLN
G 340 GLN
H 112 GLN
I 112 GLN
I 371 GLN
I 422 ASN
I 452 GLN
J 422 ASN
L 112 GLN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.183361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.117963 restraints weight = 47179.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.15
r_work: 0.3031 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  51571  Z= 0.249
  Angle     :  0.565   6.251  69576  Z= 0.315
  Chirality :  0.042   0.165   7540
  Planarity :  0.004   0.041   9191
  Dihedral  :  4.615  16.803   6942
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 12.72 %
    Favored  : 84.22 %
  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:  1.05 (0.10), residues: 6162
  helix:  1.72 (0.10), residues: 2743
  sheet:  0.97 (0.14), residues: 1144
  loop : -0.70 (0.12), residues: 2275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS K 354 
 PHE   0.030   0.002   PHE G 235 
 TYR   0.021   0.002   TYR L 218 
 ARG   0.007   0.001   ARG F 425 

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

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

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  895 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 172
    poor density    : 723
  time to evaluate  : 4.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8734 (mtt) cc_final: 0.8482 (mtt)
REVERT: A   83 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7926 (pm20)
REVERT: A  125 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7522 (mp0)
REVERT: A  183 ASN cc_start: 0.8440 (m110) cc_final: 0.8161 (m110)
REVERT: A  206 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7760 (t)
REVERT: A  213 HIS cc_start: 0.6529 (m-70) cc_final: 0.6219 (m170)
REVERT: A  286 MET cc_start: 0.8970 (ttm) cc_final: 0.8422 (mtp)
REVERT: A  429 ASN cc_start: 0.8459 (m-40) cc_final: 0.8104 (t0)
REVERT: A  452 GLN cc_start: 0.6595 (mm-40) cc_final: 0.5973 (mp-120)
REVERT: A  456 MET cc_start: 0.7404 (mtt) cc_final: 0.7185 (mtt)
REVERT: B   47 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7462 (ttmt)
REVERT: B   53 MET cc_start: 0.8599 (mtt) cc_final: 0.8266 (mtm)
REVERT: B  125 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7734 (mp0)
REVERT: B  129 ASP cc_start: 0.7264 (t0) cc_final: 0.6918 (t0)
REVERT: B  159 ASP cc_start: 0.6252 (m-30) cc_final: 0.5566 (t0)
REVERT: B  163 ARG cc_start: 0.7805 (mmm-85) cc_final: 0.7530 (mmt180)
REVERT: B  206 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.7521 (t)
REVERT: B  217 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7253 (mtt90)
REVERT: B  221 ASN cc_start: 0.7284 (p0) cc_final: 0.6946 (p0)
REVERT: B  286 MET cc_start: 0.9040 (ttm) cc_final: 0.8595 (mtp)
REVERT: B  340 GLN cc_start: 0.8754 (tp40) cc_final: 0.8481 (tm130)
REVERT: B  365 ASP cc_start: 0.7098 (m-30) cc_final: 0.6490 (m-30)
REVERT: B  429 ASN cc_start: 0.8485 (m-40) cc_final: 0.7963 (t0)
REVERT: B  440 LEU cc_start: 0.7921 (tp) cc_final: 0.7301 (tt)
REVERT: C    8 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6721 (mt-10)
REVERT: C  185 ILE cc_start: 0.8187 (mt) cc_final: 0.7787 (mt)
REVERT: C  219 LEU cc_start: 0.8212 (mp) cc_final: 0.7980 (mt)
REVERT: C  221 ASN cc_start: 0.6959 (p0) cc_final: 0.6702 (p0)
REVERT: C  279 MET cc_start: 0.9224 (mtp) cc_final: 0.8988 (mtp)
REVERT: C  362 MET cc_start: 0.8350 (ptp) cc_final: 0.7841 (ptp)
REVERT: C  363 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7328 (mmmm)
REVERT: C  365 ASP cc_start: 0.7523 (m-30) cc_final: 0.7031 (m-30)
REVERT: C  422 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7575 (m-40)
REVERT: C  429 ASN cc_start: 0.8630 (m110) cc_final: 0.8145 (t0)
REVERT: D  125 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7614 (mp0)
REVERT: D  178 ASN cc_start: 0.7360 (p0) cc_final: 0.7146 (m-40)
REVERT: D  209 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7623 (tp)
REVERT: D  221 ASN cc_start: 0.7264 (p0) cc_final: 0.6933 (p0)
REVERT: D  286 MET cc_start: 0.8967 (ttm) cc_final: 0.8462 (mtp)
REVERT: D  327 SER cc_start: 0.7792 (t) cc_final: 0.7473 (p)
REVERT: D  363 LYS cc_start: 0.8073 (mmtp) cc_final: 0.7607 (mttp)
REVERT: D  422 ASN cc_start: 0.8202 (t0) cc_final: 0.7744 (m110)
REVERT: D  452 GLN cc_start: 0.6652 (mm-40) cc_final: 0.6231 (mp10)
REVERT: E   54 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8351 (m-30)
REVERT: E  125 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7570 (mp0)
REVERT: E  143 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8418 (t0)
REVERT: E  159 ASP cc_start: 0.6435 (m-30) cc_final: 0.5651 (t0)
REVERT: E  292 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.7826 (t0)
REVERT: E  422 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7789 (m110)
REVERT: E  423 THR cc_start: 0.7585 (p) cc_final: 0.7331 (p)
REVERT: F   47 LYS cc_start: 0.7611 (tppp) cc_final: 0.7195 (tptp)
REVERT: F   53 MET cc_start: 0.8722 (mtt) cc_final: 0.8517 (mtt)
REVERT: F   83 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7909 (mp0)
REVERT: F  206 THR cc_start: 0.7804 (OUTLIER) cc_final: 0.7581 (t)
REVERT: F  365 ASP cc_start: 0.7705 (m-30) cc_final: 0.7030 (m-30)
REVERT: F  429 ASN cc_start: 0.8587 (m-40) cc_final: 0.8196 (t0)
REVERT: G   47 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7180 (ttmp)
REVERT: G   83 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7751 (mp0)
REVERT: G  129 ASP cc_start: 0.7388 (t0) cc_final: 0.6963 (t0)
REVERT: G  213 HIS cc_start: 0.5981 (m-70) cc_final: 0.5618 (m-70)
REVERT: G  221 ASN cc_start: 0.7586 (p0) cc_final: 0.7200 (p0)
REVERT: G  327 SER cc_start: 0.7674 (t) cc_final: 0.7454 (p)
REVERT: G  422 ASN cc_start: 0.7874 (t0) cc_final: 0.7592 (t0)
REVERT: G  429 ASN cc_start: 0.8429 (m-40) cc_final: 0.8015 (t0)
REVERT: G  452 GLN cc_start: 0.6896 (mm-40) cc_final: 0.6490 (mp10)
REVERT: H   54 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8377 (m-30)
REVERT: H   83 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7922 (mp0)
REVERT: H  163 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.7627 (mmt180)
REVERT: H  309 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8762 (tp)
REVERT: H  327 SER cc_start: 0.7765 (t) cc_final: 0.7404 (p)
REVERT: H  365 ASP cc_start: 0.7921 (m-30) cc_final: 0.7447 (m-30)
REVERT: H  371 GLN cc_start: 0.6720 (mt0) cc_final: 0.6477 (mt0)
REVERT: H  429 ASN cc_start: 0.8273 (m-40) cc_final: 0.7858 (t0)
REVERT: H  452 GLN cc_start: 0.6806 (mm-40) cc_final: 0.6535 (mm110)
REVERT: I    8 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6785 (mt-10)
REVERT: I  129 ASP cc_start: 0.7454 (t0) cc_final: 0.7171 (t0)
REVERT: I  170 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8910 (mtp)
REVERT: I  185 ILE cc_start: 0.8255 (mt) cc_final: 0.8026 (mt)
REVERT: I  206 THR cc_start: 0.7846 (OUTLIER) cc_final: 0.7638 (t)
REVERT: I  221 ASN cc_start: 0.6999 (p0) cc_final: 0.6686 (p0)
REVERT: I  327 SER cc_start: 0.7618 (t) cc_final: 0.7377 (p)
REVERT: I  365 ASP cc_start: 0.7475 (m-30) cc_final: 0.6921 (m-30)
REVERT: I  440 LEU cc_start: 0.8094 (tp) cc_final: 0.7543 (tt)
REVERT: I  453 THR cc_start: 0.7099 (m) cc_final: 0.6888 (t)
REVERT: J  156 ARG cc_start: 0.6954 (mmm160) cc_final: 0.6727 (mmm160)
REVERT: J  163 ARG cc_start: 0.7735 (mmm-85) cc_final: 0.7394 (mmt180)
REVERT: J  221 ASN cc_start: 0.7289 (p0) cc_final: 0.6966 (p0)
REVERT: J  309 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8571 (mp)
REVERT: J  327 SER cc_start: 0.7705 (t) cc_final: 0.7340 (p)
REVERT: J  403 LYS cc_start: 0.7719 (mttt) cc_final: 0.7427 (mttm)
REVERT: J  423 THR cc_start: 0.7659 (p) cc_final: 0.7448 (p)
REVERT: J  440 LEU cc_start: 0.8176 (tp) cc_final: 0.7588 (tt)
REVERT: J  452 GLN cc_start: 0.6490 (mm-40) cc_final: 0.6108 (mm110)
REVERT: K  125 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7808 (mp0)
REVERT: K  170 MET cc_start: 0.9169 (mtm) cc_final: 0.8876 (mtm)
REVERT: K  221 ASN cc_start: 0.7224 (p0) cc_final: 0.6736 (p0)
REVERT: K  255 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8783 (mptm)
REVERT: K  286 MET cc_start: 0.8932 (ttm) cc_final: 0.8669 (mtp)
REVERT: K  327 SER cc_start: 0.7831 (t) cc_final: 0.7570 (p)
REVERT: K  363 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7499 (mttp)
REVERT: K  422 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7684 (m-40)
REVERT: K  429 ASN cc_start: 0.8463 (m-40) cc_final: 0.7984 (t0)
REVERT: K  446 SER cc_start: 0.7037 (m) cc_final: 0.6755 (p)
REVERT: K  452 GLN cc_start: 0.6666 (mm-40) cc_final: 0.6257 (mp10)
REVERT: L   53 MET cc_start: 0.8656 (mtt) cc_final: 0.8420 (mtt)
REVERT: L   83 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7844 (mp0)
REVERT: L  143 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8563 (t0)
REVERT: L  156 ARG cc_start: 0.6576 (mmm160) cc_final: 0.6298 (mmm160)
REVERT: L  159 ASP cc_start: 0.6446 (m-30) cc_final: 0.5604 (OUTLIER)
REVERT: L  206 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7663 (t)
REVERT: L  211 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7736 (p)
REVERT: L  221 ASN cc_start: 0.7257 (p0) cc_final: 0.6871 (p0)
REVERT: L  327 SER cc_start: 0.7796 (t) cc_final: 0.7512 (p)
REVERT: L  365 ASP cc_start: 0.7611 (m-30) cc_final: 0.7283 (m-30)
REVERT: L  429 ASN cc_start: 0.8627 (m-40) cc_final: 0.8173 (t0)
REVERT: L  452 GLN cc_start: 0.6559 (mm-40) cc_final: 0.6048 (mp10)
REVERT: M   47 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7327 (tptp)
REVERT: M  217 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7569 (mtt90)
REVERT: M  255 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8753 (mptp)
REVERT: M  327 SER cc_start: 0.7730 (t) cc_final: 0.7393 (p)
REVERT: M  365 ASP cc_start: 0.7717 (m-30) cc_final: 0.7082 (m-30)
REVERT: M  422 ASN cc_start: 0.7895 (t0) cc_final: 0.7496 (t0)
REVERT: M  441 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8012 (tttt)
REVERT: M  450 ILE cc_start: 0.6785 (mp) cc_final: 0.6566 (mp)
REVERT: M  456 MET cc_start: 0.7240 (mtt) cc_final: 0.7015 (mtt)
  outliers start: 172
  outliers final: 90
  residues processed: 828
  average time/residue: 1.4013
  time to fit residues: 1431.0875
Evaluate side-chains
  833 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 122
    poor density    : 711
  time to evaluate  : 4.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain B residue   47 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  422 ASN
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  143 ASP
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  292 ASN
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  363 LYS
Chi-restraints excluded: chain C residue  422 ASN
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue  125 GLU
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  209 LEU
Chi-restraints excluded: chain D residue  262 ILE
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain E residue   54 ASP
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 GLU
Chi-restraints excluded: chain E residue  143 ASP
Chi-restraints excluded: chain E residue  262 ILE
Chi-restraints excluded: chain E residue  292 ASN
Chi-restraints excluded: chain E residue  309 LEU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  422 ASN
Chi-restraints excluded: chain F residue   54 ASP
Chi-restraints excluded: chain F residue   57 ARG
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  178 ASN
Chi-restraints excluded: chain F residue  181 GLU
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain F residue  286 MET
Chi-restraints excluded: chain F residue  315 VAL
Chi-restraints excluded: chain F residue  362 MET
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue  262 ILE
Chi-restraints excluded: chain G residue  298 VAL
Chi-restraints excluded: chain G residue  309 LEU
Chi-restraints excluded: chain G residue  315 VAL
Chi-restraints excluded: chain G residue  432 LEU
Chi-restraints excluded: chain G residue  450 ILE
Chi-restraints excluded: chain H residue   39 LEU
Chi-restraints excluded: chain H residue   54 ASP
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  133 VAL
Chi-restraints excluded: chain H residue  206 THR
Chi-restraints excluded: chain H residue  309 LEU
Chi-restraints excluded: chain H residue  396 LYS
Chi-restraints excluded: chain H residue  436 LEU
Chi-restraints excluded: chain H residue  450 ILE
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   46 SER
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  125 GLU
Chi-restraints excluded: chain I residue  170 MET
Chi-restraints excluded: chain I residue  181 GLU
Chi-restraints excluded: chain I residue  206 THR
Chi-restraints excluded: chain I residue  229 THR
Chi-restraints excluded: chain I residue  262 ILE
Chi-restraints excluded: chain I residue  362 MET
Chi-restraints excluded: chain I residue  422 ASN
Chi-restraints excluded: chain I residue  450 ILE
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue   78 THR
Chi-restraints excluded: chain J residue  292 ASN
Chi-restraints excluded: chain J residue  298 VAL
Chi-restraints excluded: chain J residue  309 LEU
Chi-restraints excluded: chain J residue  432 LEU
Chi-restraints excluded: chain K residue   47 LYS
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain K residue  181 GLU
Chi-restraints excluded: chain K residue  192 ARG
Chi-restraints excluded: chain K residue  206 THR
Chi-restraints excluded: chain K residue  255 LYS
Chi-restraints excluded: chain K residue  262 ILE
Chi-restraints excluded: chain K residue  282 LEU
Chi-restraints excluded: chain K residue  292 ASN
Chi-restraints excluded: chain K residue  363 LYS
Chi-restraints excluded: chain K residue  422 ASN
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue   96 SER
Chi-restraints excluded: chain L residue  143 ASP
Chi-restraints excluded: chain L residue  206 THR
Chi-restraints excluded: chain L residue  211 THR
Chi-restraints excluded: chain L residue  262 ILE
Chi-restraints excluded: chain L residue  286 MET
Chi-restraints excluded: chain L residue  292 ASN
Chi-restraints excluded: chain L residue  293 LEU
Chi-restraints excluded: chain L residue  298 VAL
Chi-restraints excluded: chain M residue   47 LYS
Chi-restraints excluded: chain M residue   78 THR
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue  125 GLU
Chi-restraints excluded: chain M residue  143 ASP
Chi-restraints excluded: chain M residue  206 THR
Chi-restraints excluded: chain M residue  217 ARG
Chi-restraints excluded: chain M residue  237 SER
Chi-restraints excluded: chain M residue  255 LYS
Chi-restraints excluded: chain M residue  315 VAL
Chi-restraints excluded: chain M residue  362 MET
Chi-restraints excluded: chain M residue  376 MET
Chi-restraints excluded: chain M residue  441 LYS
Chi-restraints excluded: chain M residue  452 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 611
   random chunks:
   chunk 588 optimal weight:    8.9990
   chunk 413 optimal weight:    1.9990
   chunk 524 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 217 optimal weight:    5.9990
   chunk 594 optimal weight:    0.0020
   chunk 297 optimal weight:    9.9990
   chunk 91 optimal weight:    9.9990
   chunk 536 optimal weight:    9.9990
   chunk 229 optimal weight:    0.0570
   chunk 159 optimal weight:    9.9990
   overall best weight:    2.4112

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
A 178 ASN
A 221 ASN
B 112 GLN
B 422 ASN
C 371 GLN
C 452 GLN
D 371 GLN
E 112 GLN
E 340 GLN
F 221 ASN
F 422 ASN
G 178 ASN
G 340 GLN
H 112 GLN
H 221 ASN
H 422 ASN
I 112 GLN
I 422 ASN
I 452 GLN
J 422 ASN
K 112 GLN
L 112 GLN
L 422 ASN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.183325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.117626 restraints weight = 47269.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.17
r_work: 0.2999 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  51571  Z= 0.251
  Angle     :  0.564   6.268  69576  Z= 0.315
  Chirality :  0.042   0.157   7540
  Planarity :  0.004   0.044   9191
  Dihedral  :  4.605  16.710   6942
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 13.16 %
    Favored  : 83.69 %
  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:  1.05 (0.10), residues: 6162
  helix:  1.74 (0.10), residues: 2743
  sheet:  0.97 (0.14), residues: 1144
  loop : -0.74 (0.12), residues: 2275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS K 354 
 PHE   0.031   0.002   PHE E 235 
 TYR   0.022   0.002   TYR L 218 
 ARG   0.008   0.001   ARG F 425 

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

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

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  901 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 177
    poor density    : 724
  time to evaluate  : 4.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6531 (mt-10)
REVERT: A   53 MET cc_start: 0.8765 (mtt) cc_final: 0.8534 (mtt)
REVERT: A   83 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7964 (pm20)
REVERT: A  183 ASN cc_start: 0.8457 (m110) cc_final: 0.8175 (m110)
REVERT: A  206 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7782 (t)
REVERT: A  213 HIS cc_start: 0.6528 (m-70) cc_final: 0.6216 (m170)
REVERT: A  286 MET cc_start: 0.9007 (ttm) cc_final: 0.8452 (mtp)
REVERT: A  429 ASN cc_start: 0.8491 (m-40) cc_final: 0.8115 (t0)
REVERT: A  452 GLN cc_start: 0.6536 (mm-40) cc_final: 0.5925 (mp-120)
REVERT: A  456 MET cc_start: 0.7367 (mtt) cc_final: 0.7166 (mtt)
REVERT: B   47 LYS cc_start: 0.7778 (tptp) cc_final: 0.7496 (ttmt)
REVERT: B   53 MET cc_start: 0.8619 (mtt) cc_final: 0.8287 (mtm)
REVERT: B  125 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7668 (mp0)
REVERT: B  129 ASP cc_start: 0.7291 (t0) cc_final: 0.6940 (t0)
REVERT: B  159 ASP cc_start: 0.6252 (m-30) cc_final: 0.5552 (t0)
REVERT: B  163 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7500 (mmt180)
REVERT: B  206 THR cc_start: 0.7777 (OUTLIER) cc_final: 0.7568 (t)
REVERT: B  217 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7195 (mtt90)
REVERT: B  221 ASN cc_start: 0.7248 (p0) cc_final: 0.6899 (p0)
REVERT: B  286 MET cc_start: 0.9083 (ttm) cc_final: 0.8693 (mtp)
REVERT: B  340 GLN cc_start: 0.8795 (tp40) cc_final: 0.8527 (tm130)
REVERT: B  365 ASP cc_start: 0.7072 (m-30) cc_final: 0.6467 (m-30)
REVERT: B  429 ASN cc_start: 0.8531 (m-40) cc_final: 0.7993 (t0)
REVERT: B  440 LEU cc_start: 0.7975 (tp) cc_final: 0.7357 (tt)
REVERT: C    8 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6736 (mt-10)
REVERT: C  185 ILE cc_start: 0.8227 (mt) cc_final: 0.7832 (mt)
REVERT: C  219 LEU cc_start: 0.8221 (mp) cc_final: 0.7968 (mt)
REVERT: C  279 MET cc_start: 0.9247 (mtp) cc_final: 0.8999 (mtp)
REVERT: C  362 MET cc_start: 0.8393 (ptp) cc_final: 0.7862 (ptp)
REVERT: C  363 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7359 (mmmm)
REVERT: C  365 ASP cc_start: 0.7524 (m-30) cc_final: 0.7033 (m-30)
REVERT: C  429 ASN cc_start: 0.8676 (m110) cc_final: 0.8172 (t0)
REVERT: D   32 ASP cc_start: 0.6851 (m-30) cc_final: 0.6602 (m-30)
REVERT: D  125 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7620 (mp0)
REVERT: D  209 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7664 (tp)
REVERT: D  221 ASN cc_start: 0.7317 (p0) cc_final: 0.7050 (p0)
REVERT: D  286 MET cc_start: 0.9007 (ttm) cc_final: 0.8499 (mtp)
REVERT: D  363 LYS cc_start: 0.8039 (mmtp) cc_final: 0.7550 (mttp)
REVERT: D  422 ASN cc_start: 0.8215 (t0) cc_final: 0.7841 (m-40)
REVERT: D  452 GLN cc_start: 0.6727 (mm-40) cc_final: 0.6403 (mp10)
REVERT: E   47 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7342 (mtmt)
REVERT: E   54 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8404 (m-30)
REVERT: E  125 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7600 (mp0)
REVERT: E  143 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8487 (t0)
REVERT: E  159 ASP cc_start: 0.6423 (m-30) cc_final: 0.5628 (t0)
REVERT: E  292 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.7899 (t0)
REVERT: E  422 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7817 (m110)
REVERT: E  423 THR cc_start: 0.7615 (p) cc_final: 0.7361 (p)
REVERT: E  440 LEU cc_start: 0.8148 (tp) cc_final: 0.7766 (tt)
REVERT: F   47 LYS cc_start: 0.7642 (tppp) cc_final: 0.7232 (tptp)
REVERT: F   53 MET cc_start: 0.8747 (mtt) cc_final: 0.8547 (mtt)
REVERT: F   83 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7947 (mp0)
REVERT: F  125 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7573 (mp0)
REVERT: F  206 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7623 (t)
REVERT: F  365 ASP cc_start: 0.7690 (m-30) cc_final: 0.7021 (m-30)
REVERT: F  429 ASN cc_start: 0.8621 (m-40) cc_final: 0.8218 (t0)
REVERT: G   47 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7206 (ttmp)
REVERT: G   83 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7767 (mp0)
REVERT: G  129 ASP cc_start: 0.7420 (t0) cc_final: 0.7000 (t0)
REVERT: G  213 HIS cc_start: 0.6064 (m-70) cc_final: 0.5710 (m-70)
REVERT: G  221 ASN cc_start: 0.7511 (p0) cc_final: 0.7143 (p0)
REVERT: G  327 SER cc_start: 0.7680 (t) cc_final: 0.7458 (p)
REVERT: G  422 ASN cc_start: 0.7885 (t0) cc_final: 0.7600 (t0)
REVERT: G  429 ASN cc_start: 0.8476 (m-40) cc_final: 0.8082 (t0)
REVERT: G  452 GLN cc_start: 0.6805 (mm-40) cc_final: 0.6387 (mp10)
REVERT: H   54 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8418 (m-30)
REVERT: H   83 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7956 (mp0)
REVERT: H  143 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8604 (t0)
REVERT: H  163 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7587 (mmt180)
REVERT: H  179 THR cc_start: 0.7954 (m) cc_final: 0.7578 (p)
REVERT: H  309 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8773 (tp)
REVERT: H  327 SER cc_start: 0.7764 (t) cc_final: 0.7399 (p)
REVERT: H  362 MET cc_start: 0.8402 (ptm) cc_final: 0.8175 (ptp)
REVERT: H  365 ASP cc_start: 0.7924 (m-30) cc_final: 0.7444 (m-30)
REVERT: H  371 GLN cc_start: 0.6657 (mt0) cc_final: 0.6326 (mt0)
REVERT: H  429 ASN cc_start: 0.8313 (m-40) cc_final: 0.7870 (t0)
REVERT: H  452 GLN cc_start: 0.6851 (mm-40) cc_final: 0.6576 (mm110)
REVERT: I    8 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6848 (mt-10)
REVERT: I   83 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7356 (mp0)
REVERT: I  129 ASP cc_start: 0.7479 (t0) cc_final: 0.7204 (t0)
REVERT: I  170 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8922 (mtp)
REVERT: I  185 ILE cc_start: 0.8244 (mt) cc_final: 0.8027 (mt)
REVERT: I  206 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7683 (t)
REVERT: I  221 ASN cc_start: 0.6936 (p0) cc_final: 0.6629 (p0)
REVERT: I  235 PHE cc_start: 0.7854 (t80) cc_final: 0.7280 (t80)
REVERT: I  255 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8752 (mptt)
REVERT: I  327 SER cc_start: 0.7615 (t) cc_final: 0.7364 (p)
REVERT: I  340 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8006 (tp-100)
REVERT: I  365 ASP cc_start: 0.7467 (m-30) cc_final: 0.6911 (m-30)
REVERT: I  440 LEU cc_start: 0.8053 (tp) cc_final: 0.7490 (tt)
REVERT: I  453 THR cc_start: 0.7056 (m) cc_final: 0.6835 (t)
REVERT: J  163 ARG cc_start: 0.7742 (mmm-85) cc_final: 0.7417 (mmt180)
REVERT: J  221 ASN cc_start: 0.7230 (p0) cc_final: 0.6879 (p0)
REVERT: J  309 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8585 (mp)
REVERT: J  327 SER cc_start: 0.7725 (t) cc_final: 0.7366 (p)
REVERT: J  403 LYS cc_start: 0.7756 (mttt) cc_final: 0.7480 (mttm)
REVERT: J  423 THR cc_start: 0.7666 (p) cc_final: 0.7454 (p)
REVERT: J  440 LEU cc_start: 0.8190 (tp) cc_final: 0.7603 (tt)
REVERT: J  452 GLN cc_start: 0.6390 (mm-40) cc_final: 0.6020 (mm110)
REVERT: K  143 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8543 (t0)
REVERT: K  221 ASN cc_start: 0.7157 (p0) cc_final: 0.6703 (p0)
REVERT: K  255 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8795 (mptm)
REVERT: K  286 MET cc_start: 0.8963 (ttm) cc_final: 0.8697 (mtp)
REVERT: K  327 SER cc_start: 0.7836 (t) cc_final: 0.7574 (p)
REVERT: K  363 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7481 (mttp)
REVERT: K  422 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7727 (m-40)
REVERT: K  429 ASN cc_start: 0.8484 (m-40) cc_final: 0.7982 (t0)
REVERT: K  446 SER cc_start: 0.7123 (m) cc_final: 0.6885 (p)
REVERT: K  452 GLN cc_start: 0.6722 (mm-40) cc_final: 0.6280 (mp10)
REVERT: L   53 MET cc_start: 0.8695 (mtt) cc_final: 0.8467 (mtt)
REVERT: L   83 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7876 (mp0)
REVERT: L  143 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8611 (t0)
REVERT: L  159 ASP cc_start: 0.6353 (m-30) cc_final: 0.5520 (OUTLIER)
REVERT: L  206 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7706 (t)
REVERT: L  221 ASN cc_start: 0.7206 (p0) cc_final: 0.6838 (p0)
REVERT: L  327 SER cc_start: 0.7660 (t) cc_final: 0.7379 (p)
REVERT: L  365 ASP cc_start: 0.7902 (m-30) cc_final: 0.7607 (m-30)
REVERT: L  422 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7729 (m110)
REVERT: L  429 ASN cc_start: 0.8673 (m-40) cc_final: 0.8190 (t0)
REVERT: L  440 LEU cc_start: 0.7797 (tp) cc_final: 0.7146 (tt)
REVERT: L  452 GLN cc_start: 0.6669 (mm-40) cc_final: 0.6074 (mp10)
REVERT: M   47 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7376 (tptp)
REVERT: M  217 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7590 (mtt90)
REVERT: M  255 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8769 (mptp)
REVERT: M  327 SER cc_start: 0.7733 (t) cc_final: 0.7388 (p)
REVERT: M  365 ASP cc_start: 0.7701 (m-30) cc_final: 0.7075 (m-30)
REVERT: M  422 ASN cc_start: 0.7907 (t0) cc_final: 0.7514 (t0)
REVERT: M  441 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7997 (tttt)
REVERT: M  450 ILE cc_start: 0.6739 (mp) cc_final: 0.6523 (mp)
REVERT: M  456 MET cc_start: 0.7223 (mtt) cc_final: 0.6986 (mtt)
  outliers start: 177
  outliers final: 95
  residues processed: 834
  average time/residue: 1.3778
  time to fit residues: 1419.3952
Evaluate side-chains
  842 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 131
    poor density    : 711
  time to evaluate  : 4.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   47 LYS
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  143 ASP
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  292 ASN
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  363 LYS
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue  125 GLU
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  192 ARG
Chi-restraints excluded: chain D residue  209 LEU
Chi-restraints excluded: chain D residue  229 THR
Chi-restraints excluded: chain D residue  262 ILE
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain E residue   47 LYS
Chi-restraints excluded: chain E residue   54 ASP
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 GLU
Chi-restraints excluded: chain E residue  143 ASP
Chi-restraints excluded: chain E residue  262 ILE
Chi-restraints excluded: chain E residue  292 ASN
Chi-restraints excluded: chain E residue  309 LEU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  422 ASN
Chi-restraints excluded: chain F residue   54 ASP
Chi-restraints excluded: chain F residue   57 ARG
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  143 ASP
Chi-restraints excluded: chain F residue  181 GLU
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain F residue  286 MET
Chi-restraints excluded: chain F residue  315 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue  262 ILE
Chi-restraints excluded: chain G residue  298 VAL
Chi-restraints excluded: chain G residue  309 LEU
Chi-restraints excluded: chain G residue  315 VAL
Chi-restraints excluded: chain G residue  432 LEU
Chi-restraints excluded: chain G residue  444 ILE
Chi-restraints excluded: chain G residue  450 ILE
Chi-restraints excluded: chain H residue   54 ASP
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  125 GLU
Chi-restraints excluded: chain H residue  133 VAL
Chi-restraints excluded: chain H residue  143 ASP
Chi-restraints excluded: chain H residue  206 THR
Chi-restraints excluded: chain H residue  309 LEU
Chi-restraints excluded: chain H residue  396 LYS
Chi-restraints excluded: chain H residue  436 LEU
Chi-restraints excluded: chain H residue  450 ILE
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   46 SER
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   83 GLU
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  125 GLU
Chi-restraints excluded: chain I residue  143 ASP
Chi-restraints excluded: chain I residue  170 MET
Chi-restraints excluded: chain I residue  206 THR
Chi-restraints excluded: chain I residue  229 THR
Chi-restraints excluded: chain I residue  255 LYS
Chi-restraints excluded: chain I residue  262 ILE
Chi-restraints excluded: chain I residue  286 MET
Chi-restraints excluded: chain I residue  340 GLN
Chi-restraints excluded: chain I residue  362 MET
Chi-restraints excluded: chain I residue  450 ILE
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue   78 THR
Chi-restraints excluded: chain J residue  292 ASN
Chi-restraints excluded: chain J residue  298 VAL
Chi-restraints excluded: chain J residue  309 LEU
Chi-restraints excluded: chain J residue  432 LEU
Chi-restraints excluded: chain K residue   47 LYS
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain K residue  143 ASP
Chi-restraints excluded: chain K residue  181 GLU
Chi-restraints excluded: chain K residue  192 ARG
Chi-restraints excluded: chain K residue  206 THR
Chi-restraints excluded: chain K residue  255 LYS
Chi-restraints excluded: chain K residue  262 ILE
Chi-restraints excluded: chain K residue  282 LEU
Chi-restraints excluded: chain K residue  292 ASN
Chi-restraints excluded: chain K residue  363 LYS
Chi-restraints excluded: chain K residue  422 ASN
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue   96 SER
Chi-restraints excluded: chain L residue  125 GLU
Chi-restraints excluded: chain L residue  143 ASP
Chi-restraints excluded: chain L residue  206 THR
Chi-restraints excluded: chain L residue  262 ILE
Chi-restraints excluded: chain L residue  282 LEU
Chi-restraints excluded: chain L residue  286 MET
Chi-restraints excluded: chain L residue  292 ASN
Chi-restraints excluded: chain L residue  293 LEU
Chi-restraints excluded: chain L residue  298 VAL
Chi-restraints excluded: chain L residue  422 ASN
Chi-restraints excluded: chain M residue   47 LYS
Chi-restraints excluded: chain M residue   78 THR
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue  125 GLU
Chi-restraints excluded: chain M residue  143 ASP
Chi-restraints excluded: chain M residue  206 THR
Chi-restraints excluded: chain M residue  217 ARG
Chi-restraints excluded: chain M residue  237 SER
Chi-restraints excluded: chain M residue  255 LYS
Chi-restraints excluded: chain M residue  315 VAL
Chi-restraints excluded: chain M residue  362 MET
Chi-restraints excluded: chain M residue  376 MET
Chi-restraints excluded: chain M residue  441 LYS
Chi-restraints excluded: chain M residue  452 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 611
   random chunks:
   chunk 171 optimal weight:    0.9980
   chunk 345 optimal weight:    4.9990
   chunk 506 optimal weight:    6.9990
   chunk 141 optimal weight:   20.0000
   chunk 540 optimal weight:    9.9990
   chunk 425 optimal weight:    7.9990
   chunk 400 optimal weight:    4.9990
   chunk 603 optimal weight:    3.9990
   chunk 263 optimal weight:    0.9990
   chunk 574 optimal weight:    3.9990
   chunk 441 optimal weight:    4.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
A 178 ASN
B 112 GLN
B 422 ASN
C  43 ASN
C 371 GLN
C 422 ASN
C 452 GLN
D 178 ASN
D 371 GLN
E 112 GLN
E 221 ASN
E 340 GLN
F 178 ASN
F 221 ASN
F 422 ASN
G 178 ASN
G 340 GLN
H 112 GLN
H 422 ASN
I 112 GLN
I 422 ASN
I 452 GLN
J 422 ASN
K 112 GLN
L 422 ASN
M 178 ASN
M 336 GLN

Total number of N/Q/H flips: 28

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.182662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.115841 restraints weight = 47118.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 2.32
r_work: 0.3025 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  51571  Z= 0.297
  Angle     :  0.601   7.372  69576  Z= 0.334
  Chirality :  0.044   0.159   7540
  Planarity :  0.004   0.053   9191
  Dihedral  :  4.702  17.293   6942
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 2.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 13.39 %
    Favored  : 83.35 %
  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:  1.01 (0.10), residues: 6162
  helix:  1.71 (0.10), residues: 2717
  sheet:  0.97 (0.14), residues: 1144
  loop : -0.73 (0.11), residues: 2301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS K 354 
 PHE   0.031   0.002   PHE G 235 
 TYR   0.024   0.002   TYR L 218 
 ARG   0.009   0.001   ARG F 425 

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

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

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  907 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 183
    poor density    : 724
  time to evaluate  : 4.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6511 (mt-10)
REVERT: A   53 MET cc_start: 0.8734 (mtt) cc_final: 0.8491 (mtt)
REVERT: A  125 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7494 (mp0)
REVERT: A  143 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8461 (t0)
REVERT: A  183 ASN cc_start: 0.8440 (m110) cc_final: 0.8151 (m110)
REVERT: A  206 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7801 (t)
REVERT: A  213 HIS cc_start: 0.6495 (m-70) cc_final: 0.6180 (m170)
REVERT: A  286 MET cc_start: 0.8967 (ttm) cc_final: 0.8416 (mtp)
REVERT: A  429 ASN cc_start: 0.8447 (m-40) cc_final: 0.8092 (t0)
REVERT: A  452 GLN cc_start: 0.6643 (mm-40) cc_final: 0.6060 (mp-120)
REVERT: A  456 MET cc_start: 0.7373 (mtt) cc_final: 0.7168 (mtt)
REVERT: B  125 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7531 (mp0)
REVERT: B  159 ASP cc_start: 0.6364 (m-30) cc_final: 0.5539 (t0)
REVERT: B  163 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7537 (mmt180)
REVERT: B  206 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7552 (t)
REVERT: B  217 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7122 (mtt90)
REVERT: B  221 ASN cc_start: 0.7261 (p0) cc_final: 0.6909 (p0)
REVERT: B  286 MET cc_start: 0.9069 (ttm) cc_final: 0.8614 (mtp)
REVERT: B  340 GLN cc_start: 0.8845 (tp40) cc_final: 0.8573 (tm130)
REVERT: B  365 ASP cc_start: 0.7067 (m-30) cc_final: 0.6466 (m-30)
REVERT: B  429 ASN cc_start: 0.8479 (m-40) cc_final: 0.7950 (t0)
REVERT: C    8 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6704 (mt-10)
REVERT: C  185 ILE cc_start: 0.8169 (mt) cc_final: 0.7755 (mt)
REVERT: C  279 MET cc_start: 0.9237 (mtp) cc_final: 0.8939 (mtp)
REVERT: C  327 SER cc_start: 0.7665 (t) cc_final: 0.7380 (p)
REVERT: C  362 MET cc_start: 0.8368 (ptp) cc_final: 0.7913 (ptp)
REVERT: C  363 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7362 (mmmm)
REVERT: C  365 ASP cc_start: 0.7515 (m-30) cc_final: 0.7002 (m-30)
REVERT: C  429 ASN cc_start: 0.8628 (m110) cc_final: 0.8144 (t0)
REVERT: D  125 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7724 (mp0)
REVERT: D  209 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7643 (tp)
REVERT: D  221 ASN cc_start: 0.7348 (p0) cc_final: 0.7082 (p0)
REVERT: D  286 MET cc_start: 0.8974 (ttm) cc_final: 0.8486 (mtp)
REVERT: D  363 LYS cc_start: 0.8022 (mmtp) cc_final: 0.7589 (mttp)
REVERT: D  422 ASN cc_start: 0.8223 (t0) cc_final: 0.7863 (m-40)
REVERT: D  452 GLN cc_start: 0.6799 (mm-40) cc_final: 0.6434 (mp10)
REVERT: E   47 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7326 (mtmt)
REVERT: E   54 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8340 (m-30)
REVERT: E  125 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7577 (mp0)
REVERT: E  143 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8422 (t0)
REVERT: E  159 ASP cc_start: 0.6438 (m-30) cc_final: 0.5640 (t0)
REVERT: E  255 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8449 (mptm)
REVERT: E  292 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.7811 (t0)
REVERT: E  422 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7783 (m110)
REVERT: E  423 THR cc_start: 0.7614 (p) cc_final: 0.7362 (p)
REVERT: F   47 LYS cc_start: 0.7601 (tppp) cc_final: 0.7194 (tptp)
REVERT: F   53 MET cc_start: 0.8711 (mtt) cc_final: 0.8506 (mtt)
REVERT: F   83 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7921 (mp0)
REVERT: F  206 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7586 (t)
REVERT: F  365 ASP cc_start: 0.7688 (m-30) cc_final: 0.7025 (m-30)
REVERT: F  429 ASN cc_start: 0.8574 (m-40) cc_final: 0.8182 (t0)
REVERT: G   47 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7179 (ttmp)
REVERT: G   83 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7739 (mp0)
REVERT: G  129 ASP cc_start: 0.7388 (t0) cc_final: 0.6959 (t0)
REVERT: G  213 HIS cc_start: 0.6047 (m-70) cc_final: 0.5643 (m-70)
REVERT: G  221 ASN cc_start: 0.7489 (p0) cc_final: 0.7131 (p0)
REVERT: G  327 SER cc_start: 0.7651 (t) cc_final: 0.7446 (p)
REVERT: G  422 ASN cc_start: 0.7874 (t0) cc_final: 0.7591 (t0)
REVERT: G  429 ASN cc_start: 0.8416 (m-40) cc_final: 0.7997 (t0)
REVERT: G  452 GLN cc_start: 0.6832 (mm-40) cc_final: 0.6445 (mp10)
REVERT: H   54 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8432 (m-30)
REVERT: H   83 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7930 (mp0)
REVERT: H  143 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8558 (t0)
REVERT: H  163 ARG cc_start: 0.7869 (mmm-85) cc_final: 0.7562 (mmt180)
REVERT: H  179 THR cc_start: 0.7949 (m) cc_final: 0.7624 (p)
REVERT: H  309 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8745 (tp)
REVERT: H  327 SER cc_start: 0.7757 (t) cc_final: 0.7408 (p)
REVERT: H  365 ASP cc_start: 0.7904 (m-30) cc_final: 0.7443 (m-30)
REVERT: H  371 GLN cc_start: 0.6714 (mt0) cc_final: 0.6406 (mt0)
REVERT: H  429 ASN cc_start: 0.8259 (m-40) cc_final: 0.7835 (t0)
REVERT: H  452 GLN cc_start: 0.6756 (mm-40) cc_final: 0.6519 (mm110)
REVERT: I    8 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6806 (mt-10)
REVERT: I   83 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7235 (mp0)
REVERT: I  129 ASP cc_start: 0.7458 (t0) cc_final: 0.7175 (t0)
REVERT: I  170 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8905 (mtp)
REVERT: I  185 ILE cc_start: 0.8219 (mt) cc_final: 0.8014 (mt)
REVERT: I  206 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7670 (t)
REVERT: I  221 ASN cc_start: 0.7023 (p0) cc_final: 0.6712 (p0)
REVERT: I  235 PHE cc_start: 0.7860 (t80) cc_final: 0.7389 (t80)
REVERT: I  255 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8741 (mptt)
REVERT: I  327 SER cc_start: 0.7608 (t) cc_final: 0.7364 (p)
REVERT: I  340 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7986 (tp-100)
REVERT: I  422 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7765 (m110)
REVERT: I  440 LEU cc_start: 0.8049 (tp) cc_final: 0.7470 (tt)
REVERT: I  453 THR cc_start: 0.7042 (OUTLIER) cc_final: 0.6831 (t)
REVERT: J  163 ARG cc_start: 0.7742 (mmm-85) cc_final: 0.7453 (mmt180)
REVERT: J  221 ASN cc_start: 0.7243 (p0) cc_final: 0.6896 (p0)
REVERT: J  309 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8582 (mp)
REVERT: J  327 SER cc_start: 0.7785 (t) cc_final: 0.7431 (p)
REVERT: J  403 LYS cc_start: 0.7706 (mttt) cc_final: 0.7441 (mttm)
REVERT: J  423 THR cc_start: 0.7677 (p) cc_final: 0.7468 (p)
REVERT: J  440 LEU cc_start: 0.8210 (tp) cc_final: 0.7607 (tt)
REVERT: J  452 GLN cc_start: 0.6465 (mm-40) cc_final: 0.6081 (mm110)
REVERT: K  143 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.8509 (t0)
REVERT: K  221 ASN cc_start: 0.7184 (p0) cc_final: 0.6726 (p0)
REVERT: K  255 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8865 (mptm)
REVERT: K  286 MET cc_start: 0.8942 (ttm) cc_final: 0.8677 (mtp)
REVERT: K  327 SER cc_start: 0.7834 (t) cc_final: 0.7589 (p)
REVERT: K  363 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7490 (mttp)
REVERT: K  422 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7685 (m-40)
REVERT: K  429 ASN cc_start: 0.8439 (m-40) cc_final: 0.7940 (t0)
REVERT: K  446 SER cc_start: 0.7134 (m) cc_final: 0.6923 (p)
REVERT: K  452 GLN cc_start: 0.6737 (mm-40) cc_final: 0.6270 (mp10)
REVERT: L   53 MET cc_start: 0.8684 (mtt) cc_final: 0.8461 (mtt)
REVERT: L   54 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8368 (m-30)
REVERT: L   83 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7798 (mp0)
REVERT: L  125 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7350 (mp0)
REVERT: L  143 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8538 (t0)
REVERT: L  159 ASP cc_start: 0.6370 (m-30) cc_final: 0.5548 (OUTLIER)
REVERT: L  206 THR cc_start: 0.7891 (OUTLIER) cc_final: 0.7681 (t)
REVERT: L  221 ASN cc_start: 0.7245 (p0) cc_final: 0.6868 (p0)
REVERT: L  327 SER cc_start: 0.7664 (t) cc_final: 0.7404 (p)
REVERT: L  365 ASP cc_start: 0.7946 (m-30) cc_final: 0.7633 (m-30)
REVERT: L  429 ASN cc_start: 0.8611 (m-40) cc_final: 0.8156 (t0)
REVERT: L  440 LEU cc_start: 0.7869 (tp) cc_final: 0.7236 (tt)
REVERT: L  452 GLN cc_start: 0.6713 (mm-40) cc_final: 0.6105 (mp10)
REVERT: M   47 LYS cc_start: 0.7735 (tppp) cc_final: 0.7329 (tptp)
REVERT: M  235 PHE cc_start: 0.7666 (t80) cc_final: 0.7408 (t80)
REVERT: M  327 SER cc_start: 0.7729 (t) cc_final: 0.7392 (p)
REVERT: M  365 ASP cc_start: 0.7732 (m-30) cc_final: 0.7070 (m-30)
REVERT: M  422 ASN cc_start: 0.7847 (t0) cc_final: 0.7442 (t0)
REVERT: M  441 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8009 (tttt)
REVERT: M  450 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6566 (mp)
REVERT: M  456 MET cc_start: 0.7231 (mtt) cc_final: 0.6995 (mtt)
  outliers start: 183
  outliers final: 101
  residues processed: 837
  average time/residue: 1.3858
  time to fit residues: 1434.3272
Evaluate side-chains
  851 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 141
    poor density    : 710
  time to evaluate  : 4.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   47 LYS
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  143 ASP
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  143 ASP
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  292 ASN
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  363 LYS
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue  125 GLU
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  192 ARG
Chi-restraints excluded: chain D residue  209 LEU
Chi-restraints excluded: chain D residue  229 THR
Chi-restraints excluded: chain D residue  237 SER
Chi-restraints excluded: chain D residue  262 ILE
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain E residue   47 LYS
Chi-restraints excluded: chain E residue   54 ASP
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 GLU
Chi-restraints excluded: chain E residue  143 ASP
Chi-restraints excluded: chain E residue  255 LYS
Chi-restraints excluded: chain E residue  262 ILE
Chi-restraints excluded: chain E residue  292 ASN
Chi-restraints excluded: chain E residue  309 LEU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  422 ASN
Chi-restraints excluded: chain F residue   54 ASP
Chi-restraints excluded: chain F residue   57 ARG
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  143 ASP
Chi-restraints excluded: chain F residue  181 GLU
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain F residue  262 ILE
Chi-restraints excluded: chain F residue  286 MET
Chi-restraints excluded: chain F residue  315 VAL
Chi-restraints excluded: chain F residue  362 MET
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue  229 THR
Chi-restraints excluded: chain G residue  262 ILE
Chi-restraints excluded: chain G residue  298 VAL
Chi-restraints excluded: chain G residue  309 LEU
Chi-restraints excluded: chain G residue  315 VAL
Chi-restraints excluded: chain G residue  432 LEU
Chi-restraints excluded: chain G residue  444 ILE
Chi-restraints excluded: chain G residue  450 ILE
Chi-restraints excluded: chain H residue   54 ASP
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  125 GLU
Chi-restraints excluded: chain H residue  133 VAL
Chi-restraints excluded: chain H residue  143 ASP
Chi-restraints excluded: chain H residue  206 THR
Chi-restraints excluded: chain H residue  294 ASN
Chi-restraints excluded: chain H residue  309 LEU
Chi-restraints excluded: chain H residue  396 LYS
Chi-restraints excluded: chain H residue  436 LEU
Chi-restraints excluded: chain H residue  450 ILE
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   46 SER
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   83 GLU
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  125 GLU
Chi-restraints excluded: chain I residue  143 ASP
Chi-restraints excluded: chain I residue  170 MET
Chi-restraints excluded: chain I residue  206 THR
Chi-restraints excluded: chain I residue  229 THR
Chi-restraints excluded: chain I residue  255 LYS
Chi-restraints excluded: chain I residue  262 ILE
Chi-restraints excluded: chain I residue  286 MET
Chi-restraints excluded: chain I residue  340 GLN
Chi-restraints excluded: chain I residue  362 MET
Chi-restraints excluded: chain I residue  422 ASN
Chi-restraints excluded: chain I residue  450 ILE
Chi-restraints excluded: chain I residue  453 THR
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue   78 THR
Chi-restraints excluded: chain J residue  292 ASN
Chi-restraints excluded: chain J residue  298 VAL
Chi-restraints excluded: chain J residue  309 LEU
Chi-restraints excluded: chain J residue  315 VAL
Chi-restraints excluded: chain J residue  432 LEU
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain K residue  143 ASP
Chi-restraints excluded: chain K residue  181 GLU
Chi-restraints excluded: chain K residue  192 ARG
Chi-restraints excluded: chain K residue  206 THR
Chi-restraints excluded: chain K residue  255 LYS
Chi-restraints excluded: chain K residue  262 ILE
Chi-restraints excluded: chain K residue  282 LEU
Chi-restraints excluded: chain K residue  292 ASN
Chi-restraints excluded: chain K residue  363 LYS
Chi-restraints excluded: chain K residue  422 ASN
Chi-restraints excluded: chain L residue   54 ASP
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue   96 SER
Chi-restraints excluded: chain L residue  125 GLU
Chi-restraints excluded: chain L residue  143 ASP
Chi-restraints excluded: chain L residue  206 THR
Chi-restraints excluded: chain L residue  262 ILE
Chi-restraints excluded: chain L residue  282 LEU
Chi-restraints excluded: chain L residue  286 MET
Chi-restraints excluded: chain L residue  292 ASN
Chi-restraints excluded: chain L residue  293 LEU
Chi-restraints excluded: chain L residue  298 VAL
Chi-restraints excluded: chain M residue   78 THR
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue  143 ASP
Chi-restraints excluded: chain M residue  206 THR
Chi-restraints excluded: chain M residue  237 SER
Chi-restraints excluded: chain M residue  262 ILE
Chi-restraints excluded: chain M residue  315 VAL
Chi-restraints excluded: chain M residue  362 MET
Chi-restraints excluded: chain M residue  376 MET
Chi-restraints excluded: chain M residue  441 LYS
Chi-restraints excluded: chain M residue  450 ILE
Chi-restraints excluded: chain M residue  452 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 611
   random chunks:
   chunk 191 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 112 optimal weight:   10.0000
   chunk 170 optimal weight:    0.0570
   chunk 492 optimal weight:    8.9990
   chunk 269 optimal weight:    0.9980
   chunk 257 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 363 optimal weight:    4.9990
   overall best weight:    2.6104

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
A 178 ASN
A 221 ASN
B 112 GLN
B 422 ASN
C  43 ASN
C 422 ASN
C 452 GLN
D 178 ASN
D 371 GLN
E 112 GLN
E 221 ASN
E 340 GLN
F 221 ASN
F 422 ASN
G 178 ASN
G 340 GLN
H 112 GLN
H 221 ASN
H 422 ASN
I 112 GLN
I 422 ASN
I 452 GLN
J 221 ASN
K 112 GLN
L 422 ASN

Total number of N/Q/H flips: 26

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.182992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.117217 restraints weight = 47051.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.41
r_work: 0.3027 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  51571  Z= 0.267
  Angle     :  0.575   6.416  69576  Z= 0.321
  Chirality :  0.043   0.169   7540
  Planarity :  0.004   0.043   9191
  Dihedral  :  4.662  17.115   6942
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 13.70 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.10), residues: 6162
  helix:  1.69 (0.10), residues: 2743
  sheet:  0.96 (0.14), residues: 1144
  loop : -0.82 (0.11), residues: 2275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS K 354 
 PHE   0.033   0.002   PHE H 235 
 TYR   0.024   0.002   TYR L 218 
 ARG   0.009   0.001   ARG F 425 

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

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

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  883 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 176
    poor density    : 707
  time to evaluate  : 4.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6497 (mt-10)
REVERT: A   53 MET cc_start: 0.8733 (mtt) cc_final: 0.8508 (mtt)
REVERT: A  125 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7466 (mp0)
REVERT: A  183 ASN cc_start: 0.8459 (m110) cc_final: 0.8188 (m110)
REVERT: A  206 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7758 (t)
REVERT: A  213 HIS cc_start: 0.6469 (m-70) cc_final: 0.6185 (m170)
REVERT: A  286 MET cc_start: 0.8972 (ttm) cc_final: 0.8422 (mtp)
REVERT: A  429 ASN cc_start: 0.8448 (m-40) cc_final: 0.8106 (t0)
REVERT: A  452 GLN cc_start: 0.6592 (mm-40) cc_final: 0.6008 (mp-120)
REVERT: B  125 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7551 (mp0)
REVERT: B  159 ASP cc_start: 0.6393 (m-30) cc_final: 0.5565 (t0)
REVERT: B  163 ARG cc_start: 0.7738 (mmm-85) cc_final: 0.7529 (mmt180)
REVERT: B  206 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7535 (t)
REVERT: B  217 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7125 (mtt90)
REVERT: B  221 ASN cc_start: 0.7179 (p0) cc_final: 0.6830 (p0)
REVERT: B  286 MET cc_start: 0.9050 (ttm) cc_final: 0.8605 (mtp)
REVERT: B  340 GLN cc_start: 0.8820 (tp40) cc_final: 0.8544 (tm130)
REVERT: B  365 ASP cc_start: 0.7063 (m-30) cc_final: 0.6466 (m-30)
REVERT: B  429 ASN cc_start: 0.8488 (m-40) cc_final: 0.7958 (t0)
REVERT: B  440 LEU cc_start: 0.7965 (tp) cc_final: 0.7410 (tt)
REVERT: C    8 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6707 (mt-10)
REVERT: C   83 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7788 (mp0)
REVERT: C  185 ILE cc_start: 0.8207 (mt) cc_final: 0.7798 (mt)
REVERT: C  279 MET cc_start: 0.9232 (mtp) cc_final: 0.8988 (mtp)
REVERT: C  327 SER cc_start: 0.7665 (t) cc_final: 0.7377 (p)
REVERT: C  362 MET cc_start: 0.8369 (ptp) cc_final: 0.7905 (ptp)
REVERT: C  363 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7355 (mmmm)
REVERT: C  365 ASP cc_start: 0.7500 (m-30) cc_final: 0.7009 (m-30)
REVERT: C  429 ASN cc_start: 0.8628 (m110) cc_final: 0.8150 (t0)
REVERT: D  125 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7709 (mp0)
REVERT: D  209 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7626 (tp)
REVERT: D  221 ASN cc_start: 0.7236 (p0) cc_final: 0.6993 (p0)
REVERT: D  286 MET cc_start: 0.8977 (ttm) cc_final: 0.8460 (mtp)
REVERT: D  363 LYS cc_start: 0.8010 (mmtp) cc_final: 0.7557 (mttp)
REVERT: D  422 ASN cc_start: 0.8204 (t0) cc_final: 0.7845 (m-40)
REVERT: D  452 GLN cc_start: 0.6789 (mm-40) cc_final: 0.6405 (mp10)
REVERT: E   47 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7302 (mtmt)
REVERT: E   54 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8344 (m-30)
REVERT: E  125 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7595 (mp0)
REVERT: E  143 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8435 (t0)
REVERT: E  159 ASP cc_start: 0.6429 (m-30) cc_final: 0.5624 (t0)
REVERT: E  255 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8452 (mptm)
REVERT: E  292 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.7809 (t0)
REVERT: E  422 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7801 (m110)
REVERT: E  423 THR cc_start: 0.7625 (p) cc_final: 0.7370 (p)
REVERT: E  440 LEU cc_start: 0.8057 (tp) cc_final: 0.7699 (tt)
REVERT: F   47 LYS cc_start: 0.7595 (tppp) cc_final: 0.7179 (tptp)
REVERT: F   83 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7930 (mp0)
REVERT: F  206 THR cc_start: 0.7760 (OUTLIER) cc_final: 0.7547 (t)
REVERT: F  365 ASP cc_start: 0.7676 (m-30) cc_final: 0.7015 (m-30)
REVERT: F  429 ASN cc_start: 0.8579 (m-40) cc_final: 0.8184 (t0)
REVERT: G   47 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7219 (ttmp)
REVERT: G   83 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7746 (mp0)
REVERT: G  129 ASP cc_start: 0.7392 (t0) cc_final: 0.6966 (t0)
REVERT: G  213 HIS cc_start: 0.6003 (m-70) cc_final: 0.5626 (m-70)
REVERT: G  221 ASN cc_start: 0.7348 (p0) cc_final: 0.6924 (p0)
REVERT: G  327 SER cc_start: 0.7671 (t) cc_final: 0.7457 (p)
REVERT: G  422 ASN cc_start: 0.7856 (t0) cc_final: 0.7577 (t0)
REVERT: G  429 ASN cc_start: 0.8426 (m-40) cc_final: 0.8048 (t0)
REVERT: G  452 GLN cc_start: 0.6770 (mm-40) cc_final: 0.6346 (mp10)
REVERT: H   54 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8400 (m-30)
REVERT: H   83 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7946 (mp0)
REVERT: H  143 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8548 (t0)
REVERT: H  163 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7583 (mmt180)
REVERT: H  286 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8214 (tpp)
REVERT: H  309 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8756 (tp)
REVERT: H  327 SER cc_start: 0.7749 (t) cc_final: 0.7401 (p)
REVERT: H  362 MET cc_start: 0.8389 (ptm) cc_final: 0.8155 (ptp)
REVERT: H  365 ASP cc_start: 0.7907 (m-30) cc_final: 0.7446 (m-30)
REVERT: H  371 GLN cc_start: 0.6743 (mt0) cc_final: 0.6427 (mt0)
REVERT: H  429 ASN cc_start: 0.8257 (m-40) cc_final: 0.7833 (t0)
REVERT: H  452 GLN cc_start: 0.6757 (mm-40) cc_final: 0.6519 (mm110)
REVERT: I    8 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6808 (mt-10)
REVERT: I   47 LYS cc_start: 0.7224 (mtpt) cc_final: 0.6632 (ptpt)
REVERT: I   78 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8493 (m)
REVERT: I   83 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7265 (mp0)
REVERT: I  129 ASP cc_start: 0.7453 (t0) cc_final: 0.7166 (t0)
REVERT: I  170 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8858 (mtp)
REVERT: I  185 ILE cc_start: 0.8222 (mt) cc_final: 0.8012 (mt)
REVERT: I  206 THR cc_start: 0.7836 (OUTLIER) cc_final: 0.7624 (t)
REVERT: I  221 ASN cc_start: 0.6946 (p0) cc_final: 0.6659 (p0)
REVERT: I  235 PHE cc_start: 0.7856 (t80) cc_final: 0.7435 (t80)
REVERT: I  255 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8738 (mptt)
REVERT: I  327 SER cc_start: 0.7607 (t) cc_final: 0.7360 (p)
REVERT: I  340 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7987 (tp-100)
REVERT: I  440 LEU cc_start: 0.8002 (tp) cc_final: 0.7420 (tt)
REVERT: I  453 THR cc_start: 0.7035 (OUTLIER) cc_final: 0.6823 (t)
REVERT: J  163 ARG cc_start: 0.7744 (mmm-85) cc_final: 0.7472 (mmt180)
REVERT: J  309 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8585 (mp)
REVERT: J  327 SER cc_start: 0.7781 (t) cc_final: 0.7417 (p)
REVERT: J  403 LYS cc_start: 0.7697 (mttt) cc_final: 0.7432 (mttm)
REVERT: J  423 THR cc_start: 0.7723 (p) cc_final: 0.7514 (p)
REVERT: J  440 LEU cc_start: 0.8152 (tp) cc_final: 0.7559 (tt)
REVERT: J  452 GLN cc_start: 0.6332 (mm-40) cc_final: 0.5957 (mm110)
REVERT: K  125 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7709 (mp0)
REVERT: K  143 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8533 (t0)
REVERT: K  221 ASN cc_start: 0.7092 (p0) cc_final: 0.6661 (p0)
REVERT: K  255 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8775 (mptm)
REVERT: K  286 MET cc_start: 0.8935 (ttm) cc_final: 0.8657 (mtp)
REVERT: K  327 SER cc_start: 0.7833 (t) cc_final: 0.7582 (p)
REVERT: K  363 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7476 (mttp)
REVERT: K  422 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7689 (m-40)
REVERT: K  429 ASN cc_start: 0.8447 (m-40) cc_final: 0.7953 (t0)
REVERT: K  440 LEU cc_start: 0.8183 (tp) cc_final: 0.7805 (tt)
REVERT: K  446 SER cc_start: 0.7132 (m) cc_final: 0.6931 (p)
REVERT: K  452 GLN cc_start: 0.6703 (mm-40) cc_final: 0.6226 (mp10)
REVERT: L   53 MET cc_start: 0.8691 (mtt) cc_final: 0.8466 (mtt)
REVERT: L   54 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8394 (m-30)
REVERT: L   83 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7820 (mp0)
REVERT: L  125 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7378 (mp0)
REVERT: L  143 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8558 (t0)
REVERT: L  159 ASP cc_start: 0.6414 (m-30) cc_final: 0.5550 (OUTLIER)
REVERT: L  192 ARG cc_start: 0.7751 (mmm-85) cc_final: 0.7474 (ttp80)
REVERT: L  206 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7620 (t)
REVERT: L  221 ASN cc_start: 0.7190 (p0) cc_final: 0.6830 (p0)
REVERT: L  327 SER cc_start: 0.7664 (t) cc_final: 0.7413 (p)
REVERT: L  365 ASP cc_start: 0.7951 (m-30) cc_final: 0.7637 (m-30)
REVERT: L  422 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7504 (m110)
REVERT: L  429 ASN cc_start: 0.8615 (m-40) cc_final: 0.8156 (t0)
REVERT: L  440 LEU cc_start: 0.7852 (tp) cc_final: 0.7212 (tt)
REVERT: L  452 GLN cc_start: 0.6719 (mm-40) cc_final: 0.6104 (mp10)
REVERT: M   47 LYS cc_start: 0.7739 (tppp) cc_final: 0.7333 (tptp)
REVERT: M  235 PHE cc_start: 0.7682 (t80) cc_final: 0.7457 (t80)
REVERT: M  255 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8770 (mptp)
REVERT: M  327 SER cc_start: 0.7723 (t) cc_final: 0.7386 (p)
REVERT: M  365 ASP cc_start: 0.7726 (m-30) cc_final: 0.7074 (m-30)
REVERT: M  422 ASN cc_start: 0.7844 (t0) cc_final: 0.7436 (t0)
REVERT: M  441 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7966 (tttt)
REVERT: M  450 ILE cc_start: 0.6820 (mp) cc_final: 0.6612 (mp)
REVERT: M  456 MET cc_start: 0.7168 (mtt) cc_final: 0.6929 (mtt)
  outliers start: 176
  outliers final: 107
  residues processed: 813
  average time/residue: 1.4001
  time to fit residues: 1406.2132
Evaluate side-chains
  844 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 148
    poor density    : 696
  time to evaluate  : 4.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  292 ASN
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  143 ASP
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  292 ASN
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  363 LYS
Chi-restraints excluded: chain C residue  450 ILE
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue  125 GLU
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  192 ARG
Chi-restraints excluded: chain D residue  209 LEU
Chi-restraints excluded: chain D residue  229 THR
Chi-restraints excluded: chain D residue  237 SER
Chi-restraints excluded: chain D residue  262 ILE
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain E residue   47 LYS
Chi-restraints excluded: chain E residue   54 ASP
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 GLU
Chi-restraints excluded: chain E residue  143 ASP
Chi-restraints excluded: chain E residue  255 LYS
Chi-restraints excluded: chain E residue  262 ILE
Chi-restraints excluded: chain E residue  292 ASN
Chi-restraints excluded: chain E residue  309 LEU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  422 ASN
Chi-restraints excluded: chain E residue  450 ILE
Chi-restraints excluded: chain F residue   54 ASP
Chi-restraints excluded: chain F residue   57 ARG
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  143 ASP
Chi-restraints excluded: chain F residue  178 ASN
Chi-restraints excluded: chain F residue  181 GLU
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain F residue  262 ILE
Chi-restraints excluded: chain F residue  286 MET
Chi-restraints excluded: chain F residue  315 VAL
Chi-restraints excluded: chain F residue  362 MET
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue  229 THR
Chi-restraints excluded: chain G residue  262 ILE
Chi-restraints excluded: chain G residue  298 VAL
Chi-restraints excluded: chain G residue  309 LEU
Chi-restraints excluded: chain G residue  315 VAL
Chi-restraints excluded: chain G residue  432 LEU
Chi-restraints excluded: chain G residue  450 ILE
Chi-restraints excluded: chain H residue   54 ASP
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  125 GLU
Chi-restraints excluded: chain H residue  133 VAL
Chi-restraints excluded: chain H residue  143 ASP
Chi-restraints excluded: chain H residue  206 THR
Chi-restraints excluded: chain H residue  286 MET
Chi-restraints excluded: chain H residue  294 ASN
Chi-restraints excluded: chain H residue  309 LEU
Chi-restraints excluded: chain H residue  396 LYS
Chi-restraints excluded: chain H residue  436 LEU
Chi-restraints excluded: chain H residue  450 ILE
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   46 SER
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   83 GLU
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  125 GLU
Chi-restraints excluded: chain I residue  143 ASP
Chi-restraints excluded: chain I residue  170 MET
Chi-restraints excluded: chain I residue  206 THR
Chi-restraints excluded: chain I residue  229 THR
Chi-restraints excluded: chain I residue  255 LYS
Chi-restraints excluded: chain I residue  262 ILE
Chi-restraints excluded: chain I residue  286 MET
Chi-restraints excluded: chain I residue  340 GLN
Chi-restraints excluded: chain I residue  362 MET
Chi-restraints excluded: chain I residue  450 ILE
Chi-restraints excluded: chain I residue  453 THR
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue   47 LYS
Chi-restraints excluded: chain J residue   78 THR
Chi-restraints excluded: chain J residue  143 ASP
Chi-restraints excluded: chain J residue  181 GLU
Chi-restraints excluded: chain J residue  292 ASN
Chi-restraints excluded: chain J residue  298 VAL
Chi-restraints excluded: chain J residue  309 LEU
Chi-restraints excluded: chain J residue  315 VAL
Chi-restraints excluded: chain J residue  432 LEU
Chi-restraints excluded: chain K residue   47 LYS
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain K residue  143 ASP
Chi-restraints excluded: chain K residue  181 GLU
Chi-restraints excluded: chain K residue  192 ARG
Chi-restraints excluded: chain K residue  206 THR
Chi-restraints excluded: chain K residue  255 LYS
Chi-restraints excluded: chain K residue  262 ILE
Chi-restraints excluded: chain K residue  282 LEU
Chi-restraints excluded: chain K residue  292 ASN
Chi-restraints excluded: chain K residue  363 LYS
Chi-restraints excluded: chain K residue  422 ASN
Chi-restraints excluded: chain L residue   54 ASP
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue   96 SER
Chi-restraints excluded: chain L residue  125 GLU
Chi-restraints excluded: chain L residue  143 ASP
Chi-restraints excluded: chain L residue  206 THR
Chi-restraints excluded: chain L residue  262 ILE
Chi-restraints excluded: chain L residue  282 LEU
Chi-restraints excluded: chain L residue  286 MET
Chi-restraints excluded: chain L residue  292 ASN
Chi-restraints excluded: chain L residue  293 LEU
Chi-restraints excluded: chain L residue  298 VAL
Chi-restraints excluded: chain L residue  422 ASN
Chi-restraints excluded: chain M residue   78 THR
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue  125 GLU
Chi-restraints excluded: chain M residue  143 ASP
Chi-restraints excluded: chain M residue  206 THR
Chi-restraints excluded: chain M residue  237 SER
Chi-restraints excluded: chain M residue  255 LYS
Chi-restraints excluded: chain M residue  262 ILE
Chi-restraints excluded: chain M residue  315 VAL
Chi-restraints excluded: chain M residue  362 MET
Chi-restraints excluded: chain M residue  376 MET
Chi-restraints excluded: chain M residue  441 LYS
Chi-restraints excluded: chain M residue  452 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 611
   random chunks:
   chunk 192 optimal weight:   10.0000
   chunk 358 optimal weight:    0.0470
   chunk 44 optimal weight:    6.9990
   chunk 453 optimal weight:    2.9990
   chunk 187 optimal weight:    9.9990
   chunk 433 optimal weight:    0.6980
   chunk 445 optimal weight:    5.9990
   chunk 476 optimal weight:    0.9990
   chunk 322 optimal weight:    8.9990
   chunk 267 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.5484

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
B 112 GLN
B 422 ASN
C  43 ASN
C 112 GLN
C 422 ASN
C 452 GLN
D 178 ASN
E 112 GLN
E 221 ASN
E 340 GLN
F 221 ASN
F 422 ASN
G 178 ASN
G 340 GLN
H 112 GLN
H 422 ASN
I 112 GLN
I 371 GLN
I 422 ASN
I 452 GLN
J 221 ASN
K 112 GLN
L 422 ASN
M  22 ASN
M 178 ASN

Total number of N/Q/H flips: 26

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.184314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.118991 restraints weight = 47273.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.12
r_work: 0.3028 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  51571  Z= 0.188
  Angle     :  0.514   6.092  69576  Z= 0.289
  Chirality :  0.040   0.164   7540
  Planarity :  0.003   0.037   9191
  Dihedral  :  4.468  17.109   6942
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.34 %
    Favored  : 83.09 %
  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:  1.17 (0.10), residues: 6162
  helix:  1.95 (0.10), residues: 2730
  sheet:  1.00 (0.14), residues: 1144
  loop : -0.80 (0.12), residues: 2288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS M 354 
 PHE   0.023   0.002   PHE A 235 
 TYR   0.024   0.002   TYR L 218 
 ARG   0.009   0.000   ARG F 425 

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

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

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  12324 Ramachandran restraints generated.
    6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  842 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 145
    poor density    : 697
  time to evaluate  : 4.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6534 (mt-10)
REVERT: A   53 MET cc_start: 0.8747 (mtt) cc_final: 0.8502 (mtt)
REVERT: A  183 ASN cc_start: 0.8482 (m110) cc_final: 0.8202 (m110)
REVERT: A  206 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7788 (t)
REVERT: A  213 HIS cc_start: 0.6495 (m-70) cc_final: 0.6202 (m90)
REVERT: A  286 MET cc_start: 0.8975 (ttm) cc_final: 0.8405 (mtp)
REVERT: A  403 LYS cc_start: 0.7859 (mttt) cc_final: 0.7454 (mtpt)
REVERT: A  429 ASN cc_start: 0.8543 (m-40) cc_final: 0.8194 (t0)
REVERT: A  452 GLN cc_start: 0.6442 (mm-40) cc_final: 0.6142 (mp-120)
REVERT: B   53 MET cc_start: 0.8653 (mtt) cc_final: 0.8306 (mtm)
REVERT: B  125 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7528 (mp0)
REVERT: B  129 ASP cc_start: 0.7139 (t0) cc_final: 0.6800 (t0)
REVERT: B  159 ASP cc_start: 0.6346 (m-30) cc_final: 0.5513 (t0)
REVERT: B  163 ARG cc_start: 0.7715 (mmm-85) cc_final: 0.7492 (mmt180)
REVERT: B  206 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7516 (t)
REVERT: B  217 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7152 (mtt90)
REVERT: B  221 ASN cc_start: 0.7125 (p0) cc_final: 0.6841 (p0)
REVERT: B  286 MET cc_start: 0.9051 (ttm) cc_final: 0.8595 (mtp)
REVERT: B  340 GLN cc_start: 0.8759 (tp40) cc_final: 0.8496 (tm130)
REVERT: B  365 ASP cc_start: 0.7054 (m-30) cc_final: 0.6462 (m-30)
REVERT: B  429 ASN cc_start: 0.8528 (m-40) cc_final: 0.7991 (t0)
REVERT: B  440 LEU cc_start: 0.8007 (tp) cc_final: 0.7471 (tt)
REVERT: C    8 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6677 (mt-10)
REVERT: C   83 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7806 (mp0)
REVERT: C  185 ILE cc_start: 0.8247 (mt) cc_final: 0.7820 (mt)
REVERT: C  235 PHE cc_start: 0.7682 (t80) cc_final: 0.7378 (t80)
REVERT: C  279 MET cc_start: 0.9196 (mtp) cc_final: 0.8901 (mtp)
REVERT: C  363 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7388 (mmmm)
REVERT: C  365 ASP cc_start: 0.7511 (m-30) cc_final: 0.7033 (m-30)
REVERT: C  429 ASN cc_start: 0.8696 (m110) cc_final: 0.8188 (t0)
REVERT: D  125 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7663 (mp0)
REVERT: D  192 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6712 (ttp-170)
REVERT: D  209 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7651 (tp)
REVERT: D  221 ASN cc_start: 0.7214 (p0) cc_final: 0.6966 (p0)
REVERT: D  286 MET cc_start: 0.8987 (ttm) cc_final: 0.8466 (mtp)
REVERT: D  363 LYS cc_start: 0.7978 (mmtp) cc_final: 0.7550 (mttp)
REVERT: D  422 ASN cc_start: 0.8199 (t0) cc_final: 0.7806 (m110)
REVERT: D  452 GLN cc_start: 0.6836 (mm-40) cc_final: 0.6442 (mp10)
REVERT: E   54 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8377 (m-30)
REVERT: E  125 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7592 (mp0)
REVERT: E  159 ASP cc_start: 0.6430 (m-30) cc_final: 0.5621 (t0)
REVERT: E  255 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8437 (mptm)
REVERT: E  292 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.7895 (t0)
REVERT: E  422 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7778 (m110)
REVERT: E  423 THR cc_start: 0.7607 (p) cc_final: 0.7354 (p)
REVERT: E  440 LEU cc_start: 0.8124 (tp) cc_final: 0.7773 (tt)
REVERT: F   47 LYS cc_start: 0.7619 (tppp) cc_final: 0.7203 (tptp)
REVERT: F   83 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7954 (mp0)
REVERT: F  365 ASP cc_start: 0.7673 (m-30) cc_final: 0.6982 (m-30)
REVERT: F  429 ASN cc_start: 0.8610 (m-40) cc_final: 0.8202 (t0)
REVERT: G   47 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7288 (ttmp)
REVERT: G   83 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7721 (mp0)
REVERT: G  129 ASP cc_start: 0.7444 (t0) cc_final: 0.6999 (t0)
REVERT: G  213 HIS cc_start: 0.6007 (m-70) cc_final: 0.5625 (m-70)
REVERT: G  221 ASN cc_start: 0.7294 (p0) cc_final: 0.6892 (p0)
REVERT: G  422 ASN cc_start: 0.7863 (t0) cc_final: 0.7585 (t0)
REVERT: G  429 ASN cc_start: 0.8448 (m-40) cc_final: 0.8061 (t0)
REVERT: G  452 GLN cc_start: 0.6854 (mm-40) cc_final: 0.6414 (mp10)
REVERT: H   54 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8401 (m-30)
REVERT: H   83 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7948 (mp0)
REVERT: H  163 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7592 (mmt180)
REVERT: H  309 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8765 (tp)
REVERT: H  327 SER cc_start: 0.7794 (t) cc_final: 0.7447 (p)
REVERT: H  365 ASP cc_start: 0.7917 (m-30) cc_final: 0.7357 (m-30)
REVERT: H  371 GLN cc_start: 0.6665 (mt0) cc_final: 0.6350 (mt0)
REVERT: H  429 ASN cc_start: 0.8288 (m-40) cc_final: 0.7844 (t0)
REVERT: H  452 GLN cc_start: 0.6735 (mm-40) cc_final: 0.6457 (mm110)
REVERT: I    8 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6809 (mt-10)
REVERT: I   47 LYS cc_start: 0.7237 (mtpt) cc_final: 0.6851 (ptpt)
REVERT: I   78 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8518 (m)
REVERT: I   83 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7352 (mp0)
REVERT: I  129 ASP cc_start: 0.7449 (t0) cc_final: 0.7184 (t0)
REVERT: I  143 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8565 (t0)
REVERT: I  185 ILE cc_start: 0.8234 (mt) cc_final: 0.7992 (mt)
REVERT: I  206 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7633 (t)
REVERT: I  221 ASN cc_start: 0.6879 (p0) cc_final: 0.6616 (p0)
REVERT: I  235 PHE cc_start: 0.7810 (t80) cc_final: 0.7412 (t80)
REVERT: I  255 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8736 (mptt)
REVERT: I  340 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7940 (tp-100)
REVERT: I  365 ASP cc_start: 0.7466 (m-30) cc_final: 0.6911 (m-30)
REVERT: I  440 LEU cc_start: 0.8117 (tp) cc_final: 0.7559 (tt)
REVERT: I  441 LYS cc_start: 0.8354 (tttp) cc_final: 0.8113 (tptt)
REVERT: I  453 THR cc_start: 0.7059 (OUTLIER) cc_final: 0.6836 (t)
REVERT: J   47 LYS cc_start: 0.7369 (mtmp) cc_final: 0.6866 (ptpt)
REVERT: J  163 ARG cc_start: 0.7714 (mmm-85) cc_final: 0.7448 (mmt180)
REVERT: J  327 SER cc_start: 0.7753 (t) cc_final: 0.7411 (p)
REVERT: J  403 LYS cc_start: 0.7670 (mttt) cc_final: 0.7094 (mppt)
REVERT: J  423 THR cc_start: 0.7736 (p) cc_final: 0.7525 (p)
REVERT: J  440 LEU cc_start: 0.8190 (tp) cc_final: 0.7597 (tt)
REVERT: J  452 GLN cc_start: 0.6484 (mm-40) cc_final: 0.6207 (mm110)
REVERT: K  125 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7732 (mp0)
REVERT: K  143 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8541 (t0)
REVERT: K  221 ASN cc_start: 0.7096 (p0) cc_final: 0.6682 (p0)
REVERT: K  255 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8776 (mptm)
REVERT: K  286 MET cc_start: 0.8938 (ttm) cc_final: 0.8645 (mtp)
REVERT: K  327 SER cc_start: 0.7856 (t) cc_final: 0.7631 (p)
REVERT: K  363 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7469 (mttp)
REVERT: K  422 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7738 (m-40)
REVERT: K  429 ASN cc_start: 0.8481 (m-40) cc_final: 0.7974 (t0)
REVERT: K  440 LEU cc_start: 0.8149 (tp) cc_final: 0.7718 (tt)
REVERT: K  452 GLN cc_start: 0.6700 (mm-40) cc_final: 0.6213 (mp10)
REVERT: L   53 MET cc_start: 0.8632 (mtt) cc_final: 0.8398 (mtt)
REVERT: L   54 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8399 (m-30)
REVERT: L   83 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7862 (mp0)
REVERT: L  125 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7443 (mp0)
REVERT: L  143 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8615 (t0)
REVERT: L  192 ARG cc_start: 0.7758 (mmm-85) cc_final: 0.7475 (ttp80)
REVERT: L  206 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7684 (t)
REVERT: L  221 ASN cc_start: 0.7159 (p0) cc_final: 0.6823 (p0)
REVERT: L  365 ASP cc_start: 0.7585 (m-30) cc_final: 0.7254 (m-30)
REVERT: L  422 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7897 (m110)
REVERT: L  429 ASN cc_start: 0.8665 (m-40) cc_final: 0.8177 (t0)
REVERT: L  440 LEU cc_start: 0.7831 (tp) cc_final: 0.7176 (tt)
REVERT: L  452 GLN cc_start: 0.6646 (mm-40) cc_final: 0.6027 (mp10)
REVERT: M   47 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7375 (tptp)
REVERT: M  255 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8793 (mptp)
REVERT: M  327 SER cc_start: 0.7734 (t) cc_final: 0.7402 (p)
REVERT: M  365 ASP cc_start: 0.7702 (m-30) cc_final: 0.7079 (m-30)
REVERT: M  422 ASN cc_start: 0.7876 (t0) cc_final: 0.7440 (t0)
REVERT: M  441 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8039 (tttt)
REVERT: M  450 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6604 (mp)
REVERT: M  456 MET cc_start: 0.7213 (mtt) cc_final: 0.6942 (mtt)
  outliers start: 145
  outliers final: 78
  residues processed: 788
  average time/residue: 1.4112
  time to fit residues: 1368.2787
Evaluate side-chains
  810 residues out of total 5629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 116
    poor density    : 694
  time to evaluate  : 4.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  292 ASN
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  363 LYS
Chi-restraints excluded: chain C residue  450 ILE
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue  125 GLU
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  192 ARG
Chi-restraints excluded: chain D residue  209 LEU
Chi-restraints excluded: chain D residue  237 SER
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain E residue   54 ASP
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 GLU
Chi-restraints excluded: chain E residue  255 LYS
Chi-restraints excluded: chain E residue  292 ASN
Chi-restraints excluded: chain E residue  309 LEU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  422 ASN
Chi-restraints excluded: chain F residue   57 ARG
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  143 ASP
Chi-restraints excluded: chain F residue  181 GLU
Chi-restraints excluded: chain F residue  286 MET
Chi-restraints excluded: chain F residue  315 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue  298 VAL
Chi-restraints excluded: chain G residue  309 LEU
Chi-restraints excluded: chain G residue  315 VAL
Chi-restraints excluded: chain G residue  450 ILE
Chi-restraints excluded: chain H residue   54 ASP
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  125 GLU
Chi-restraints excluded: chain H residue  133 VAL
Chi-restraints excluded: chain H residue  206 THR
Chi-restraints excluded: chain H residue  294 ASN
Chi-restraints excluded: chain H residue  309 LEU
Chi-restraints excluded: chain H residue  396 LYS
Chi-restraints excluded: chain H residue  436 LEU
Chi-restraints excluded: chain H residue  450 ILE
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   22 ASN
Chi-restraints excluded: chain I residue   46 SER
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   83 GLU
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  125 GLU
Chi-restraints excluded: chain I residue  143 ASP
Chi-restraints excluded: chain I residue  206 THR
Chi-restraints excluded: chain I residue  255 LYS
Chi-restraints excluded: chain I residue  340 GLN
Chi-restraints excluded: chain I residue  362 MET
Chi-restraints excluded: chain I residue  450 ILE
Chi-restraints excluded: chain I residue  453 THR
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue   78 THR
Chi-restraints excluded: chain J residue  292 ASN
Chi-restraints excluded: chain J residue  298 VAL
Chi-restraints excluded: chain J residue  309 LEU
Chi-restraints excluded: chain K residue   47 LYS
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain K residue  143 ASP
Chi-restraints excluded: chain K residue  181 GLU
Chi-restraints excluded: chain K residue  192 ARG
Chi-restraints excluded: chain K residue  255 LYS
Chi-restraints excluded: chain K residue  292 ASN
Chi-restraints excluded: chain K residue  363 LYS
Chi-restraints excluded: chain K residue  422 ASN
Chi-restraints excluded: chain K residue  450 ILE
Chi-restraints excluded: chain L residue   54 ASP
Chi-restraints excluded: chain L residue   96 SER
Chi-restraints excluded: chain L residue  125 GLU
Chi-restraints excluded: chain L residue  143 ASP
Chi-restraints excluded: chain L residue  206 THR
Chi-restraints excluded: chain L residue  282 LEU
Chi-restraints excluded: chain L residue  286 MET
Chi-restraints excluded: chain L residue  292 ASN
Chi-restraints excluded: chain L residue  298 VAL
Chi-restraints excluded: chain L residue  376 MET
Chi-restraints excluded: chain L residue  422 ASN
Chi-restraints excluded: chain M residue   47 LYS
Chi-restraints excluded: chain M residue   78 THR
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue  125 GLU
Chi-restraints excluded: chain M residue  206 THR
Chi-restraints excluded: chain M residue  237 SER
Chi-restraints excluded: chain M residue  255 LYS
Chi-restraints excluded: chain M residue  315 VAL
Chi-restraints excluded: chain M residue  376 MET
Chi-restraints excluded: chain M residue  441 LYS
Chi-restraints excluded: chain M residue  450 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 611
   random chunks:
   chunk 561 optimal weight:    9.9990
   chunk 44 optimal weight:    0.0670
   chunk 602 optimal weight:    1.9990
   chunk 233 optimal weight:    6.9990
   chunk 225 optimal weight:    2.9990
   chunk 538 optimal weight:    9.9990
   chunk 427 optimal weight:   10.0000
   chunk 439 optimal weight:    0.8980
   chunk 251 optimal weight:    3.9990
   chunk 410 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    1.9924

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
A 178 ASN
B 112 GLN
B 422 ASN
C  43 ASN
C 112 GLN
C 422 ASN
C 452 GLN
D 178 ASN
E 112 GLN
E 340 GLN
F 221 ASN
F 422 ASN
G 178 ASN
G 340 GLN
H 112 GLN
H 422 ASN
I 112 GLN
I 371 GLN
I 452 GLN
K 112 GLN
L 422 ASN
M  22 ASN

Total number of N/Q/H flips: 23

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.183693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.118593 restraints weight = 47089.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.12
r_work: 0.3038 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.2867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  51571  Z= 0.221
  Angle     :  0.539   5.693  69576  Z= 0.301
  Chirality :  0.041   0.172   7540
  Planarity :  0.004   0.039   9191
  Dihedral  :  4.494  17.114   6942
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 14.60 %
    Favored  : 82.91 %
  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:  1.15 (0.10), residues: 6162
  helix:  1.90 (0.10), residues: 2743
  sheet:  0.99 (0.14), residues: 1144
  loop : -0.79 (0.12), residues: 2275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS K 354 
 PHE   0.031   0.002   PHE H 235 
 TYR   0.024   0.002   TYR L 218 
 ARG   0.009   0.000   ARG F 425 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 43444.74 seconds
wall clock time: 739 minutes 53.47 seconds (44393.47 seconds total)