Starting phenix.real_space_refine
on Thu Feb 15 13:10:15 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c70_7352/02_2024/6c70_7352_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c70_7352/02_2024/6c70_7352.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c70_7352/02_2024/6c70_7352.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c70_7352/02_2024/6c70_7352.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c70_7352/02_2024/6c70_7352_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c70_7352/02_2024/6c70_7352_neut.pdb"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

  Symmetric amino acids flipped
    Residue "A ARG  130": "NH1" <-> "NH2"
    Residue "A ARG  174": "NH1" <-> "NH2"
    Residue "A PHE  449": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  130": "NH1" <-> "NH2"
    Residue "B ARG  174": "NH1" <-> "NH2"
    Residue "B PHE  449": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  130": "NH1" <-> "NH2"
    Residue "C ARG  174": "NH1" <-> "NH2"
    Residue "C PHE  449": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG  130": "NH1" <-> "NH2"
    Residue "D ARG  174": "NH1" <-> "NH2"
    Residue "D PHE  449": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 12368
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3092
          Classifications: {'peptide': 388}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 377}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3092
          Classifications: {'peptide': 388}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 377}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3092
          Classifications: {'peptide': 388}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 377}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 3092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3092
          Classifications: {'peptide': 388}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 377}
          Chain breaks: 2
  Time building chain proxies: 6.45, per 1000 atoms: 0.52
  Number of scatterers: 12368
  At special positions: 0
  Unit cell: (121, 121, 101, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     108     16.00
     O    2116      8.00
     N    1992      7.00
     C    8152      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 4.86
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 4 sheets defined
      81.4% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 11
    Processing helix  chain 'A' and resid 12 through 23
      removed outlier: 3.560A  pdb=" N   MET A  19 " --> pdb=" O   ASN A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 33
      No H-bonds generated for 'chain 'A' and resid 31 through 33'
    Processing helix  chain 'A' and resid 34 through 63
      removed outlier: 3.533A  pdb=" N   ILE A  40 " --> pdb=" O   PHE A  36 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   TYR A  41 " --> pdb=" O   PRO A  37 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ALA A  57 " --> pdb=" O   TYR A  53 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL A  58 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN A  59 " --> pdb=" O   MET A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 80
    Processing helix  chain 'A' and resid 81 through 93
      removed outlier: 3.696A  pdb=" N   MET A  87 " --> pdb=" O   PRO A  83 " (cutoff:3.500A)
      Proline residue:  A  91  - end of helix
    Processing helix  chain 'A' and resid 94 through 102
    Processing helix  chain 'A' and resid 113 through 115
      No H-bonds generated for 'chain 'A' and resid 113 through 115'
    Processing helix  chain 'A' and resid 116 through 151
      removed outlier: 3.589A  pdb=" N   PHE A 120 " --> pdb=" O   SER A 116 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A 123 " --> pdb=" O   ARG A 119 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 132 " --> pdb=" O   MET A 128 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   ILE A 149 " --> pdb=" O   SER A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 190
      No H-bonds generated for 'chain 'A' and resid 188 through 190'
    Processing helix  chain 'A' and resid 191 through 233
      removed outlier: 3.907A  pdb=" N   ASN A 210 " --> pdb=" O   MET A 206 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU A 212 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU A 221 " --> pdb=" O   CYS A 217 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA A 232 " --> pdb=" O   GLN A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 315 through 347
      removed outlier: 3.522A  pdb=" N   ALA A 342 " --> pdb=" O   ARG A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 371
      removed outlier: 3.530A  pdb=" N   ILE A 360 " --> pdb=" O   LEU A 356 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU A 364 " --> pdb=" O   ILE A 360 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   TYR A 367 " --> pdb=" O   THR A 363 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LYS A 371 " --> pdb=" O   TYR A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 416
      removed outlier: 4.305A  pdb=" N   TYR A 388 " --> pdb=" O   GLY A 384 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A 393 " --> pdb=" O   THR A 389 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE A 396 " --> pdb=" O   GLN A 392 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   PHE A 399 " --> pdb=" O   LEU A 395 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET A 411 " --> pdb=" O   SER A 407 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU A 412 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 422
      removed outlier: 3.541A  pdb=" N   ASP A 421 " --> pdb=" O   HIS A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 437
      removed outlier: 3.605A  pdb=" N   ILE A 432 " --> pdb=" O   THR A 428 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN A 435 " --> pdb=" O   GLN A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 471
      removed outlier: 3.717A  pdb=" N   PHE A 456 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 11
    Processing helix  chain 'B' and resid 12 through 23
      removed outlier: 3.560A  pdb=" N   MET B  19 " --> pdb=" O   ASN B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 33
      No H-bonds generated for 'chain 'B' and resid 31 through 33'
    Processing helix  chain 'B' and resid 34 through 63
      removed outlier: 3.534A  pdb=" N   ILE B  40 " --> pdb=" O   PHE B  36 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   TYR B  41 " --> pdb=" O   PRO B  37 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN B  52 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA B  57 " --> pdb=" O   TYR B  53 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL B  58 " --> pdb=" O   GLY B  54 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ASN B  59 " --> pdb=" O   MET B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 80
    Processing helix  chain 'B' and resid 81 through 93
      removed outlier: 3.696A  pdb=" N   MET B  87 " --> pdb=" O   PRO B  83 " (cutoff:3.500A)
      Proline residue:  B  91  - end of helix
    Processing helix  chain 'B' and resid 94 through 102
    Processing helix  chain 'B' and resid 113 through 115
      No H-bonds generated for 'chain 'B' and resid 113 through 115'
    Processing helix  chain 'B' and resid 116 through 151
      removed outlier: 3.589A  pdb=" N   PHE B 120 " --> pdb=" O   SER B 116 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU B 123 " --> pdb=" O   ARG B 119 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU B 132 " --> pdb=" O   MET B 128 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY B 137 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   ILE B 149 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 190
      No H-bonds generated for 'chain 'B' and resid 188 through 190'
    Processing helix  chain 'B' and resid 191 through 233
      removed outlier: 3.908A  pdb=" N   ASN B 210 " --> pdb=" O   MET B 206 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU B 212 " --> pdb=" O   VAL B 208 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU B 221 " --> pdb=" O   CYS B 217 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA B 232 " --> pdb=" O   GLN B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 239
    Processing helix  chain 'B' and resid 315 through 347
      removed outlier: 3.522A  pdb=" N   ALA B 342 " --> pdb=" O   ARG B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 371
      removed outlier: 3.530A  pdb=" N   ILE B 360 " --> pdb=" O   LEU B 356 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU B 364 " --> pdb=" O   ILE B 360 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   TYR B 367 " --> pdb=" O   THR B 363 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LYS B 371 " --> pdb=" O   TYR B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 378 through 416
      removed outlier: 4.305A  pdb=" N   TYR B 388 " --> pdb=" O   GLY B 384 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL B 393 " --> pdb=" O   THR B 389 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE B 396 " --> pdb=" O   GLN B 392 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   PHE B 399 " --> pdb=" O   LEU B 395 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET B 411 " --> pdb=" O   SER B 407 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLU B 412 " --> pdb=" O   SER B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 422
      removed outlier: 3.541A  pdb=" N   ASP B 421 " --> pdb=" O   HIS B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 437
      removed outlier: 3.605A  pdb=" N   ILE B 432 " --> pdb=" O   THR B 428 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLN B 435 " --> pdb=" O   GLN B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 471
      removed outlier: 3.717A  pdb=" N   PHE B 456 " --> pdb=" O   SER B 452 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 11
    Processing helix  chain 'C' and resid 12 through 23
      removed outlier: 3.561A  pdb=" N   MET C  19 " --> pdb=" O   ASN C  15 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 33
      No H-bonds generated for 'chain 'C' and resid 31 through 33'
    Processing helix  chain 'C' and resid 34 through 63
      removed outlier: 3.534A  pdb=" N   ILE C  40 " --> pdb=" O   PHE C  36 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   TYR C  41 " --> pdb=" O   PRO C  37 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN C  52 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA C  57 " --> pdb=" O   TYR C  53 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL C  58 " --> pdb=" O   GLY C  54 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN C  59 " --> pdb=" O   MET C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 80
    Processing helix  chain 'C' and resid 81 through 93
      removed outlier: 3.697A  pdb=" N   MET C  87 " --> pdb=" O   PRO C  83 " (cutoff:3.500A)
      Proline residue:  C  91  - end of helix
    Processing helix  chain 'C' and resid 94 through 102
    Processing helix  chain 'C' and resid 113 through 115
      No H-bonds generated for 'chain 'C' and resid 113 through 115'
    Processing helix  chain 'C' and resid 116 through 151
      removed outlier: 3.589A  pdb=" N   PHE C 120 " --> pdb=" O   SER C 116 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU C 123 " --> pdb=" O   ARG C 119 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU C 132 " --> pdb=" O   MET C 128 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY C 137 " --> pdb=" O   PHE C 133 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   ILE C 149 " --> pdb=" O   SER C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 188 through 190
      No H-bonds generated for 'chain 'C' and resid 188 through 190'
    Processing helix  chain 'C' and resid 191 through 233
      removed outlier: 3.907A  pdb=" N   ASN C 210 " --> pdb=" O   MET C 206 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU C 212 " --> pdb=" O   VAL C 208 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU C 221 " --> pdb=" O   CYS C 217 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA C 232 " --> pdb=" O   GLN C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 239
    Processing helix  chain 'C' and resid 315 through 347
      removed outlier: 3.522A  pdb=" N   ALA C 342 " --> pdb=" O   ARG C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 347 through 371
      removed outlier: 3.530A  pdb=" N   ILE C 360 " --> pdb=" O   LEU C 356 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU C 364 " --> pdb=" O   ILE C 360 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   TYR C 367 " --> pdb=" O   THR C 363 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LYS C 371 " --> pdb=" O   TYR C 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 378 through 416
      removed outlier: 4.305A  pdb=" N   TYR C 388 " --> pdb=" O   GLY C 384 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL C 393 " --> pdb=" O   THR C 389 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE C 396 " --> pdb=" O   GLN C 392 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   PHE C 399 " --> pdb=" O   LEU C 395 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET C 411 " --> pdb=" O   SER C 407 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU C 412 " --> pdb=" O   SER C 408 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 418 through 422
      removed outlier: 3.541A  pdb=" N   ASP C 421 " --> pdb=" O   HIS C 418 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 423 through 437
      removed outlier: 3.606A  pdb=" N   ILE C 432 " --> pdb=" O   THR C 428 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN C 435 " --> pdb=" O   GLN C 431 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 471
      removed outlier: 3.717A  pdb=" N   PHE C 456 " --> pdb=" O   SER C 452 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 11
    Processing helix  chain 'D' and resid 12 through 23
      removed outlier: 3.560A  pdb=" N   MET D  19 " --> pdb=" O   ASN D  15 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 33
      No H-bonds generated for 'chain 'D' and resid 31 through 33'
    Processing helix  chain 'D' and resid 34 through 63
      removed outlier: 3.534A  pdb=" N   ILE D  40 " --> pdb=" O   PHE D  36 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   TYR D  41 " --> pdb=" O   PRO D  37 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN D  52 " --> pdb=" O   LEU D  48 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA D  57 " --> pdb=" O   TYR D  53 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL D  58 " --> pdb=" O   GLY D  54 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN D  59 " --> pdb=" O   MET D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 80
    Processing helix  chain 'D' and resid 81 through 93
      removed outlier: 3.696A  pdb=" N   MET D  87 " --> pdb=" O   PRO D  83 " (cutoff:3.500A)
      Proline residue:  D  91  - end of helix
    Processing helix  chain 'D' and resid 94 through 102
    Processing helix  chain 'D' and resid 113 through 115
      No H-bonds generated for 'chain 'D' and resid 113 through 115'
    Processing helix  chain 'D' and resid 116 through 151
      removed outlier: 3.589A  pdb=" N   PHE D 120 " --> pdb=" O   SER D 116 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU D 123 " --> pdb=" O   ARG D 119 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU D 132 " --> pdb=" O   MET D 128 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLY D 137 " --> pdb=" O   PHE D 133 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   ILE D 149 " --> pdb=" O   SER D 145 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 190
      No H-bonds generated for 'chain 'D' and resid 188 through 190'
    Processing helix  chain 'D' and resid 191 through 233
      removed outlier: 3.908A  pdb=" N   ASN D 210 " --> pdb=" O   MET D 206 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU D 212 " --> pdb=" O   VAL D 208 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU D 221 " --> pdb=" O   CYS D 217 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA D 232 " --> pdb=" O   GLN D 228 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 239
    Processing helix  chain 'D' and resid 315 through 347
      removed outlier: 3.522A  pdb=" N   ALA D 342 " --> pdb=" O   ARG D 338 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 347 through 371
      removed outlier: 3.530A  pdb=" N   ILE D 360 " --> pdb=" O   LEU D 356 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU D 364 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   TYR D 367 " --> pdb=" O   THR D 363 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LYS D 371 " --> pdb=" O   TYR D 367 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 378 through 416
      removed outlier: 4.305A  pdb=" N   TYR D 388 " --> pdb=" O   GLY D 384 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL D 393 " --> pdb=" O   THR D 389 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE D 396 " --> pdb=" O   GLN D 392 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   PHE D 399 " --> pdb=" O   LEU D 395 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET D 411 " --> pdb=" O   SER D 407 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU D 412 " --> pdb=" O   SER D 408 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 418 through 422
      removed outlier: 3.540A  pdb=" N   ASP D 421 " --> pdb=" O   HIS D 418 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 423 through 437
      removed outlier: 3.604A  pdb=" N   ILE D 432 " --> pdb=" O   THR D 428 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLN D 435 " --> pdb=" O   GLN D 431 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 452 through 471
      removed outlier: 3.716A  pdb=" N   PHE D 456 " --> pdb=" O   SER D 452 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 444 through 445
      removed outlier: 4.079A  pdb=" N   PHE A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 444 through 445
      removed outlier: 4.079A  pdb=" N   PHE B 449 " --> pdb=" O   GLY B 445 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 444 through 445
      removed outlier: 4.080A  pdb=" N   PHE C 449 " --> pdb=" O   GLY C 445 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 444 through 445
      removed outlier: 4.079A  pdb=" N   PHE D 449 " --> pdb=" O   GLY D 445 " (cutoff:3.500A)

    860 hydrogen bonds defined for protein.
    2544 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.48

  Time building geometry restraints manager: 5.25 seconds

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

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

  Histogram of bond angle deviations from ideal:
       96.02 -   103.67: 156
      103.67 -   111.31: 5424
      111.31 -   118.96: 4779
      118.96 -   126.60: 6660
      126.60 -   134.25: 153
  Bond angle restraints: 17172
  Sorted by residual:
  angle pdb=" CA  PRO B  83 "
        pdb=" N   PRO B  83 "
        pdb=" CD  PRO B  83 "
      ideal   model   delta    sigma   weight residual
     112.00  107.81    4.19 1.40e+00 5.10e-01 8.96e+00
  angle pdb=" N   CYS A 417 "
        pdb=" CA  CYS A 417 "
        pdb=" C   CYS A 417 "
      ideal   model   delta    sigma   weight residual
     109.81  105.27    4.54 1.53e+00 4.27e-01 8.80e+00
  angle pdb=" CA  PRO A  83 "
        pdb=" N   PRO A  83 "
        pdb=" CD  PRO A  83 "
      ideal   model   delta    sigma   weight residual
     112.00  107.85    4.15 1.40e+00 5.10e-01 8.77e+00
  angle pdb=" CA  PRO D  83 "
        pdb=" N   PRO D  83 "
        pdb=" CD  PRO D  83 "
      ideal   model   delta    sigma   weight residual
     112.00  107.85    4.15 1.40e+00 5.10e-01 8.77e+00
  angle pdb=" N   CYS B 417 "
        pdb=" CA  CYS B 417 "
        pdb=" C   CYS B 417 "
      ideal   model   delta    sigma   weight residual
     109.81  105.30    4.51 1.53e+00 4.27e-01 8.67e+00
  ... (remaining 17167 not shown)

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

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

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

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1571
        2.74 -     3.28: 12895
        3.28 -     3.82: 21457
        3.82 -     4.36: 25337
        4.36 -     4.90: 42002
  Nonbonded interactions: 103262
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B  68 "
            pdb=" NZ  LYS B 371 "
     model   vdw
     2.197 2.520
  nonbonded pdb=" OD1 ASP C  68 "
            pdb=" NZ  LYS C 371 "
     model   vdw
     2.197 2.520
  nonbonded pdb=" OD1 ASP A  68 "
            pdb=" NZ  LYS A 371 "
     model   vdw
     2.197 2.520
  nonbonded pdb=" OD1 ASP D  68 "
            pdb=" NZ  LYS D 371 "
     model   vdw
     2.197 2.520
  nonbonded pdb=" NE2 GLN C 436 "
            pdb=" O   MET D 411 "
     model   vdw
     2.263 2.520
  ... (remaining 103257 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.950
  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:             0.000
  Extract box with map and model:          11.960
  Check model and map are aligned:         0.190
  Set scattering table:                    0.110
  Process input model:                     33.530
  Find NCS groups from input model:        0.750
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.073  12668  Z= 0.679
  Angle     :  1.093   9.890  17172  Z= 0.565
  Chirality :  0.057   0.213   2008
  Planarity :  0.007   0.049   2080
  Dihedral  : 11.204  76.836   4464
  Min Nonbonded Distance : 2.197

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

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.23 (0.14), residues: 1528
  helix: -3.33 (0.09), residues: 1188
  sheet:  None (None), residues: 0
  loop : -2.93 (0.27), residues: 340

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

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

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  392 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 392
  time to evaluate  : 1.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.8905 (ttm) cc_final: 0.7858 (ttm)
REVERT: A  106 ASN cc_start: 0.8940 (t0) cc_final: 0.8648 (t0)
REVERT: A  134 CYS cc_start: 0.9196 (m) cc_final: 0.8971 (m)
REVERT: A  345 ASP cc_start: 0.8813 (t70) cc_final: 0.8598 (t70)
REVERT: A  424 GLU cc_start: 0.8789 (tp30) cc_final: 0.8496 (tp30)
REVERT: A  474 LYS cc_start: 0.7247 (tmtm) cc_final: 0.7012 (tttm)
REVERT: B   13 LEU cc_start: 0.8930 (mt) cc_final: 0.8684 (mt)
REVERT: B   19 MET cc_start: 0.8932 (ttm) cc_final: 0.8569 (ttm)
REVERT: B   22 VAL cc_start: 0.9703 (p) cc_final: 0.9490 (p)
REVERT: B  106 ASN cc_start: 0.8955 (t0) cc_final: 0.8649 (t0)
REVERT: B  134 CYS cc_start: 0.9135 (m) cc_final: 0.8857 (m)
REVERT: B  239 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8596 (mm-30)
REVERT: B  331 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8254 (mm-30)
REVERT: B  345 ASP cc_start: 0.8764 (t70) cc_final: 0.8554 (t70)
REVERT: B  363 THR cc_start: 0.9029 (p) cc_final: 0.8808 (t)
REVERT: B  424 GLU cc_start: 0.8758 (tp30) cc_final: 0.8433 (tp30)
REVERT: B  474 LYS cc_start: 0.7295 (tmtm) cc_final: 0.7072 (tttm)
REVERT: C   19 MET cc_start: 0.8885 (ttm) cc_final: 0.8105 (ttm)
REVERT: C  134 CYS cc_start: 0.9168 (m) cc_final: 0.8803 (m)
REVERT: C  345 ASP cc_start: 0.8758 (t70) cc_final: 0.8537 (t70)
REVERT: C  424 GLU cc_start: 0.8686 (tp30) cc_final: 0.8475 (tp30)
REVERT: C  437 CYS cc_start: 0.8670 (m) cc_final: 0.8352 (m)
REVERT: C  474 LYS cc_start: 0.7492 (tmtm) cc_final: 0.7180 (tttm)
REVERT: D   19 MET cc_start: 0.8936 (ttm) cc_final: 0.7990 (ttm)
REVERT: D  106 ASN cc_start: 0.8896 (t0) cc_final: 0.8627 (t0)
REVERT: D  134 CYS cc_start: 0.9239 (m) cc_final: 0.8873 (m)
REVERT: D  331 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8400 (mm-30)
REVERT: D  437 CYS cc_start: 0.8623 (m) cc_final: 0.8372 (m)
REVERT: D  474 LYS cc_start: 0.7578 (tmtm) cc_final: 0.7262 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 392
  average time/residue: 0.2115
  time to fit residues: 122.6567
Evaluate side-chains
  251 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 1.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 61 optimal weight:    0.1980
   chunk 119 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0980
   chunk 72 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 138 optimal weight:    0.8980
   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  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 GLN
A 401 ASN
A 431 GLN
B   5 HIS
** B  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 401 ASN
** C  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 401 ASN
D 431 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.3005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  12668  Z= 0.189
  Angle     :  0.624   8.247  17172  Z= 0.325
  Chirality :  0.039   0.136   2008
  Planarity :  0.004   0.029   2080
  Dihedral  :  5.073  18.788   1668
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 12.02 %
    Favored  : 86.65 %
  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: -1.87 (0.19), residues: 1528
  helix: -0.74 (0.14), residues: 1216
  sheet:  None (None), residues: 0
  loop : -2.70 (0.31), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 104 
 HIS   0.003   0.001   HIS D 335 
 PHE   0.016   0.002   PHE D 394 
 TYR   0.011   0.001   TYR A 201 
 ARG   0.002   0.000   ARG B 323 

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

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 348
  time to evaluate  : 1.304 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 PHE cc_start: 0.8988 (t80) cc_final: 0.8686 (t80)
REVERT: A  206 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8566 (ttp)
REVERT: A  424 GLU cc_start: 0.8700 (tp30) cc_final: 0.8390 (tp30)
REVERT: A  437 CYS cc_start: 0.8456 (m) cc_final: 0.8199 (m)
REVERT: A  474 LYS cc_start: 0.7263 (tmtm) cc_final: 0.6934 (tttm)
REVERT: B   48 LEU cc_start: 0.9416 (mt) cc_final: 0.9112 (pp)
REVERT: B  141 PHE cc_start: 0.8944 (t80) cc_final: 0.8612 (t80)
REVERT: B  239 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8448 (mm-30)
REVERT: B  331 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8620 (mm-30)
REVERT: B  355 MET cc_start: 0.8794 (mmm) cc_final: 0.8535 (mmm)
REVERT: B  406 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8356 (mm-30)
REVERT: B  424 GLU cc_start: 0.8645 (tp30) cc_final: 0.8289 (tp30)
REVERT: B  437 CYS cc_start: 0.8525 (m) cc_final: 0.8202 (m)
REVERT: B  474 LYS cc_start: 0.7198 (tmtm) cc_final: 0.6903 (tttm)
REVERT: C   29 TYR cc_start: 0.8399 (m-80) cc_final: 0.8025 (m-80)
REVERT: C  131 LEU cc_start: 0.9625 (tp) cc_final: 0.9375 (tp)
REVERT: C  134 CYS cc_start: 0.9294 (m) cc_final: 0.9001 (m)
REVERT: C  201 TYR cc_start: 0.8946 (t80) cc_final: 0.8735 (t80)
REVERT: C  215 LEU cc_start: 0.9362 (tp) cc_final: 0.9151 (tt)
REVERT: C  345 ASP cc_start: 0.8381 (t70) cc_final: 0.8152 (t70)
REVERT: C  406 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8204 (mm-30)
REVERT: C  408 SER cc_start: 0.9423 (m) cc_final: 0.9048 (p)
REVERT: C  424 GLU cc_start: 0.8673 (tp30) cc_final: 0.8371 (tp30)
REVERT: C  437 CYS cc_start: 0.8660 (m) cc_final: 0.8387 (m)
REVERT: C  474 LYS cc_start: 0.7212 (tmtm) cc_final: 0.6897 (tttm)
REVERT: D   77 MET cc_start: 0.8199 (ttm) cc_final: 0.7966 (ttp)
REVERT: D  131 LEU cc_start: 0.9622 (tp) cc_final: 0.9401 (tp)
REVERT: D  134 CYS cc_start: 0.9259 (m) cc_final: 0.9003 (m)
REVERT: D  141 PHE cc_start: 0.8973 (t80) cc_final: 0.8715 (t80)
REVERT: D  215 LEU cc_start: 0.9382 (tp) cc_final: 0.9162 (tt)
REVERT: D  239 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8494 (mm-30)
REVERT: D  355 MET cc_start: 0.9066 (mmm) cc_final: 0.8835 (mmm)
REVERT: D  406 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8326 (mm-30)
REVERT: D  437 CYS cc_start: 0.8500 (m) cc_final: 0.8185 (m)
REVERT: D  474 LYS cc_start: 0.7362 (tmtm) cc_final: 0.6991 (tttm)
  outliers start: 18
  outliers final: 9
  residues processed: 357
  average time/residue: 0.1804
  time to fit residues: 100.8984
Evaluate side-chains
  287 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 277
  time to evaluate  : 1.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue  351 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 114 optimal weight:    7.9990
   chunk 93 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 138 optimal weight:    0.9990
   chunk 149 optimal weight:    6.9990
   chunk 123 optimal weight:    4.9990
   chunk 137 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9990
   overall best weight:    1.5788

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12668  Z= 0.267
  Angle     :  0.605  13.338  17172  Z= 0.318
  Chirality :  0.040   0.160   2008
  Planarity :  0.003   0.030   2080
  Dihedral  :  4.601  16.963   1668
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 14.02 %
    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: -0.18 (0.21), residues: 1528
  helix:  0.55 (0.15), residues: 1212
  sheet:  None (None), residues: 0
  loop : -2.58 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 104 
 HIS   0.004   0.001   HIS D 229 
 PHE   0.020   0.002   PHE C 141 
 TYR   0.012   0.001   TYR C  53 
 ARG   0.002   0.000   ARG A 338 

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

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 296
  time to evaluate  : 1.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 PHE cc_start: 0.8984 (t80) cc_final: 0.8655 (t80)
REVERT: A  149 ILE cc_start: 0.9059 (mm) cc_final: 0.8817 (mt)
REVERT: A  206 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8626 (ttp)
REVERT: A  215 LEU cc_start: 0.9411 (tp) cc_final: 0.9208 (tt)
REVERT: A  474 LYS cc_start: 0.7330 (tmtm) cc_final: 0.6972 (tttm)
REVERT: B   53 TYR cc_start: 0.7980 (t80) cc_final: 0.7574 (t80)
REVERT: B   77 MET cc_start: 0.8448 (tpp) cc_final: 0.8226 (tpp)
REVERT: B  141 PHE cc_start: 0.8926 (t80) cc_final: 0.8622 (t80)
REVERT: B  215 LEU cc_start: 0.9410 (tp) cc_final: 0.9163 (tt)
REVERT: B  239 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8509 (mm-30)
REVERT: B  355 MET cc_start: 0.8948 (mmm) cc_final: 0.8683 (mmm)
REVERT: B  424 GLU cc_start: 0.8630 (tp30) cc_final: 0.8294 (tp30)
REVERT: B  474 LYS cc_start: 0.7332 (tmtm) cc_final: 0.7003 (tttm)
REVERT: C  128 MET cc_start: 0.8847 (mtp) cc_final: 0.8602 (mtp)
REVERT: C  134 CYS cc_start: 0.9312 (m) cc_final: 0.9046 (m)
REVERT: C  149 ILE cc_start: 0.8864 (mm) cc_final: 0.8655 (mt)
REVERT: C  215 LEU cc_start: 0.9434 (tp) cc_final: 0.9227 (tt)
REVERT: C  345 ASP cc_start: 0.8419 (t70) cc_final: 0.8188 (t70)
REVERT: C  408 SER cc_start: 0.9423 (m) cc_final: 0.9095 (p)
REVERT: C  424 GLU cc_start: 0.8724 (tp30) cc_final: 0.8401 (tp30)
REVERT: C  474 LYS cc_start: 0.7382 (tmtm) cc_final: 0.7032 (tttm)
REVERT: D  131 LEU cc_start: 0.9656 (tp) cc_final: 0.9443 (tp)
REVERT: D  134 CYS cc_start: 0.9262 (m) cc_final: 0.9038 (m)
REVERT: D  141 PHE cc_start: 0.8981 (t80) cc_final: 0.8695 (t80)
REVERT: D  215 LEU cc_start: 0.9462 (tp) cc_final: 0.9236 (tt)
REVERT: D  239 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8538 (mm-30)
REVERT: D  355 MET cc_start: 0.9128 (mmm) cc_final: 0.8906 (mmm)
REVERT: D  408 SER cc_start: 0.9413 (m) cc_final: 0.9191 (p)
REVERT: D  474 LYS cc_start: 0.7377 (tmtm) cc_final: 0.7050 (tttm)
  outliers start: 39
  outliers final: 20
  residues processed: 317
  average time/residue: 0.1896
  time to fit residues: 92.6410
Evaluate side-chains
  287 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 266
  time to evaluate  : 1.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain C residue    4 LYS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   65 ASP
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  224 CYS
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain D residue    4 LYS
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  351 LEU
Chi-restraints excluded: chain D residue  442 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 136 optimal weight:    0.0570
   chunk 103 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0030
   chunk 65 optimal weight:    0.8980
   chunk 92 optimal weight:    0.0000
   chunk 138 optimal weight:    3.9990
   chunk 146 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 131 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.3312

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.4076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12668  Z= 0.155
  Angle     :  0.571  16.122  17172  Z= 0.288
  Chirality :  0.039   0.189   2008
  Planarity :  0.003   0.027   2080
  Dihedral  :  4.385  18.672   1668
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.43 %
    Favored  : 82.42 %
  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:  0.67 (0.22), residues: 1528
  helix:  1.21 (0.15), residues: 1212
  sheet:  None (None), residues: 0
  loop : -2.54 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 219 
 HIS   0.003   0.001   HIS B  82 
 PHE   0.015   0.001   PHE A 394 
 TYR   0.011   0.001   TYR D 385 
 ARG   0.002   0.000   ARG A 178 

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

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 332
  time to evaluate  : 1.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.9505 (mt) cc_final: 0.9205 (pp)
REVERT: A   77 MET cc_start: 0.7967 (ttp) cc_final: 0.7662 (ttm)
REVERT: A  141 PHE cc_start: 0.8945 (t80) cc_final: 0.8661 (t80)
REVERT: A  204 ILE cc_start: 0.9567 (tp) cc_final: 0.9354 (tp)
REVERT: A  225 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8447 (mm-30)
REVERT: A  355 MET cc_start: 0.8997 (mmm) cc_final: 0.8796 (mmm)
REVERT: A  387 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8953 (mt)
REVERT: A  424 GLU cc_start: 0.8589 (tp30) cc_final: 0.8254 (tp30)
REVERT: A  474 LYS cc_start: 0.7222 (tmtm) cc_final: 0.6916 (tttm)
REVERT: B  141 PHE cc_start: 0.8875 (t80) cc_final: 0.8597 (t80)
REVERT: B  149 ILE cc_start: 0.8614 (mt) cc_final: 0.8408 (tp)
REVERT: B  215 LEU cc_start: 0.9408 (tp) cc_final: 0.9205 (tt)
REVERT: B  239 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8499 (mm-30)
REVERT: B  355 MET cc_start: 0.9004 (mmm) cc_final: 0.8753 (mmm)
REVERT: B  401 ASN cc_start: 0.9174 (t0) cc_final: 0.8964 (t0)
REVERT: B  424 GLU cc_start: 0.8565 (tp30) cc_final: 0.8224 (tp30)
REVERT: B  474 LYS cc_start: 0.7178 (tmtm) cc_final: 0.6825 (tttm)
REVERT: C   48 LEU cc_start: 0.9498 (mt) cc_final: 0.9238 (pp)
REVERT: C   53 TYR cc_start: 0.7708 (t80) cc_final: 0.7037 (t80)
REVERT: C   77 MET cc_start: 0.8570 (tpp) cc_final: 0.7955 (mmm)
REVERT: C  134 CYS cc_start: 0.9237 (m) cc_final: 0.9023 (m)
REVERT: C  149 ILE cc_start: 0.8820 (mm) cc_final: 0.8570 (tp)
REVERT: C  345 ASP cc_start: 0.8351 (t70) cc_final: 0.8060 (t70)
REVERT: C  408 SER cc_start: 0.9352 (m) cc_final: 0.8989 (p)
REVERT: C  415 TYR cc_start: 0.8896 (t80) cc_final: 0.8414 (t80)
REVERT: C  474 LYS cc_start: 0.7180 (tmtm) cc_final: 0.6844 (tttm)
REVERT: D   53 TYR cc_start: 0.7887 (t80) cc_final: 0.7661 (t80)
REVERT: D  131 LEU cc_start: 0.9620 (tp) cc_final: 0.9409 (tp)
REVERT: D  141 PHE cc_start: 0.8923 (t80) cc_final: 0.8700 (t80)
REVERT: D  201 TYR cc_start: 0.8935 (t80) cc_final: 0.8705 (t80)
REVERT: D  239 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8538 (mm-30)
REVERT: D  355 MET cc_start: 0.9149 (mmm) cc_final: 0.8906 (mmm)
REVERT: D  408 SER cc_start: 0.9336 (m) cc_final: 0.9003 (p)
REVERT: D  474 LYS cc_start: 0.7167 (tmtm) cc_final: 0.6900 (tttm)
  outliers start: 29
  outliers final: 19
  residues processed: 345
  average time/residue: 0.1869
  time to fit residues: 100.2210
Evaluate side-chains
  305 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 285
  time to evaluate  : 1.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain C residue    4 LYS
Chi-restraints excluded: chain C residue   26 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain D residue    4 LYS
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  217 CYS
Chi-restraints excluded: chain D residue  321 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 122 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 109 optimal weight:    5.9990
   chunk 60 optimal weight:    5.9990
   chunk 125 optimal weight:    0.0570
   chunk 101 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 131 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    1.1102

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12668  Z= 0.214
  Angle     :  0.578   9.527  17172  Z= 0.298
  Chirality :  0.040   0.196   2008
  Planarity :  0.003   0.026   2080
  Dihedral  :  4.164  17.304   1668
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 18.62 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.22), residues: 1528
  helix:  1.53 (0.15), residues: 1212
  sheet:  None (None), residues: 0
  loop : -2.61 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 219 
 HIS   0.003   0.001   HIS D   5 
 PHE   0.020   0.001   PHE C 141 
 TYR   0.013   0.001   TYR B 201 
 ARG   0.002   0.000   ARG D 338 

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

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 293
  time to evaluate  : 1.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.8753 (pp) cc_final: 0.8537 (pp)
REVERT: A  141 PHE cc_start: 0.8946 (t80) cc_final: 0.8614 (t80)
REVERT: A  176 MET cc_start: 0.6625 (tpp) cc_final: 0.6191 (tpt)
REVERT: A  204 ILE cc_start: 0.9629 (tp) cc_final: 0.9365 (tp)
REVERT: A  215 LEU cc_start: 0.9380 (tp) cc_final: 0.9116 (tt)
REVERT: A  387 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8984 (mt)
REVERT: A  474 LYS cc_start: 0.7334 (tmtm) cc_final: 0.6979 (tttm)
REVERT: B   77 MET cc_start: 0.8310 (tpp) cc_final: 0.7865 (mmm)
REVERT: B  141 PHE cc_start: 0.8846 (t80) cc_final: 0.8566 (t80)
REVERT: B  149 ILE cc_start: 0.8473 (mt) cc_final: 0.8157 (tp)
REVERT: B  204 ILE cc_start: 0.9631 (tp) cc_final: 0.9426 (tp)
REVERT: B  215 LEU cc_start: 0.9421 (tp) cc_final: 0.9134 (tt)
REVERT: B  239 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8527 (mm-30)
REVERT: B  355 MET cc_start: 0.9043 (mmm) cc_final: 0.8792 (mmm)
REVERT: B  401 ASN cc_start: 0.9183 (t0) cc_final: 0.8969 (t0)
REVERT: B  474 LYS cc_start: 0.7312 (tmtm) cc_final: 0.6964 (tttm)
REVERT: C   53 TYR cc_start: 0.7923 (t80) cc_final: 0.6638 (t80)
REVERT: C   77 MET cc_start: 0.8543 (tpp) cc_final: 0.7853 (tmm)
REVERT: C  134 CYS cc_start: 0.9281 (m) cc_final: 0.9055 (m)
REVERT: C  345 ASP cc_start: 0.8402 (t70) cc_final: 0.8131 (t70)
REVERT: C  408 SER cc_start: 0.9410 (m) cc_final: 0.9045 (p)
REVERT: C  415 TYR cc_start: 0.8882 (t80) cc_final: 0.8492 (t80)
REVERT: C  435 GLN cc_start: 0.8193 (mt0) cc_final: 0.7799 (mt0)
REVERT: C  474 LYS cc_start: 0.7289 (tmtm) cc_final: 0.6953 (tttm)
REVERT: D  128 MET cc_start: 0.8933 (mtp) cc_final: 0.8617 (mtp)
REVERT: D  141 PHE cc_start: 0.8930 (t80) cc_final: 0.8660 (t80)
REVERT: D  239 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8548 (mm-30)
REVERT: D  355 MET cc_start: 0.9153 (mmm) cc_final: 0.8898 (mmm)
REVERT: D  408 SER cc_start: 0.9351 (m) cc_final: 0.9058 (p)
REVERT: D  474 LYS cc_start: 0.7298 (tmtm) cc_final: 0.7012 (tttm)
  outliers start: 33
  outliers final: 26
  residues processed: 310
  average time/residue: 0.1878
  time to fit residues: 90.5123
Evaluate side-chains
  296 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 269
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ASP
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  398 ILE
Chi-restraints excluded: chain B residue  450 THR
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain C residue    4 LYS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain D residue    4 LYS
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  217 CYS
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  442 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 49 optimal weight:    0.0020
   chunk 132 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 36 optimal weight:    0.3980
   chunk 147 optimal weight:    7.9990
   chunk 122 optimal weight:    0.0670
   chunk 68 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0670
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.2664

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  15 ASN
A 333 HIS
B   5 HIS
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  15 ASN
C 401 ASN
D   6 GLN
D  15 ASN
** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.4723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12668  Z= 0.154
  Angle     :  0.573  10.756  17172  Z= 0.290
  Chirality :  0.040   0.195   2008
  Planarity :  0.003   0.026   2080
  Dihedral  :  4.028  15.536   1668
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 19.88 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.22), residues: 1528
  helix:  1.77 (0.15), residues: 1212
  sheet:  None (None), residues: 0
  loop : -2.58 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 219 
 HIS   0.002   0.001   HIS C 354 
 PHE   0.015   0.001   PHE A 394 
 TYR   0.014   0.001   TYR A  53 
 ARG   0.002   0.000   ARG B 129 

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

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 306
  time to evaluate  : 1.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.8758 (pp) cc_final: 0.8514 (pp)
REVERT: A   48 LEU cc_start: 0.9460 (mt) cc_final: 0.9189 (pp)
REVERT: A  141 PHE cc_start: 0.8895 (t80) cc_final: 0.8590 (t80)
REVERT: A  204 ILE cc_start: 0.9597 (tp) cc_final: 0.9324 (tp)
REVERT: A  387 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.9004 (mt)
REVERT: A  415 TYR cc_start: 0.8625 (t80) cc_final: 0.8199 (t80)
REVERT: A  474 LYS cc_start: 0.7209 (tmtm) cc_final: 0.6903 (tttm)
REVERT: B   53 TYR cc_start: 0.7293 (t80) cc_final: 0.6388 (t80)
REVERT: B   77 MET cc_start: 0.8324 (tpp) cc_final: 0.7978 (mmm)
REVERT: B  141 PHE cc_start: 0.8781 (t80) cc_final: 0.8512 (t80)
REVERT: B  149 ILE cc_start: 0.8293 (mt) cc_final: 0.7940 (tp)
REVERT: B  201 TYR cc_start: 0.9014 (t80) cc_final: 0.8778 (t80)
REVERT: B  239 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8480 (mm-30)
REVERT: B  355 MET cc_start: 0.9075 (mmm) cc_final: 0.8838 (mmm)
REVERT: B  474 LYS cc_start: 0.7135 (tmtm) cc_final: 0.6803 (tttm)
REVERT: C   53 TYR cc_start: 0.7664 (t80) cc_final: 0.6912 (t80)
REVERT: C   77 MET cc_start: 0.8518 (tpp) cc_final: 0.7824 (tmm)
REVERT: C  408 SER cc_start: 0.9347 (m) cc_final: 0.8929 (p)
REVERT: C  415 TYR cc_start: 0.8811 (t80) cc_final: 0.8375 (t80)
REVERT: C  474 LYS cc_start: 0.7207 (tmtm) cc_final: 0.6876 (tttm)
REVERT: D   13 LEU cc_start: 0.9087 (mm) cc_final: 0.8740 (mm)
REVERT: D  141 PHE cc_start: 0.8847 (t80) cc_final: 0.8565 (t80)
REVERT: D  239 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8499 (mm-30)
REVERT: D  355 MET cc_start: 0.9191 (mmm) cc_final: 0.8949 (mmm)
REVERT: D  408 SER cc_start: 0.9290 (m) cc_final: 0.8971 (p)
REVERT: D  474 LYS cc_start: 0.7147 (tmtm) cc_final: 0.6891 (tttm)
  outliers start: 35
  outliers final: 23
  residues processed: 322
  average time/residue: 0.1846
  time to fit residues: 92.6475
Evaluate side-chains
  294 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 270
  time to evaluate  : 1.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  398 ILE
Chi-restraints excluded: chain B residue  450 THR
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain C residue    4 LYS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  217 CYS
Chi-restraints excluded: chain D residue  321 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 141 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0870
   chunk 83 optimal weight:    0.8980
   chunk 107 optimal weight:    0.5980
   chunk 123 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 146 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   chunk 89 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  15 ASN
B   5 HIS
B  15 ASN
B 401 ASN
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  15 ASN
C 333 HIS
C 401 ASN
D  15 ASN
** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.4850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12668  Z= 0.176
  Angle     :  0.612   9.919  17172  Z= 0.305
  Chirality :  0.041   0.201   2008
  Planarity :  0.003   0.027   2080
  Dihedral  :  3.948  14.843   1668
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.10 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.52 (0.22), residues: 1528
  helix:  1.86 (0.15), residues: 1216
  sheet:  None (None), residues: 0
  loop : -2.55 (0.31), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 219 
 HIS   0.003   0.001   HIS B   5 
 PHE   0.019   0.001   PHE C 141 
 TYR   0.013   0.001   TYR B  53 
 ARG   0.002   0.000   ARG A 178 

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

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 284
  time to evaluate  : 1.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.8753 (pp) cc_final: 0.8523 (pp)
REVERT: A  141 PHE cc_start: 0.8836 (t80) cc_final: 0.8579 (t80)
REVERT: A  204 ILE cc_start: 0.9592 (tp) cc_final: 0.9336 (tp)
REVERT: A  215 LEU cc_start: 0.9355 (tp) cc_final: 0.9118 (tt)
REVERT: A  387 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9015 (mt)
REVERT: A  474 LYS cc_start: 0.7232 (tmtm) cc_final: 0.6915 (tttm)
REVERT: B   13 LEU cc_start: 0.9085 (mm) cc_final: 0.8651 (pp)
REVERT: B   77 MET cc_start: 0.8326 (tpp) cc_final: 0.7970 (mmm)
REVERT: B  141 PHE cc_start: 0.8736 (t80) cc_final: 0.8506 (t80)
REVERT: B  215 LEU cc_start: 0.9345 (tp) cc_final: 0.9101 (tt)
REVERT: B  239 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8543 (mm-30)
REVERT: B  355 MET cc_start: 0.9069 (mmm) cc_final: 0.8844 (mmm)
REVERT: B  474 LYS cc_start: 0.7150 (tmtm) cc_final: 0.6843 (tttm)
REVERT: C   53 TYR cc_start: 0.7827 (t80) cc_final: 0.6710 (t80)
REVERT: C   77 MET cc_start: 0.8535 (tpp) cc_final: 0.7907 (tmm)
REVERT: C  215 LEU cc_start: 0.9371 (tp) cc_final: 0.9122 (tt)
REVERT: C  408 SER cc_start: 0.9346 (m) cc_final: 0.8950 (p)
REVERT: C  474 LYS cc_start: 0.7212 (tmtm) cc_final: 0.6897 (tttm)
REVERT: D   13 LEU cc_start: 0.9120 (mm) cc_final: 0.8754 (mm)
REVERT: D  141 PHE cc_start: 0.8807 (t80) cc_final: 0.8536 (t80)
REVERT: D  239 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8537 (mm-30)
REVERT: D  355 MET cc_start: 0.9174 (mmm) cc_final: 0.8920 (mmm)
REVERT: D  408 SER cc_start: 0.9302 (m) cc_final: 0.8973 (p)
REVERT: D  474 LYS cc_start: 0.7174 (tmtm) cc_final: 0.6911 (tttm)
  outliers start: 40
  outliers final: 29
  residues processed: 302
  average time/residue: 0.1845
  time to fit residues: 86.8297
Evaluate side-chains
  299 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 269
  time to evaluate  : 1.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain C residue    4 LYS
Chi-restraints excluded: chain C residue   26 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   65 ASP
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain D residue    4 LYS
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  217 CYS
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  450 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0000
   chunk 44 optimal weight:    6.9990
   chunk 28 optimal weight:    0.5980
   chunk 93 optimal weight:    8.9990
   chunk 99 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 115 optimal weight:    1.9990
   chunk 133 optimal weight:    0.5980
   chunk 140 optimal weight:    0.7980
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
B  15 ASN
B 333 HIS
B 401 ASN
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  15 ASN
C 401 ASN
D  15 ASN
** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.5002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12668  Z= 0.174
  Angle     :  0.621   9.882  17172  Z= 0.311
  Chirality :  0.041   0.204   2008
  Planarity :  0.003   0.027   2080
  Dihedral  :  3.920  14.947   1668
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 20.40 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.22), residues: 1528
  helix:  1.94 (0.15), residues: 1216
  sheet:  None (None), residues: 0
  loop : -2.59 (0.31), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 146 
 HIS   0.002   0.001   HIS C   5 
 PHE   0.017   0.001   PHE C 394 
 TYR   0.013   0.001   TYR A  53 
 ARG   0.001   0.000   ARG C 178 

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

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 280
  time to evaluate  : 1.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 PHE cc_start: 0.8818 (t80) cc_final: 0.8603 (t80)
REVERT: A  204 ILE cc_start: 0.9593 (tp) cc_final: 0.9335 (tp)
REVERT: A  215 LEU cc_start: 0.9359 (tp) cc_final: 0.9127 (tt)
REVERT: A  387 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9025 (mt)
REVERT: A  415 TYR cc_start: 0.8587 (t80) cc_final: 0.8293 (t80)
REVERT: A  474 LYS cc_start: 0.7223 (tmtm) cc_final: 0.6911 (tttm)
REVERT: B   13 LEU cc_start: 0.9117 (mm) cc_final: 0.8695 (pp)
REVERT: B   53 TYR cc_start: 0.7653 (t80) cc_final: 0.6587 (t80)
REVERT: B   77 MET cc_start: 0.8309 (tpp) cc_final: 0.7989 (mmm)
REVERT: B  141 PHE cc_start: 0.8747 (t80) cc_final: 0.8507 (t80)
REVERT: B  215 LEU cc_start: 0.9359 (tp) cc_final: 0.9127 (tt)
REVERT: B  239 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8548 (mm-30)
REVERT: B  355 MET cc_start: 0.9092 (mmm) cc_final: 0.8858 (mmm)
REVERT: B  398 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8952 (mm)
REVERT: B  408 SER cc_start: 0.9451 (m) cc_final: 0.9236 (m)
REVERT: B  474 LYS cc_start: 0.7107 (tmtm) cc_final: 0.6804 (tttm)
REVERT: C   53 TYR cc_start: 0.7673 (t80) cc_final: 0.7013 (t80)
REVERT: C   77 MET cc_start: 0.8575 (tpp) cc_final: 0.7861 (mmm)
REVERT: C  408 SER cc_start: 0.9347 (m) cc_final: 0.8947 (p)
REVERT: C  415 TYR cc_start: 0.8509 (t80) cc_final: 0.8301 (t80)
REVERT: C  474 LYS cc_start: 0.7161 (tmtm) cc_final: 0.6916 (tttm)
REVERT: D   13 LEU cc_start: 0.9123 (mm) cc_final: 0.8783 (mm)
REVERT: D  141 PHE cc_start: 0.8811 (t80) cc_final: 0.8536 (t80)
REVERT: D  239 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8522 (mm-30)
REVERT: D  355 MET cc_start: 0.9173 (mmm) cc_final: 0.8926 (mmm)
REVERT: D  408 SER cc_start: 0.9301 (m) cc_final: 0.8934 (p)
REVERT: D  474 LYS cc_start: 0.7188 (tmtm) cc_final: 0.6928 (tttm)
  outliers start: 46
  outliers final: 32
  residues processed: 298
  average time/residue: 0.1845
  time to fit residues: 85.5371
Evaluate side-chains
  297 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 263
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  398 ILE
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain C residue    4 LYS
Chi-restraints excluded: chain C residue   26 MET
Chi-restraints excluded: chain C residue   65 ASP
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain D residue    4 LYS
Chi-restraints excluded: chain D residue   11 ASP
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  217 CYS
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  450 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    0.9980
   chunk 136 optimal weight:    0.0770
   chunk 140 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 107 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9980
   chunk 129 optimal weight:    7.9990
   chunk 89 optimal weight:    0.7980
   chunk 144 optimal weight:    1.9990
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  15 ASN
C  15 ASN
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 401 ASN
D   6 GLN
D  15 ASN
** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12668  Z= 0.184
  Angle     :  0.661   9.715  17172  Z= 0.327
  Chirality :  0.041   0.214   2008
  Planarity :  0.003   0.027   2080
  Dihedral  :  3.888  14.701   1668
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 20.85 %
    Favored  : 75.89 %
  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:  1.73 (0.22), residues: 1528
  helix:  2.05 (0.15), residues: 1208
  sheet:  None (None), residues: 0
  loop : -2.54 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 219 
 HIS   0.002   0.001   HIS C   5 
 PHE   0.030   0.001   PHE A 180 
 TYR   0.017   0.001   TYR A  53 
 ARG   0.001   0.000   ARG A 178 

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

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 275
  time to evaluate  : 1.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 PHE cc_start: 0.8770 (t80) cc_final: 0.8553 (t80)
REVERT: A  204 ILE cc_start: 0.9595 (tp) cc_final: 0.9340 (tp)
REVERT: A  215 LEU cc_start: 0.9373 (tp) cc_final: 0.9138 (tt)
REVERT: A  387 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9020 (mt)
REVERT: A  474 LYS cc_start: 0.7239 (tmtm) cc_final: 0.6934 (tttm)
REVERT: B   13 LEU cc_start: 0.9079 (mm) cc_final: 0.8666 (pp)
REVERT: B   53 TYR cc_start: 0.7613 (t80) cc_final: 0.6464 (t80)
REVERT: B   77 MET cc_start: 0.8297 (tpp) cc_final: 0.7992 (mmm)
REVERT: B  141 PHE cc_start: 0.8746 (t80) cc_final: 0.8501 (t80)
REVERT: B  186 MET cc_start: 0.1968 (mmp) cc_final: 0.1762 (mmp)
REVERT: B  215 LEU cc_start: 0.9377 (tp) cc_final: 0.9131 (tt)
REVERT: B  239 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8585 (mm-30)
REVERT: B  355 MET cc_start: 0.9106 (mmm) cc_final: 0.8877 (mmm)
REVERT: B  408 SER cc_start: 0.9448 (m) cc_final: 0.9248 (m)
REVERT: B  474 LYS cc_start: 0.7126 (tmtm) cc_final: 0.6824 (tttm)
REVERT: C   53 TYR cc_start: 0.7586 (t80) cc_final: 0.6788 (t80)
REVERT: C   77 MET cc_start: 0.8552 (tpp) cc_final: 0.7859 (tmm)
REVERT: C  408 SER cc_start: 0.9336 (m) cc_final: 0.8979 (p)
REVERT: C  474 LYS cc_start: 0.7184 (tmtm) cc_final: 0.6937 (tttm)
REVERT: D   13 LEU cc_start: 0.9141 (mm) cc_final: 0.8794 (mm)
REVERT: D   77 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7922 (mmm)
REVERT: D  141 PHE cc_start: 0.8805 (t80) cc_final: 0.8520 (t80)
REVERT: D  355 MET cc_start: 0.9174 (mmm) cc_final: 0.8921 (mmm)
REVERT: D  408 SER cc_start: 0.9298 (m) cc_final: 0.8929 (p)
REVERT: D  474 LYS cc_start: 0.7229 (tmtm) cc_final: 0.6962 (tttm)
  outliers start: 44
  outliers final: 32
  residues processed: 296
  average time/residue: 0.1816
  time to fit residues: 84.3763
Evaluate side-chains
  301 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 267
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain C residue    4 LYS
Chi-restraints excluded: chain C residue   26 MET
Chi-restraints excluded: chain C residue   65 ASP
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  450 THR
Chi-restraints excluded: chain D residue    4 LYS
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain D residue   77 MET
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  351 LEU
Chi-restraints excluded: chain D residue  450 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 88 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 100 optimal weight:    0.8980
   chunk 151 optimal weight:    0.8980
   chunk 139 optimal weight:    0.8980
   chunk 120 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 93 optimal weight:    6.9990
   chunk 73 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 128 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
B  15 ASN
C  15 ASN
C 401 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.5162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12668  Z= 0.197
  Angle     :  0.682  11.394  17172  Z= 0.335
  Chirality :  0.041   0.225   2008
  Planarity :  0.003   0.046   2080
  Dihedral  :  3.903  16.658   1668
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 21.74 %
    Favored  : 75.45 %
  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:  1.79 (0.22), residues: 1528
  helix:  2.08 (0.15), residues: 1208
  sheet:  None (None), residues: 0
  loop : -2.49 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 219 
 HIS   0.002   0.001   HIS D   5 
 PHE   0.024   0.001   PHE A 180 
 TYR   0.015   0.001   TYR A  53 
 ARG   0.002   0.000   ARG B 178 

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

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 278
  time to evaluate  : 1.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.9503 (mt) cc_final: 0.9218 (pp)
REVERT: A  128 MET cc_start: 0.8789 (mtp) cc_final: 0.8544 (mtp)
REVERT: A  141 PHE cc_start: 0.8777 (t80) cc_final: 0.8545 (t80)
REVERT: A  204 ILE cc_start: 0.9599 (tp) cc_final: 0.9335 (tp)
REVERT: A  215 LEU cc_start: 0.9381 (tp) cc_final: 0.9153 (tt)
REVERT: A  415 TYR cc_start: 0.8532 (t80) cc_final: 0.8168 (t80)
REVERT: A  474 LYS cc_start: 0.7269 (tmtm) cc_final: 0.6956 (tttm)
REVERT: B   13 LEU cc_start: 0.9115 (mm) cc_final: 0.8682 (pp)
REVERT: B   53 TYR cc_start: 0.7313 (t80) cc_final: 0.6297 (t80)
REVERT: B  141 PHE cc_start: 0.8752 (t80) cc_final: 0.8497 (t80)
REVERT: B  215 LEU cc_start: 0.9388 (tp) cc_final: 0.9160 (tt)
REVERT: B  239 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8570 (mm-30)
REVERT: B  355 MET cc_start: 0.9123 (mmm) cc_final: 0.8892 (mmm)
REVERT: B  408 SER cc_start: 0.9461 (m) cc_final: 0.9260 (m)
REVERT: B  415 TYR cc_start: 0.8467 (t80) cc_final: 0.8076 (t80)
REVERT: B  474 LYS cc_start: 0.7184 (tmtm) cc_final: 0.6885 (tttm)
REVERT: C   48 LEU cc_start: 0.9502 (mt) cc_final: 0.9234 (pp)
REVERT: C   53 TYR cc_start: 0.7539 (t80) cc_final: 0.6749 (t80)
REVERT: C   77 MET cc_start: 0.8565 (tpp) cc_final: 0.7897 (tmm)
REVERT: C  408 SER cc_start: 0.9368 (m) cc_final: 0.8993 (p)
REVERT: C  415 TYR cc_start: 0.8414 (t80) cc_final: 0.8096 (t80)
REVERT: C  474 LYS cc_start: 0.7223 (tmtm) cc_final: 0.6962 (tttm)
REVERT: D   13 LEU cc_start: 0.9159 (mm) cc_final: 0.8814 (mm)
REVERT: D   77 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7885 (mmm)
REVERT: D  141 PHE cc_start: 0.8782 (t80) cc_final: 0.8479 (t80)
REVERT: D  355 MET cc_start: 0.9168 (mmm) cc_final: 0.8924 (mmm)
REVERT: D  408 SER cc_start: 0.9309 (m) cc_final: 0.8961 (p)
REVERT: D  474 LYS cc_start: 0.7273 (tmtm) cc_final: 0.6998 (tttm)
  outliers start: 38
  outliers final: 29
  residues processed: 296
  average time/residue: 0.1853
  time to fit residues: 85.4141
Evaluate side-chains
  294 residues out of total 1348 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 264
  time to evaluate  : 1.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 MET
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain C residue    4 LYS
Chi-restraints excluded: chain C residue   26 MET
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain D residue    4 LYS
Chi-restraints excluded: chain D residue   26 MET
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain D residue   77 MET
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  450 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 111 optimal weight:    0.9980
   chunk 17 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 124 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 106 optimal weight:    0.2980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
B  15 ASN
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  15 ASN
C 401 ASN
D   6 GLN
** D  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.076050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.067764 restraints weight = 42322.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.069657 restraints weight = 19721.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.070854 restraints weight = 11214.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.5256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12668  Z= 0.180
  Angle     :  0.679   9.861  17172  Z= 0.334
  Chirality :  0.041   0.203   2008
  Planarity :  0.003   0.036   2080
  Dihedral  :  3.846  15.220   1668
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.59 %
    Favored  : 75.67 %
  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:  1.85 (0.22), residues: 1528
  helix:  2.12 (0.15), residues: 1208
  sheet:  None (None), residues: 0
  loop : -2.45 (0.30), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 219 
 HIS   0.002   0.001   HIS C   5 
 PHE   0.023   0.001   PHE C 141 
 TYR   0.014   0.001   TYR B 385 
 ARG   0.003   0.000   ARG D 178 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2680.96 seconds
wall clock time: 50 minutes 4.24 seconds (3004.24 seconds total)