Starting phenix.real_space_refine
on Sun Sep 29 21:57:07 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/09_2024/3jd4_6633.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/09_2024/3jd4_6633.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/09_2024/3jd4_6633.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/09_2024/3jd4_6633.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/09_2024/3jd4_6633.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/09_2024/3jd4_6633.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     P      42      5.49       5
     S     114      5.16       5
     C   15060      2.51       5
     N    4194      2.21       5
     O    4644      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 24054
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 3889
          Classifications: {'peptide': 497}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475}
    Chain: "C"
      Number of atoms: 3889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 3889
          Classifications: {'peptide': 497}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475}
    Chain: "A"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 120
          Unusual residues: {'GTP': 1, 'NAI': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 120
          Unusual residues: {'GTP': 1, 'NAI': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B, D, E, F
  Time building chain proxies: 14.86, per 1000 atoms: 0.62
  Number of scatterers: 24054
  At special positions: 0
  Unit cell: (114.12, 129.421, 165.123, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     114     16.00
     P      42     15.00
     O    4644      8.00
     N    4194      7.00
     C   15060      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 5.87
  Conformation dependent library (CDL) restraints added in 2.9 seconds
  

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5412

  Finding SS restraints...
    Secondary structure from input PDB file:
      132 helices and 24 sheets defined
      56.7% alpha, 8.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 30
      removed outlier: 3.615A  pdb=" N   ILE A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   ASP A  26 " --> pdb=" O   SER A  22 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   LYS A  27 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLU A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 53
      removed outlier: 3.998A  pdb=" N   SER A  47 " --> pdb=" O   ASN A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 118
      removed outlier: 4.091A  pdb=" N   ALA A 106 " --> pdb=" O   ASP A 102 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA A 116 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 155
      removed outlier: 3.526A  pdb=" N   LYS A 155 " --> pdb=" O   GLU A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 187
      removed outlier: 3.569A  pdb=" N   TRP A 178 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 198
      removed outlier: 4.275A  pdb=" N   VAL A 198 " --> pdb=" O   HIS A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 206
    Processing helix  chain 'A' and resid 213 through 228
    Processing helix  chain 'A' and resid 229 through 237
      removed outlier: 4.201A  pdb=" N   ILE A 235 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 265
    Processing helix  chain 'A' and resid 287 through 298
      removed outlier: 3.558A  pdb=" N   PHE A 294 " --> pdb=" O   GLU A 290 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU A 296 " --> pdb=" O   GLU A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 335 through 339
      removed outlier: 3.572A  pdb=" N   VAL A 339 " --> pdb=" O   ALA A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 363
      removed outlier: 3.859A  pdb=" N   LYS A 358 " --> pdb=" O   PRO A 354 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE A 359 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 374
    Processing helix  chain 'A' and resid 374 through 388
      removed outlier: 4.313A  pdb=" N   VAL A 378 " --> pdb=" O   ASN A 374 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   PHE A 383 " --> pdb=" O   THR A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 397
      No H-bonds generated for 'chain 'A' and resid 395 through 397'
    Processing helix  chain 'A' and resid 398 through 421
      removed outlier: 3.731A  pdb=" N   GLU A 402 " --> pdb=" O   THR A 398 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   MET A 411 " --> pdb=" O   TYR A 407 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS A 420 " --> pdb=" O   SER A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 425
    Processing helix  chain 'A' and resid 433 through 439
      removed outlier: 3.752A  pdb=" N   ASP A 438 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG A 439 " --> pdb=" O   GLU A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 471
      removed outlier: 3.645A  pdb=" N   VAL A 449 " --> pdb=" O   GLU A 445 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ALA A 454 " --> pdb=" O   HIS A 450 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ALA A 461 " --> pdb=" O   MET A 457 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS A 470 " --> pdb=" O   ARG A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 496
      removed outlier: 3.531A  pdb=" N   ARG A 491 " --> pdb=" O   GLU A 487 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A 492 " --> pdb=" O   LYS A 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 30
      removed outlier: 3.615A  pdb=" N   ILE B  23 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   ASP B  26 " --> pdb=" O   SER B  22 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   LYS B  27 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL B  29 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLU B  30 " --> pdb=" O   ASP B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 53
      removed outlier: 3.998A  pdb=" N   SER B  47 " --> pdb=" O   ASN B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 118
      removed outlier: 4.091A  pdb=" N   ALA B 106 " --> pdb=" O   ASP B 102 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA B 116 " --> pdb=" O   THR B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 155
      removed outlier: 3.525A  pdb=" N   LYS B 155 " --> pdb=" O   GLU B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 187
      removed outlier: 3.570A  pdb=" N   TRP B 178 " --> pdb=" O   ARG B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 198
      removed outlier: 4.274A  pdb=" N   VAL B 198 " --> pdb=" O   HIS B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 206
    Processing helix  chain 'B' and resid 213 through 228
    Processing helix  chain 'B' and resid 229 through 237
      removed outlier: 4.201A  pdb=" N   ILE B 235 " --> pdb=" O   SER B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 265
    Processing helix  chain 'B' and resid 287 through 298
      removed outlier: 3.558A  pdb=" N   PHE B 294 " --> pdb=" O   GLU B 290 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU B 296 " --> pdb=" O   GLU B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 317
    Processing helix  chain 'B' and resid 335 through 339
      removed outlier: 3.573A  pdb=" N   VAL B 339 " --> pdb=" O   ALA B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 363
      removed outlier: 3.858A  pdb=" N   LYS B 358 " --> pdb=" O   PRO B 354 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE B 359 " --> pdb=" O   GLU B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 374
    Processing helix  chain 'B' and resid 374 through 388
      removed outlier: 4.314A  pdb=" N   VAL B 378 " --> pdb=" O   ASN B 374 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   PHE B 383 " --> pdb=" O   THR B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 397
      No H-bonds generated for 'chain 'B' and resid 395 through 397'
    Processing helix  chain 'B' and resid 398 through 421
      removed outlier: 3.731A  pdb=" N   GLU B 402 " --> pdb=" O   THR B 398 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   MET B 411 " --> pdb=" O   TYR B 407 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG B 419 " --> pdb=" O   GLU B 415 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS B 420 " --> pdb=" O   SER B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 425
    Processing helix  chain 'B' and resid 433 through 439
      removed outlier: 3.752A  pdb=" N   ASP B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG B 439 " --> pdb=" O   GLU B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 471
      removed outlier: 3.645A  pdb=" N   VAL B 449 " --> pdb=" O   GLU B 445 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ALA B 454 " --> pdb=" O   HIS B 450 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ALA B 461 " --> pdb=" O   MET B 457 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS B 470 " --> pdb=" O   ARG B 466 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 496
      removed outlier: 3.531A  pdb=" N   ARG B 491 " --> pdb=" O   GLU B 487 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL B 492 " --> pdb=" O   LYS B 488 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 30
      removed outlier: 3.615A  pdb=" N   ILE C  23 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   ASP C  26 " --> pdb=" O   SER C  22 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   LYS C  27 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL C  29 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU C  30 " --> pdb=" O   ASP C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 53
      removed outlier: 3.998A  pdb=" N   SER C  47 " --> pdb=" O   ASN C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 118
      removed outlier: 4.091A  pdb=" N   ALA C 106 " --> pdb=" O   ASP C 102 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA C 116 " --> pdb=" O   THR C 112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 155
      removed outlier: 3.526A  pdb=" N   LYS C 155 " --> pdb=" O   GLU C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 187
      removed outlier: 3.570A  pdb=" N   TRP C 178 " --> pdb=" O   ARG C 174 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 193 through 198
      removed outlier: 4.275A  pdb=" N   VAL C 198 " --> pdb=" O   HIS C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 206
    Processing helix  chain 'C' and resid 213 through 228
    Processing helix  chain 'C' and resid 229 through 237
      removed outlier: 4.201A  pdb=" N   ILE C 235 " --> pdb=" O   SER C 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 253 through 265
    Processing helix  chain 'C' and resid 287 through 298
      removed outlier: 3.558A  pdb=" N   PHE C 294 " --> pdb=" O   GLU C 290 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU C 296 " --> pdb=" O   GLU C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 313 through 317
    Processing helix  chain 'C' and resid 335 through 339
      removed outlier: 3.572A  pdb=" N   VAL C 339 " --> pdb=" O   ALA C 336 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 353 through 363
      removed outlier: 3.858A  pdb=" N   LYS C 358 " --> pdb=" O   PRO C 354 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE C 359 " --> pdb=" O   GLU C 355 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 369 through 374
    Processing helix  chain 'C' and resid 374 through 388
      removed outlier: 4.314A  pdb=" N   VAL C 378 " --> pdb=" O   ASN C 374 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   PHE C 383 " --> pdb=" O   THR C 379 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 395 through 397
      No H-bonds generated for 'chain 'C' and resid 395 through 397'
    Processing helix  chain 'C' and resid 398 through 421
      removed outlier: 3.731A  pdb=" N   GLU C 402 " --> pdb=" O   THR C 398 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   MET C 411 " --> pdb=" O   TYR C 407 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG C 419 " --> pdb=" O   GLU C 415 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS C 420 " --> pdb=" O   SER C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 422 through 425
    Processing helix  chain 'C' and resid 433 through 439
      removed outlier: 3.752A  pdb=" N   ASP C 438 " --> pdb=" O   ALA C 434 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ARG C 439 " --> pdb=" O   GLU C 435 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 444 through 471
      removed outlier: 3.645A  pdb=" N   VAL C 449 " --> pdb=" O   GLU C 445 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA C 454 " --> pdb=" O   HIS C 450 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ALA C 461 " --> pdb=" O   MET C 457 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LYS C 470 " --> pdb=" O   ARG C 466 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 476 through 496
      removed outlier: 3.532A  pdb=" N   ARG C 491 " --> pdb=" O   GLU C 487 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL C 492 " --> pdb=" O   LYS C 488 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 8 through 30
      removed outlier: 3.614A  pdb=" N   ILE D  23 " --> pdb=" O   ARG D  19 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   ASP D  26 " --> pdb=" O   SER D  22 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   LYS D  27 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL D  29 " --> pdb=" O   GLU D  25 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU D  30 " --> pdb=" O   ASP D  26 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 53
      removed outlier: 3.998A  pdb=" N   SER D  47 " --> pdb=" O   ASN D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 118
      removed outlier: 4.091A  pdb=" N   ALA D 106 " --> pdb=" O   ASP D 102 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA D 116 " --> pdb=" O   THR D 112 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 155
      removed outlier: 3.526A  pdb=" N   LYS D 155 " --> pdb=" O   GLU D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 172 through 187
      removed outlier: 3.569A  pdb=" N   TRP D 178 " --> pdb=" O   ARG D 174 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 193 through 198
      removed outlier: 4.275A  pdb=" N   VAL D 198 " --> pdb=" O   HIS D 195 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 206
    Processing helix  chain 'D' and resid 213 through 228
    Processing helix  chain 'D' and resid 229 through 237
      removed outlier: 4.201A  pdb=" N   ILE D 235 " --> pdb=" O   SER D 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 253 through 265
    Processing helix  chain 'D' and resid 287 through 298
      removed outlier: 3.557A  pdb=" N   PHE D 294 " --> pdb=" O   GLU D 290 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU D 296 " --> pdb=" O   GLU D 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 313 through 317
    Processing helix  chain 'D' and resid 335 through 339
      removed outlier: 3.573A  pdb=" N   VAL D 339 " --> pdb=" O   ALA D 336 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 353 through 363
      removed outlier: 3.859A  pdb=" N   LYS D 358 " --> pdb=" O   PRO D 354 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE D 359 " --> pdb=" O   GLU D 355 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 369 through 374
    Processing helix  chain 'D' and resid 374 through 388
      removed outlier: 4.313A  pdb=" N   VAL D 378 " --> pdb=" O   ASN D 374 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   PHE D 383 " --> pdb=" O   THR D 379 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 395 through 397
      No H-bonds generated for 'chain 'D' and resid 395 through 397'
    Processing helix  chain 'D' and resid 398 through 421
      removed outlier: 3.731A  pdb=" N   GLU D 402 " --> pdb=" O   THR D 398 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   MET D 411 " --> pdb=" O   TYR D 407 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG D 419 " --> pdb=" O   GLU D 415 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS D 420 " --> pdb=" O   SER D 416 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 422 through 425
    Processing helix  chain 'D' and resid 433 through 439
      removed outlier: 3.752A  pdb=" N   ASP D 438 " --> pdb=" O   ALA D 434 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG D 439 " --> pdb=" O   GLU D 435 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 444 through 471
      removed outlier: 3.645A  pdb=" N   VAL D 449 " --> pdb=" O   GLU D 445 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA D 454 " --> pdb=" O   HIS D 450 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ALA D 461 " --> pdb=" O   MET D 457 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS D 470 " --> pdb=" O   ARG D 466 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 476 through 496
      removed outlier: 3.530A  pdb=" N   ARG D 491 " --> pdb=" O   GLU D 487 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL D 492 " --> pdb=" O   LYS D 488 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 8 through 30
      removed outlier: 3.614A  pdb=" N   ILE E  23 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   ASP E  26 " --> pdb=" O   SER E  22 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   LYS E  27 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL E  29 " --> pdb=" O   GLU E  25 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU E  30 " --> pdb=" O   ASP E  26 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 37 through 53
      removed outlier: 3.998A  pdb=" N   SER E  47 " --> pdb=" O   ASN E  43 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 100 through 118
      removed outlier: 4.092A  pdb=" N   ALA E 106 " --> pdb=" O   ASP E 102 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA E 116 " --> pdb=" O   THR E 112 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 139 through 155
      removed outlier: 3.525A  pdb=" N   LYS E 155 " --> pdb=" O   GLU E 151 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 172 through 187
      removed outlier: 3.569A  pdb=" N   TRP E 178 " --> pdb=" O   ARG E 174 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 193 through 198
      removed outlier: 4.275A  pdb=" N   VAL E 198 " --> pdb=" O   HIS E 195 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 202 through 206
    Processing helix  chain 'E' and resid 213 through 228
    Processing helix  chain 'E' and resid 229 through 237
      removed outlier: 4.200A  pdb=" N   ILE E 235 " --> pdb=" O   SER E 231 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 253 through 265
    Processing helix  chain 'E' and resid 287 through 298
      removed outlier: 3.558A  pdb=" N   PHE E 294 " --> pdb=" O   GLU E 290 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU E 296 " --> pdb=" O   GLU E 292 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 313 through 317
    Processing helix  chain 'E' and resid 335 through 339
      removed outlier: 3.573A  pdb=" N   VAL E 339 " --> pdb=" O   ALA E 336 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 353 through 363
      removed outlier: 3.859A  pdb=" N   LYS E 358 " --> pdb=" O   PRO E 354 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE E 359 " --> pdb=" O   GLU E 355 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 369 through 374
    Processing helix  chain 'E' and resid 374 through 388
      removed outlier: 4.313A  pdb=" N   VAL E 378 " --> pdb=" O   ASN E 374 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   PHE E 383 " --> pdb=" O   THR E 379 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 395 through 397
      No H-bonds generated for 'chain 'E' and resid 395 through 397'
    Processing helix  chain 'E' and resid 398 through 421
      removed outlier: 3.730A  pdb=" N   GLU E 402 " --> pdb=" O   THR E 398 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   MET E 411 " --> pdb=" O   TYR E 407 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG E 419 " --> pdb=" O   GLU E 415 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS E 420 " --> pdb=" O   SER E 416 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 422 through 425
    Processing helix  chain 'E' and resid 433 through 439
      removed outlier: 3.753A  pdb=" N   ASP E 438 " --> pdb=" O   ALA E 434 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG E 439 " --> pdb=" O   GLU E 435 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 444 through 471
      removed outlier: 3.645A  pdb=" N   VAL E 449 " --> pdb=" O   GLU E 445 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA E 454 " --> pdb=" O   HIS E 450 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ALA E 461 " --> pdb=" O   MET E 457 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LYS E 470 " --> pdb=" O   ARG E 466 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 476 through 496
      removed outlier: 3.530A  pdb=" N   ARG E 491 " --> pdb=" O   GLU E 487 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL E 492 " --> pdb=" O   LYS E 488 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 8 through 30
      removed outlier: 3.615A  pdb=" N   ILE F  23 " --> pdb=" O   ARG F  19 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   ASP F  26 " --> pdb=" O   SER F  22 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   LYS F  27 " --> pdb=" O   ILE F  23 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL F  29 " --> pdb=" O   GLU F  25 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU F  30 " --> pdb=" O   ASP F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 37 through 53
      removed outlier: 3.998A  pdb=" N   SER F  47 " --> pdb=" O   ASN F  43 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 100 through 118
      removed outlier: 4.092A  pdb=" N   ALA F 106 " --> pdb=" O   ASP F 102 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA F 116 " --> pdb=" O   THR F 112 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 139 through 155
      removed outlier: 3.526A  pdb=" N   LYS F 155 " --> pdb=" O   GLU F 151 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 172 through 187
      removed outlier: 3.570A  pdb=" N   TRP F 178 " --> pdb=" O   ARG F 174 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 193 through 198
      removed outlier: 4.275A  pdb=" N   VAL F 198 " --> pdb=" O   HIS F 195 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 202 through 206
    Processing helix  chain 'F' and resid 213 through 228
    Processing helix  chain 'F' and resid 229 through 237
      removed outlier: 4.201A  pdb=" N   ILE F 235 " --> pdb=" O   SER F 231 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 253 through 265
    Processing helix  chain 'F' and resid 287 through 298
      removed outlier: 3.558A  pdb=" N   PHE F 294 " --> pdb=" O   GLU F 290 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU F 296 " --> pdb=" O   GLU F 292 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 313 through 317
    Processing helix  chain 'F' and resid 335 through 339
      removed outlier: 3.573A  pdb=" N   VAL F 339 " --> pdb=" O   ALA F 336 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 353 through 363
      removed outlier: 3.859A  pdb=" N   LYS F 358 " --> pdb=" O   PRO F 354 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE F 359 " --> pdb=" O   GLU F 355 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 369 through 374
    Processing helix  chain 'F' and resid 374 through 388
      removed outlier: 4.314A  pdb=" N   VAL F 378 " --> pdb=" O   ASN F 374 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   PHE F 383 " --> pdb=" O   THR F 379 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 395 through 397
      No H-bonds generated for 'chain 'F' and resid 395 through 397'
    Processing helix  chain 'F' and resid 398 through 421
      removed outlier: 3.731A  pdb=" N   GLU F 402 " --> pdb=" O   THR F 398 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   MET F 411 " --> pdb=" O   TYR F 407 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG F 419 " --> pdb=" O   GLU F 415 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS F 420 " --> pdb=" O   SER F 416 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 422 through 425
    Processing helix  chain 'F' and resid 433 through 439
      removed outlier: 3.752A  pdb=" N   ASP F 438 " --> pdb=" O   ALA F 434 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ARG F 439 " --> pdb=" O   GLU F 435 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 444 through 471
      removed outlier: 3.644A  pdb=" N   VAL F 449 " --> pdb=" O   GLU F 445 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA F 454 " --> pdb=" O   HIS F 450 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ALA F 461 " --> pdb=" O   MET F 457 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LYS F 470 " --> pdb=" O   ARG F 466 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 476 through 496
      removed outlier: 3.531A  pdb=" N   ARG F 491 " --> pdb=" O   GLU F 487 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL F 492 " --> pdb=" O   LYS F 488 " (cutoff:3.500A)
    Processing sheet with id=A, first strand: chain 'A' and resid 57 through 60
      removed outlier: 4.407A  pdb=" N   GLY A  92 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   CYS A  89 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   ALA A 166 " --> pdb=" O   CYS A  89 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLY A  91 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
    Processing sheet with id=B, first strand: chain 'A' and resid 65 through 66
    Processing sheet with id=C, first strand: chain 'A' and resid 246 through 250
      removed outlier: 7.824A  pdb=" N   PHE A 247 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   VAL A 273 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   VAL A 249 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   SER A 279 " --> pdb=" O   TYR A 310 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS A 308 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
    Processing sheet with id=D, first strand: chain 'A' and resid 321 through 322
    Processing sheet with id=E, first strand: chain 'B' and resid 57 through 60
      removed outlier: 4.408A  pdb=" N   GLY B  92 " --> pdb=" O   ALA B 125 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   CYS B  89 " --> pdb=" O   VAL B 164 " (cutoff:3.500A)
      removed outlier: 7.634A  pdb=" N   ALA B 166 " --> pdb=" O   CYS B  89 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLY B  91 " --> pdb=" O   ALA B 166 " (cutoff:3.500A)
    Processing sheet with id=F, first strand: chain 'B' and resid 65 through 66
    Processing sheet with id=G, first strand: chain 'B' and resid 246 through 250
      removed outlier: 7.825A  pdb=" N   PHE B 247 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   VAL B 273 " --> pdb=" O   PHE B 247 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   VAL B 249 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   SER B 279 " --> pdb=" O   TYR B 310 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LYS B 308 " --> pdb=" O   TRP B 281 " (cutoff:3.500A)
    Processing sheet with id=H, first strand: chain 'B' and resid 321 through 322
    Processing sheet with id=I, first strand: chain 'C' and resid 57 through 60
      removed outlier: 4.407A  pdb=" N   GLY C  92 " --> pdb=" O   ALA C 125 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   CYS C  89 " --> pdb=" O   VAL C 164 " (cutoff:3.500A)
      removed outlier: 7.634A  pdb=" N   ALA C 166 " --> pdb=" O   CYS C  89 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLY C  91 " --> pdb=" O   ALA C 166 " (cutoff:3.500A)
    Processing sheet with id=J, first strand: chain 'C' and resid 65 through 66
    Processing sheet with id=K, first strand: chain 'C' and resid 246 through 250
      removed outlier: 7.825A  pdb=" N   PHE C 247 " --> pdb=" O   ILE C 271 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   VAL C 273 " --> pdb=" O   PHE C 247 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   VAL C 249 " --> pdb=" O   VAL C 273 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   SER C 279 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LYS C 308 " --> pdb=" O   TRP C 281 " (cutoff:3.500A)
    Processing sheet with id=L, first strand: chain 'C' and resid 321 through 322
    Processing sheet with id=M, first strand: chain 'D' and resid 57 through 60
      removed outlier: 4.407A  pdb=" N   GLY D  92 " --> pdb=" O   ALA D 125 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   CYS D  89 " --> pdb=" O   VAL D 164 " (cutoff:3.500A)
      removed outlier: 7.634A  pdb=" N   ALA D 166 " --> pdb=" O   CYS D  89 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLY D  91 " --> pdb=" O   ALA D 166 " (cutoff:3.500A)
    Processing sheet with id=N, first strand: chain 'D' and resid 65 through 66
    Processing sheet with id=O, first strand: chain 'D' and resid 246 through 250
      removed outlier: 7.824A  pdb=" N   PHE D 247 " --> pdb=" O   ILE D 271 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   VAL D 273 " --> pdb=" O   PHE D 247 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   VAL D 249 " --> pdb=" O   VAL D 273 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   SER D 279 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS D 308 " --> pdb=" O   TRP D 281 " (cutoff:3.500A)
    Processing sheet with id=P, first strand: chain 'D' and resid 321 through 322
    Processing sheet with id=Q, first strand: chain 'E' and resid 57 through 60
      removed outlier: 4.407A  pdb=" N   GLY E  92 " --> pdb=" O   ALA E 125 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   CYS E  89 " --> pdb=" O   VAL E 164 " (cutoff:3.500A)
      removed outlier: 7.634A  pdb=" N   ALA E 166 " --> pdb=" O   CYS E  89 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLY E  91 " --> pdb=" O   ALA E 166 " (cutoff:3.500A)
    Processing sheet with id=R, first strand: chain 'E' and resid 65 through 66
    Processing sheet with id=S, first strand: chain 'E' and resid 246 through 250
      removed outlier: 7.825A  pdb=" N   PHE E 247 " --> pdb=" O   ILE E 271 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   VAL E 273 " --> pdb=" O   PHE E 247 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   VAL E 249 " --> pdb=" O   VAL E 273 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   SER E 279 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LYS E 308 " --> pdb=" O   TRP E 281 " (cutoff:3.500A)
    Processing sheet with id=T, first strand: chain 'E' and resid 321 through 322
    Processing sheet with id=U, first strand: chain 'F' and resid 57 through 60
      removed outlier: 4.408A  pdb=" N   GLY F  92 " --> pdb=" O   ALA F 125 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   CYS F  89 " --> pdb=" O   VAL F 164 " (cutoff:3.500A)
      removed outlier: 7.634A  pdb=" N   ALA F 166 " --> pdb=" O   CYS F  89 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLY F  91 " --> pdb=" O   ALA F 166 " (cutoff:3.500A)
    Processing sheet with id=V, first strand: chain 'F' and resid 65 through 66
    Processing sheet with id=W, first strand: chain 'F' and resid 246 through 250
      removed outlier: 7.824A  pdb=" N   PHE F 247 " --> pdb=" O   ILE F 271 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   VAL F 273 " --> pdb=" O   PHE F 247 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   VAL F 249 " --> pdb=" O   VAL F 273 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   SER F 279 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS F 308 " --> pdb=" O   TRP F 281 " (cutoff:3.500A)
    Processing sheet with id=X, first strand: chain 'F' and resid 321 through 322

    1140 hydrogen bonds defined for protein.
    3240 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: 8.38

  Time building geometry restraints manager: 6.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 7511
        1.33 -     1.45: 3456
        1.45 -     1.57: 13375
        1.57 -     1.68: 78
        1.68 -     1.80: 192
  Bond restraints: 24612
  Sorted by residual:
  bond pdb=" C4A NAI A 601 "
       pdb=" C5A NAI A 601 "
    ideal  model  delta    sigma   weight residual
    1.386  1.466 -0.080 2.00e-02 2.50e+03 1.62e+01
  bond pdb=" N   PRO F 429 "
       pdb=" CD  PRO F 429 "
    ideal  model  delta    sigma   weight residual
    1.473  1.529 -0.056 1.40e-02 5.10e+03 1.60e+01
  bond pdb=" C4A NAI B 602 "
       pdb=" C5A NAI B 602 "
    ideal  model  delta    sigma   weight residual
    1.386  1.466 -0.080 2.00e-02 2.50e+03 1.60e+01
  bond pdb=" C4A NAI C 602 "
       pdb=" C5A NAI C 602 "
    ideal  model  delta    sigma   weight residual
    1.386  1.466 -0.080 2.00e-02 2.50e+03 1.59e+01
  bond pdb=" C4A NAI E 602 "
       pdb=" C5A NAI E 602 "
    ideal  model  delta    sigma   weight residual
    1.386  1.466 -0.080 2.00e-02 2.50e+03 1.59e+01
  ... (remaining 24607 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.86: 32776
        2.86 -     5.73: 507
        5.73 -     8.59: 74
        8.59 -    11.46: 15
       11.46 -    14.32: 12
  Bond angle restraints: 33384
  Sorted by residual:
  angle pdb=" C   ILE A 428 "
        pdb=" N   PRO A 429 "
        pdb=" CA  PRO A 429 "
      ideal   model   delta    sigma   weight residual
     119.84  114.17    5.67 1.25e+00 6.40e-01 2.06e+01
  angle pdb=" C   ILE C 428 "
        pdb=" N   PRO C 429 "
        pdb=" CA  PRO C 429 "
      ideal   model   delta    sigma   weight residual
     119.84  114.19    5.65 1.25e+00 6.40e-01 2.04e+01
  angle pdb=" C   ILE E 428 "
        pdb=" N   PRO E 429 "
        pdb=" CA  PRO E 429 "
      ideal   model   delta    sigma   weight residual
     119.84  114.20    5.64 1.25e+00 6.40e-01 2.04e+01
  angle pdb=" C   ILE B 428 "
        pdb=" N   PRO B 429 "
        pdb=" CA  PRO B 429 "
      ideal   model   delta    sigma   weight residual
     119.84  114.20    5.64 1.25e+00 6.40e-01 2.03e+01
  angle pdb=" C   ILE F 428 "
        pdb=" N   PRO F 429 "
        pdb=" CA  PRO F 429 "
      ideal   model   delta    sigma   weight residual
     119.84  114.21    5.63 1.25e+00 6.40e-01 2.03e+01
  ... (remaining 33379 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.47: 14779
       33.47 -    66.95: 293
       66.95 -   100.42: 12
      100.42 -   133.89: 6
      133.89 -   167.37: 6
  Dihedral angle restraints: 15096
    sinusoidal: 6600
      harmonic: 8496
  Sorted by residual:
  dihedral pdb=" C8  GTP D 602 "
           pdb=" C1' GTP D 602 "
           pdb=" N9  GTP D 602 "
           pdb=" O4' GTP D 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -62.77  167.37     1      2.00e+01 2.50e-03 4.74e+01
  dihedral pdb=" C8  GTP F 603 "
           pdb=" C1' GTP F 603 "
           pdb=" N9  GTP F 603 "
           pdb=" O4' GTP F 603 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -62.72  167.32     1      2.00e+01 2.50e-03 4.74e+01
  dihedral pdb=" C8  GTP C 603 "
           pdb=" C1' GTP C 603 "
           pdb=" N9  GTP C 603 "
           pdb=" O4' GTP C 603 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -62.72  167.31     1      2.00e+01 2.50e-03 4.74e+01
  ... (remaining 15093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 2508
       0.049 -    0.097: 930
       0.097 -    0.146: 135
       0.146 -    0.195: 31
       0.195 -    0.244: 14
  Chirality restraints: 3618
  Sorted by residual:
  chirality pdb=" C1B NAI E 602 "
            pdb=" C2B NAI E 602 "
            pdb=" N9A NAI E 602 "
            pdb=" O4B NAI E 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.31    2.55   -0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" C1B NAI D 601 "
            pdb=" C2B NAI D 601 "
            pdb=" N9A NAI D 601 "
            pdb=" O4B NAI D 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.31    2.55   -0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" C1B NAI B 602 "
            pdb=" C2B NAI B 602 "
            pdb=" N9A NAI B 602 "
            pdb=" O4B NAI B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.31    2.55   -0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 3615 not shown)

  Planarity restraints: 4242
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D 282 "    0.034 5.00e-02 4.00e+02   5.12e-02 4.20e+00
        pdb=" N   PRO D 283 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO D 283 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO D 283 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN F 282 "   -0.034 5.00e-02 4.00e+02   5.12e-02 4.19e+00
        pdb=" N   PRO F 283 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO F 283 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO F 283 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 282 "    0.034 5.00e-02 4.00e+02   5.11e-02 4.18e+00
        pdb=" N   PRO A 283 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 283 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 283 "    0.028 5.00e-02 4.00e+02
  ... (remaining 4239 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 1144
        2.71 -     3.25: 26307
        3.25 -     3.80: 38827
        3.80 -     4.35: 52983
        4.35 -     4.90: 86076
  Nonbonded interactions: 205337
  Sorted by model distance:
  nonbonded pdb=" O   HIS D 195 "
            pdb=" NZ  LYS D 201 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" O   HIS C 195 "
            pdb=" NZ  LYS C 201 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" O   HIS A 195 "
            pdb=" NZ  LYS A 201 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" O   HIS B 195 "
            pdb=" NZ  LYS B 201 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" O   HIS E 195 "
            pdb=" NZ  LYS E 201 "
     model   vdw
     2.158 3.120
  ... (remaining 205332 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 5 through 501 or resid 601))
  selection = (chain 'B' and (resid 5 through 501 or resid 602))
  selection = (chain 'C' and (resid 5 through 501 or resid 601))
  selection = (chain 'D' and (resid 5 through 501 or resid 601))
  selection = (chain 'E' and (resid 5 through 501 or resid 602))
  selection = (chain 'F' and (resid 5 through 501 or resid 601))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          1.000
  Check model and map are aligned:         0.150
  Set scattering table:                    0.190
  Process input model:                     52.220
  Find NCS groups from input model:        1.330
  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:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
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      :  0.009   0.080  24612  Z= 0.578
  Angle     :  0.963  14.319  33384  Z= 0.498
  Chirality :  0.052   0.244   3618
  Planarity :  0.004   0.051   4242
  Dihedral  : 12.302 167.367   9684
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.84 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -4.82 (0.12), residues: 2970
  helix: -3.67 (0.08), residues: 1320
  sheet: -3.54 (0.22), residues: 312
  loop : -2.42 (0.16), residues: 1338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP D 178 
 HIS   0.010   0.002   HIS E 450 
 PHE   0.034   0.003   PHE C 122 
 TYR   0.033   0.003   TYR A  78 
 ARG   0.005   0.001   ARG F  86 

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

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

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  542 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 542
  time to evaluate  : 2.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.8401 (t0) cc_final: 0.7931 (m-30)
REVERT: A   33 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7929 (mtmt)
REVERT: A   72 TRP cc_start: 0.8354 (m100) cc_final: 0.8147 (m100)
REVERT: A   84 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8073 (mm-40)
REVERT: A  181 ASP cc_start: 0.8449 (t70) cc_final: 0.7995 (t0)
REVERT: A  308 LYS cc_start: 0.7902 (pttt) cc_final: 0.7414 (mttp)
REVERT: B    6 ASP cc_start: 0.8394 (t0) cc_final: 0.7865 (m-30)
REVERT: B   33 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7871 (mtmt)
REVERT: B   72 TRP cc_start: 0.8365 (m100) cc_final: 0.8084 (m100)
REVERT: B   84 GLN cc_start: 0.8301 (mm-40) cc_final: 0.8059 (mm-40)
REVERT: B  181 ASP cc_start: 0.8531 (t70) cc_final: 0.8037 (t0)
REVERT: B  308 LYS cc_start: 0.8002 (pttt) cc_final: 0.7518 (mttp)
REVERT: C    6 ASP cc_start: 0.8424 (t0) cc_final: 0.7900 (m-30)
REVERT: C   72 TRP cc_start: 0.8371 (m100) cc_final: 0.8043 (m100)
REVERT: C  181 ASP cc_start: 0.8463 (t70) cc_final: 0.7995 (t0)
REVERT: C  292 GLU cc_start: 0.8434 (tt0) cc_final: 0.7976 (tm-30)
REVERT: C  308 LYS cc_start: 0.7915 (pttt) cc_final: 0.7436 (mttp)
REVERT: C  372 TYR cc_start: 0.8003 (t80) cc_final: 0.7674 (t80)
REVERT: D    6 ASP cc_start: 0.8395 (t0) cc_final: 0.7892 (m-30)
REVERT: D   33 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7957 (mtmt)
REVERT: D   72 TRP cc_start: 0.8354 (m100) cc_final: 0.8107 (m100)
REVERT: D   84 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8086 (mm-40)
REVERT: D  181 ASP cc_start: 0.8470 (t70) cc_final: 0.8018 (t0)
REVERT: D  308 LYS cc_start: 0.7913 (pttt) cc_final: 0.7442 (mttp)
REVERT: E    6 ASP cc_start: 0.8388 (t0) cc_final: 0.7857 (m-30)
REVERT: E   33 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7874 (mtmt)
REVERT: E   72 TRP cc_start: 0.8356 (m100) cc_final: 0.8077 (m100)
REVERT: E   84 GLN cc_start: 0.8303 (mm-40) cc_final: 0.8055 (mm-40)
REVERT: E  181 ASP cc_start: 0.8533 (t70) cc_final: 0.8043 (t0)
REVERT: E  308 LYS cc_start: 0.8011 (pttt) cc_final: 0.7533 (mttp)
REVERT: F    6 ASP cc_start: 0.8423 (t0) cc_final: 0.7897 (m-30)
REVERT: F   72 TRP cc_start: 0.8369 (m100) cc_final: 0.8044 (m100)
REVERT: F  181 ASP cc_start: 0.8463 (t70) cc_final: 0.7991 (t0)
REVERT: F  292 GLU cc_start: 0.8430 (tt0) cc_final: 0.7974 (tm-30)
REVERT: F  308 LYS cc_start: 0.7915 (pttt) cc_final: 0.7439 (mttp)
REVERT: F  372 TYR cc_start: 0.7999 (t80) cc_final: 0.7670 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 542
  average time/residue: 0.4180
  time to fit residues: 333.3527
Evaluate side-chains
  299 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 299
  time to evaluate  : 2.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 294
   random chunks:
   chunk 248 optimal weight:    7.9990
   chunk 222 optimal weight:   10.0000
   chunk 123 optimal weight:    5.9990
   chunk 76 optimal weight:    9.9990
   chunk 150 optimal weight:    7.9990
   chunk 119 optimal weight:    5.9990
   chunk 230 optimal weight:   10.0000
   chunk 89 optimal weight:    5.9990
   chunk 140 optimal weight:   20.0000
   chunk 171 optimal weight:    6.9990
   chunk 266 optimal weight:    8.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
A  85 HIS
** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 ASN
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 408 HIS
B  85 HIS
B 189 HIS
B 228 ASN
** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 408 HIS
** C  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 HIS
C 189 HIS
** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 408 HIS
D  81 GLN
D  84 GLN
D  85 HIS
** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 193 ASN
** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 408 HIS
E  81 GLN
E  84 GLN
E  85 HIS
E 189 HIS
** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 408 HIS
** F  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  85 HIS
F 189 HIS
** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 408 HIS

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  24612  Z= 0.385
  Angle     :  0.719  10.557  33384  Z= 0.364
  Chirality :  0.049   0.199   3618
  Planarity :  0.005   0.044   4242
  Dihedral  : 14.145 164.226   4080
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  7.19 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.23 (0.14), residues: 2970
  helix: -1.00 (0.12), residues: 1380
  sheet: -2.79 (0.22), residues: 372
  loop : -1.39 (0.18), residues: 1218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 281 
 HIS   0.009   0.002   HIS E 450 
 PHE   0.022   0.003   PHE A  16 
 TYR   0.024   0.002   TYR F  78 
 ARG   0.005   0.001   ARG C  19 

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

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

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  450 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 63
    poor density    : 387
  time to evaluate  : 2.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.8228 (t0) cc_final: 0.7639 (m-30)
REVERT: A   33 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7867 (mtmt)
REVERT: A   72 TRP cc_start: 0.8399 (m100) cc_final: 0.7290 (m100)
REVERT: A   81 GLN cc_start: 0.8209 (mt0) cc_final: 0.7928 (mt0)
REVERT: A   84 GLN cc_start: 0.8299 (mm110) cc_final: 0.8064 (mm-40)
REVERT: A  181 ASP cc_start: 0.8479 (t70) cc_final: 0.8066 (t0)
REVERT: A  308 LYS cc_start: 0.7823 (pttt) cc_final: 0.7368 (mttp)
REVERT: A  495 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8151 (mt-10)
REVERT: B    6 ASP cc_start: 0.8244 (t0) cc_final: 0.7646 (m-30)
REVERT: B   33 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7890 (mtmt)
REVERT: B   72 TRP cc_start: 0.8373 (m100) cc_final: 0.7166 (m100)
REVERT: B   81 GLN cc_start: 0.8381 (mt0) cc_final: 0.7570 (mt0)
REVERT: B   84 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8007 (mm-40)
REVERT: B  163 ASP cc_start: 0.8227 (m-30) cc_final: 0.7372 (m-30)
REVERT: B  181 ASP cc_start: 0.8525 (t70) cc_final: 0.8110 (t0)
REVERT: B  308 LYS cc_start: 0.7957 (pttt) cc_final: 0.7486 (mttp)
REVERT: C    6 ASP cc_start: 0.8287 (t0) cc_final: 0.7687 (m-30)
REVERT: C   72 TRP cc_start: 0.8412 (m100) cc_final: 0.7950 (m100)
REVERT: C   81 GLN cc_start: 0.8235 (mt0) cc_final: 0.7950 (mt0)
REVERT: C  181 ASP cc_start: 0.8503 (t70) cc_final: 0.8300 (t0)
REVERT: C  308 LYS cc_start: 0.7862 (pttt) cc_final: 0.7380 (mttp)
REVERT: C  372 TYR cc_start: 0.8415 (t80) cc_final: 0.8190 (t80)
REVERT: C  457 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7852 (mtm)
REVERT: C  495 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8164 (mt-10)
REVERT: D    6 ASP cc_start: 0.8199 (t0) cc_final: 0.7609 (m-30)
REVERT: D   33 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7884 (mtmt)
REVERT: D   72 TRP cc_start: 0.8384 (m100) cc_final: 0.7298 (m100)
REVERT: D   81 GLN cc_start: 0.8116 (mt0) cc_final: 0.7877 (mt0)
REVERT: D  181 ASP cc_start: 0.8488 (t70) cc_final: 0.8072 (t0)
REVERT: D  308 LYS cc_start: 0.7813 (pttt) cc_final: 0.7369 (mttp)
REVERT: D  495 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8160 (mt-10)
REVERT: E    6 ASP cc_start: 0.8243 (t0) cc_final: 0.7648 (m-30)
REVERT: E   33 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7890 (mtmt)
REVERT: E   72 TRP cc_start: 0.8367 (m100) cc_final: 0.7221 (m100)
REVERT: E   81 GLN cc_start: 0.8138 (mt0) cc_final: 0.7923 (mt0)
REVERT: E   84 GLN cc_start: 0.8225 (mm110) cc_final: 0.7988 (mm-40)
REVERT: E  181 ASP cc_start: 0.8532 (t70) cc_final: 0.8126 (t0)
REVERT: E  308 LYS cc_start: 0.7950 (pttt) cc_final: 0.7486 (mttp)
REVERT: F    6 ASP cc_start: 0.8281 (t0) cc_final: 0.7670 (m-30)
REVERT: F   72 TRP cc_start: 0.8411 (m100) cc_final: 0.7958 (m100)
REVERT: F   81 GLN cc_start: 0.8233 (mt0) cc_final: 0.7934 (mt0)
REVERT: F  181 ASP cc_start: 0.8498 (t70) cc_final: 0.8297 (t0)
REVERT: F  308 LYS cc_start: 0.7863 (pttt) cc_final: 0.7382 (mttp)
REVERT: F  372 TYR cc_start: 0.8414 (t80) cc_final: 0.8187 (t80)
REVERT: F  457 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7849 (mtm)
REVERT: F  495 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8171 (mt-10)
  outliers start: 63
  outliers final: 48
  residues processed: 437
  average time/residue: 0.3419
  time to fit residues: 235.1606
Evaluate side-chains
  334 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 284
  time to evaluate  : 2.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  277 ASP
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  277 ASP
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  427 THR
Chi-restraints excluded: chain C residue  457 MET
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  158 ILE
Chi-restraints excluded: chain D residue  219 VAL
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain D residue  413 VAL
Chi-restraints excluded: chain E residue   32 LEU
Chi-restraints excluded: chain E residue   97 THR
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  277 ASP
Chi-restraints excluded: chain E residue  309 ILE
Chi-restraints excluded: chain E residue  339 VAL
Chi-restraints excluded: chain E residue  361 LEU
Chi-restraints excluded: chain E residue  413 VAL
Chi-restraints excluded: chain F residue   32 LEU
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain F residue  277 ASP
Chi-restraints excluded: chain F residue  309 ILE
Chi-restraints excluded: chain F residue  413 VAL
Chi-restraints excluded: chain F residue  427 THR
Chi-restraints excluded: chain F residue  457 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 294
   random chunks:
   chunk 148 optimal weight:    0.3980
   chunk 82 optimal weight:    0.0870
   chunk 222 optimal weight:    0.9980
   chunk 181 optimal weight:   30.0000
   chunk 73 optimal weight:    5.9990
   chunk 267 optimal weight:   10.0000
   chunk 288 optimal weight:    7.9990
   chunk 238 optimal weight:    3.9990
   chunk 265 optimal weight:    7.9990
   chunk 91 optimal weight:    0.0670
   chunk 214 optimal weight:    4.9990
   overall best weight:    1.1098

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
A 189 HIS
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 221 HIS
** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 221 HIS
** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  24612  Z= 0.156
  Angle     :  0.574   7.454  33384  Z= 0.290
  Chirality :  0.044   0.201   3618
  Planarity :  0.004   0.038   4242
  Dihedral  : 12.958 162.674   4080
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 10.15 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -0.66 (0.15), residues: 2970
  helix:  0.50 (0.13), residues: 1410
  sheet: -2.34 (0.23), residues: 384
  loop : -0.75 (0.19), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  72 
 HIS   0.006   0.001   HIS E 450 
 PHE   0.019   0.002   PHE E   9 
 TYR   0.012   0.001   TYR F 401 
 ARG   0.004   0.000   ARG A 261 

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

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

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  424 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 368
  time to evaluate  : 2.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7847 (mtmt)
REVERT: A   84 GLN cc_start: 0.8222 (mm110) cc_final: 0.7966 (mm-40)
REVERT: A  150 MET cc_start: 0.8054 (tpp) cc_final: 0.7830 (mpp)
REVERT: A  181 ASP cc_start: 0.8446 (t70) cc_final: 0.8075 (t0)
REVERT: A  308 LYS cc_start: 0.7795 (pttt) cc_final: 0.7556 (mttp)
REVERT: B    6 ASP cc_start: 0.7938 (t0) cc_final: 0.7321 (m-30)
REVERT: B   33 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7784 (mtmt)
REVERT: B   81 GLN cc_start: 0.8221 (mt0) cc_final: 0.7382 (mt0)
REVERT: B   84 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7979 (mp10)
REVERT: B  163 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7154 (m-30)
REVERT: B  181 ASP cc_start: 0.8456 (t70) cc_final: 0.8087 (t0)
REVERT: B  308 LYS cc_start: 0.7885 (pttt) cc_final: 0.7641 (mttp)
REVERT: C    6 ASP cc_start: 0.7890 (t0) cc_final: 0.7228 (m-30)
REVERT: C   72 TRP cc_start: 0.8331 (m100) cc_final: 0.7998 (m100)
REVERT: C  181 ASP cc_start: 0.8464 (t70) cc_final: 0.8059 (t0)
REVERT: C  292 GLU cc_start: 0.8209 (tt0) cc_final: 0.7698 (tm-30)
REVERT: C  308 LYS cc_start: 0.7839 (pttt) cc_final: 0.7591 (mttp)
REVERT: D   33 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7820 (mtmt)
REVERT: D  150 MET cc_start: 0.8063 (tpp) cc_final: 0.7837 (mpp)
REVERT: D  181 ASP cc_start: 0.8456 (t70) cc_final: 0.8109 (t0)
REVERT: D  308 LYS cc_start: 0.7756 (pttt) cc_final: 0.7550 (mttp)
REVERT: E   33 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7786 (mtmt)
REVERT: E  181 ASP cc_start: 0.8462 (t70) cc_final: 0.8097 (t0)
REVERT: E  308 LYS cc_start: 0.7880 (pttt) cc_final: 0.7640 (mttp)
REVERT: F    6 ASP cc_start: 0.7892 (t0) cc_final: 0.7233 (m-30)
REVERT: F   72 TRP cc_start: 0.8325 (m100) cc_final: 0.7973 (m100)
REVERT: F  181 ASP cc_start: 0.8459 (t70) cc_final: 0.8053 (t0)
REVERT: F  308 LYS cc_start: 0.7837 (pttt) cc_final: 0.7592 (mttp)
  outliers start: 56
  outliers final: 27
  residues processed: 403
  average time/residue: 0.3343
  time to fit residues: 215.1601
Evaluate side-chains
  313 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 285
  time to evaluate  : 2.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  277 ASP
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain C residue  427 THR
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  272 THR
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain E residue   32 LEU
Chi-restraints excluded: chain E residue   97 THR
Chi-restraints excluded: chain E residue  277 ASP
Chi-restraints excluded: chain E residue  339 VAL
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain F residue  248 VAL
Chi-restraints excluded: chain F residue  272 THR
Chi-restraints excluded: chain F residue  322 LEU
Chi-restraints excluded: chain F residue  427 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 294
   random chunks:
   chunk 264 optimal weight:    7.9990
   chunk 201 optimal weight:    0.0670
   chunk 138 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 127 optimal weight:    6.9990
   chunk 179 optimal weight:   30.0000
   chunk 268 optimal weight:    8.9990
   chunk 284 optimal weight:    9.9990
   chunk 140 optimal weight:   20.0000
   chunk 254 optimal weight:    0.0870
   chunk 76 optimal weight:    2.9990
   overall best weight:    2.6302

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

Flipped N/Q/H residues before XYZ refinement:
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 ASN
B 388 ASN
B 391 HIS
C  56 ASN
** C  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 297 GLN
** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 388 ASN
C 391 HIS
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 388 ASN
E 391 HIS
F  56 ASN
** F  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 297 GLN
** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 388 ASN
F 391 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.3678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  24612  Z= 0.194
  Angle     :  0.560   8.308  33384  Z= 0.278
  Chirality :  0.044   0.172   3618
  Planarity :  0.004   0.035   4242
  Dihedral  : 12.586 160.260   4080
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 12.07 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 (0.16), residues: 2970
  helix:  1.15 (0.14), residues: 1374
  sheet: -1.53 (0.25), residues: 402
  loop : -0.37 (0.20), residues: 1194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP E  72 
 HIS   0.006   0.001   HIS D 450 
 PHE   0.014   0.002   PHE B 148 
 TYR   0.012   0.001   TYR B 262 
 ARG   0.003   0.000   ARG C 261 

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

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

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  392 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 78
    poor density    : 314
  time to evaluate  : 2.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7853 (mtmt)
REVERT: A   84 GLN cc_start: 0.8299 (mm110) cc_final: 0.7878 (mp10)
REVERT: A  181 ASP cc_start: 0.8459 (t70) cc_final: 0.8070 (t0)
REVERT: A  308 LYS cc_start: 0.7810 (pttt) cc_final: 0.7597 (mttp)
REVERT: B   33 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7805 (mtmt)
REVERT: B   72 TRP cc_start: 0.8186 (m100) cc_final: 0.7940 (m100)
REVERT: B   81 GLN cc_start: 0.8337 (mt0) cc_final: 0.7470 (mt0)
REVERT: B   84 GLN cc_start: 0.8302 (mm-40) cc_final: 0.8040 (mp10)
REVERT: B  163 ASP cc_start: 0.8152 (m-30) cc_final: 0.7261 (m-30)
REVERT: B  181 ASP cc_start: 0.8417 (t70) cc_final: 0.8022 (t0)
REVERT: B  308 LYS cc_start: 0.7846 (pttt) cc_final: 0.7628 (mttp)
REVERT: C    6 ASP cc_start: 0.7928 (t0) cc_final: 0.7302 (m-30)
REVERT: C   72 TRP cc_start: 0.8349 (m100) cc_final: 0.7988 (m100)
REVERT: C  181 ASP cc_start: 0.8465 (t70) cc_final: 0.8060 (t0)
REVERT: C  308 LYS cc_start: 0.7834 (pttt) cc_final: 0.7586 (mttp)
REVERT: C  372 TYR cc_start: 0.8295 (t80) cc_final: 0.8084 (t80)
REVERT: C  457 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7541 (mtm)
REVERT: D   33 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7859 (mtmt)
REVERT: D  181 ASP cc_start: 0.8471 (t70) cc_final: 0.8083 (t0)
REVERT: E   33 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7809 (mtmt)
REVERT: E   72 TRP cc_start: 0.8175 (m100) cc_final: 0.7917 (m100)
REVERT: E  181 ASP cc_start: 0.8420 (t70) cc_final: 0.8038 (t0)
REVERT: E  308 LYS cc_start: 0.7837 (pttt) cc_final: 0.7620 (mttp)
REVERT: F    6 ASP cc_start: 0.7938 (t0) cc_final: 0.7317 (m-30)
REVERT: F   72 TRP cc_start: 0.8348 (m100) cc_final: 0.7990 (m100)
REVERT: F  181 ASP cc_start: 0.8456 (t70) cc_final: 0.8062 (t0)
REVERT: F  308 LYS cc_start: 0.7831 (pttt) cc_final: 0.7588 (mttp)
REVERT: F  372 TYR cc_start: 0.8296 (t80) cc_final: 0.8084 (t80)
REVERT: F  457 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7534 (mtm)
  outliers start: 78
  outliers final: 47
  residues processed: 363
  average time/residue: 0.3558
  time to fit residues: 201.6873
Evaluate side-chains
  319 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 270
  time to evaluate  : 2.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  277 ASP
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  239 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  249 VAL
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain C residue  457 MET
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  239 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  272 THR
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain E residue   90 LYS
Chi-restraints excluded: chain E residue   97 THR
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  277 ASP
Chi-restraints excluded: chain E residue  322 LEU
Chi-restraints excluded: chain E residue  339 VAL
Chi-restraints excluded: chain F residue   90 LYS
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain F residue  239 THR
Chi-restraints excluded: chain F residue  248 VAL
Chi-restraints excluded: chain F residue  249 VAL
Chi-restraints excluded: chain F residue  272 THR
Chi-restraints excluded: chain F residue  322 LEU
Chi-restraints excluded: chain F residue  427 THR
Chi-restraints excluded: chain F residue  457 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 294
   random chunks:
   chunk 236 optimal weight:    5.9990
   chunk 161 optimal weight:    7.9990
   chunk 4 optimal weight:    7.9990
   chunk 211 optimal weight:    5.9990
   chunk 117 optimal weight:    5.9990
   chunk 242 optimal weight:    8.9990
   chunk 196 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 145 optimal weight:    5.9990
   chunk 255 optimal weight:    0.9990
   chunk 71 optimal weight:   10.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  56 ASN
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 254 ASN
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 221 HIS
B 254 ASN
** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 388 ASN
C  56 ASN
** C  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 ASN
** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 388 ASN
** D  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 254 ASN
** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 221 HIS
** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 388 ASN
F  56 ASN
** F  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 254 ASN
** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 388 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.3766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  24612  Z= 0.290
  Angle     :  0.599   9.101  33384  Z= 0.299
  Chirality :  0.046   0.156   3618
  Planarity :  0.004   0.036   4242
  Dihedral  : 12.480 157.801   4080
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 11.71 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.22 (0.16), residues: 2970
  helix:  1.19 (0.14), residues: 1410
  sheet: -1.53 (0.25), residues: 402
  loop : -0.40 (0.20), residues: 1158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP D  72 
 HIS   0.007   0.001   HIS E 450 
 PHE   0.017   0.002   PHE A 122 
 TYR   0.015   0.002   TYR A  78 
 ARG   0.003   0.000   ARG F 459 

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

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

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  363 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 88
    poor density    : 275
  time to evaluate  : 2.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7836 (mtmt)
REVERT: A   84 GLN cc_start: 0.8359 (mm110) cc_final: 0.8104 (mp10)
REVERT: A  181 ASP cc_start: 0.8488 (t70) cc_final: 0.8081 (t0)
REVERT: A  308 LYS cc_start: 0.7803 (pttt) cc_final: 0.7527 (mttp)
REVERT: B   33 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7839 (mtmt)
REVERT: B   81 GLN cc_start: 0.8421 (mt0) cc_final: 0.7540 (mt0)
REVERT: B   84 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8140 (mp10)
REVERT: B  163 ASP cc_start: 0.8189 (m-30) cc_final: 0.7316 (m-30)
REVERT: B  181 ASP cc_start: 0.8426 (t70) cc_final: 0.8019 (t0)
REVERT: B  308 LYS cc_start: 0.7898 (pttt) cc_final: 0.7619 (mttp)
REVERT: C    6 ASP cc_start: 0.8012 (t0) cc_final: 0.7512 (m-30)
REVERT: C   72 TRP cc_start: 0.8357 (m100) cc_final: 0.8006 (m100)
REVERT: C  140 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7875 (mt-10)
REVERT: C  308 LYS cc_start: 0.7867 (pttt) cc_final: 0.7543 (mttp)
REVERT: C  372 TYR cc_start: 0.8357 (t80) cc_final: 0.8146 (t80)
REVERT: C  457 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7518 (mtm)
REVERT: D   33 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7857 (mtmt)
REVERT: D  181 ASP cc_start: 0.8494 (t70) cc_final: 0.8088 (t0)
REVERT: E   33 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7857 (mtmt)
REVERT: E  181 ASP cc_start: 0.8447 (t70) cc_final: 0.8049 (t0)
REVERT: E  308 LYS cc_start: 0.7902 (pttt) cc_final: 0.7632 (mttp)
REVERT: E  411 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8378 (tpt)
REVERT: F    6 ASP cc_start: 0.7998 (t0) cc_final: 0.7442 (m-30)
REVERT: F   72 TRP cc_start: 0.8359 (m100) cc_final: 0.8019 (m100)
REVERT: F  140 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7866 (mt-10)
REVERT: F  308 LYS cc_start: 0.7866 (pttt) cc_final: 0.7545 (mttp)
REVERT: F  457 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7924 (mtm)
  outliers start: 88
  outliers final: 61
  residues processed: 338
  average time/residue: 0.3354
  time to fit residues: 185.8498
Evaluate side-chains
  332 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 66
    poor density    : 266
  time to evaluate  : 2.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  277 ASP
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  140 GLU
Chi-restraints excluded: chain C residue  239 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  277 ASP
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain C residue  457 MET
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  239 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  249 VAL
Chi-restraints excluded: chain D residue  272 THR
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain D residue  413 VAL
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain E residue   97 THR
Chi-restraints excluded: chain E residue  158 ILE
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  272 THR
Chi-restraints excluded: chain E residue  277 ASP
Chi-restraints excluded: chain E residue  309 ILE
Chi-restraints excluded: chain E residue  322 LEU
Chi-restraints excluded: chain E residue  339 VAL
Chi-restraints excluded: chain E residue  411 MET
Chi-restraints excluded: chain F residue   90 LYS
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain F residue  239 THR
Chi-restraints excluded: chain F residue  248 VAL
Chi-restraints excluded: chain F residue  272 THR
Chi-restraints excluded: chain F residue  277 ASP
Chi-restraints excluded: chain F residue  309 ILE
Chi-restraints excluded: chain F residue  322 LEU
Chi-restraints excluded: chain F residue  427 THR
Chi-restraints excluded: chain F residue  457 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 294
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 255 optimal weight:    0.9980
   chunk 56 optimal weight:    7.9990
   chunk 166 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 284 optimal weight:    8.9990
   chunk 236 optimal weight:    5.9990
   chunk 131 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 94 optimal weight:    2.9990
   chunk 149 optimal weight:   20.0000
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.4054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  24612  Z= 0.179
  Angle     :  0.550   9.638  33384  Z= 0.272
  Chirality :  0.043   0.150   3618
  Planarity :  0.004   0.036   4242
  Dihedral  : 12.150 155.908   4080
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 12.71 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.64 (0.16), residues: 2970
  helix:  1.58 (0.14), residues: 1374
  sheet: -1.47 (0.26), residues: 402
  loop : -0.13 (0.20), residues: 1194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP D  72 
 HIS   0.005   0.001   HIS E 450 
 PHE   0.014   0.001   PHE D   9 
 TYR   0.009   0.001   TYR C 401 
 ARG   0.002   0.000   ARG C 261 

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

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

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  374 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 77
    poor density    : 297
  time to evaluate  : 2.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7843 (mtmt)
REVERT: A   84 GLN cc_start: 0.8338 (mm110) cc_final: 0.8090 (mp10)
REVERT: A  181 ASP cc_start: 0.8445 (t70) cc_final: 0.8216 (t0)
REVERT: B   33 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7820 (mtmt)
REVERT: B   72 TRP cc_start: 0.8348 (m100) cc_final: 0.7943 (m100)
REVERT: B   81 GLN cc_start: 0.8356 (mt0) cc_final: 0.7487 (mt0)
REVERT: B   84 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8082 (mp10)
REVERT: B  140 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7942 (mt-10)
REVERT: B  163 ASP cc_start: 0.8162 (m-30) cc_final: 0.7275 (m-30)
REVERT: C    6 ASP cc_start: 0.7914 (t0) cc_final: 0.7429 (m-30)
REVERT: C   72 TRP cc_start: 0.8328 (m100) cc_final: 0.7939 (m100)
REVERT: C  308 LYS cc_start: 0.7820 (pttt) cc_final: 0.7603 (mttp)
REVERT: C  491 ARG cc_start: 0.8225 (mtp180) cc_final: 0.7980 (mtm-85)
REVERT: D   33 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7808 (mtmt)
REVERT: D  181 ASP cc_start: 0.8453 (t70) cc_final: 0.8227 (t0)
REVERT: E   33 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7863 (mtmt)
REVERT: E   72 TRP cc_start: 0.8350 (m100) cc_final: 0.7936 (m100)
REVERT: E  140 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7954 (mt-10)
REVERT: F    6 ASP cc_start: 0.7958 (t0) cc_final: 0.7481 (m-30)
REVERT: F   72 TRP cc_start: 0.8339 (m100) cc_final: 0.7949 (m100)
REVERT: F  308 LYS cc_start: 0.7818 (pttt) cc_final: 0.7607 (mttp)
  outliers start: 77
  outliers final: 49
  residues processed: 346
  average time/residue: 0.3287
  time to fit residues: 183.5265
Evaluate side-chains
  313 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 262
  time to evaluate  : 2.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  140 GLU
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  260 MET
Chi-restraints excluded: chain B residue  277 ASP
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  239 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  249 VAL
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  277 ASP
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  158 ILE
Chi-restraints excluded: chain D residue  239 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  249 VAL
Chi-restraints excluded: chain D residue  272 THR
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain E residue   97 THR
Chi-restraints excluded: chain E residue  140 GLU
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  260 MET
Chi-restraints excluded: chain E residue  277 ASP
Chi-restraints excluded: chain E residue  322 LEU
Chi-restraints excluded: chain F residue   90 LYS
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain F residue  239 THR
Chi-restraints excluded: chain F residue  248 VAL
Chi-restraints excluded: chain F residue  249 VAL
Chi-restraints excluded: chain F residue  272 THR
Chi-restraints excluded: chain F residue  277 ASP
Chi-restraints excluded: chain F residue  322 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 294
   random chunks:
   chunk 274 optimal weight:   20.0000
   chunk 32 optimal weight:    2.9990
   chunk 162 optimal weight:    9.9990
   chunk 207 optimal weight:    0.9990
   chunk 160 optimal weight:   10.0000
   chunk 239 optimal weight:    3.9990
   chunk 158 optimal weight:    0.9990
   chunk 283 optimal weight:    4.9990
   chunk 177 optimal weight:    1.9990
   chunk 172 optimal weight:    9.9990
   chunk 130 optimal weight:    8.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 ASN
** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 254 ASN
** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  81 GLN
F 254 ASN
** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.4207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  24612  Z= 0.176
  Angle     :  0.550   9.755  33384  Z= 0.273
  Chirality :  0.043   0.151   3618
  Planarity :  0.004   0.036   4242
  Dihedral  : 11.823 153.361   4080
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.15 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.75 (0.16), residues: 2970
  helix:  1.59 (0.14), residues: 1386
  sheet: -1.31 (0.26), residues: 402
  loop : -0.02 (0.20), residues: 1182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D  72 
 HIS   0.005   0.001   HIS E 450 
 PHE   0.012   0.001   PHE B 148 
 TYR   0.009   0.001   TYR F 493 
 ARG   0.007   0.000   ARG E 338 

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

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

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 68
    poor density    : 278
  time to evaluate  : 2.880 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7779 (mtmt)
REVERT: A   84 GLN cc_start: 0.8340 (mm110) cc_final: 0.8102 (mp10)
REVERT: A  181 ASP cc_start: 0.8413 (t70) cc_final: 0.8185 (t0)
REVERT: B   33 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7843 (mtmt)
REVERT: B   72 TRP cc_start: 0.8334 (m100) cc_final: 0.7913 (m100)
REVERT: B   81 GLN cc_start: 0.8350 (mt0) cc_final: 0.7467 (mt0)
REVERT: B   84 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8101 (mp10)
REVERT: B  140 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7907 (mt-10)
REVERT: B  163 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7283 (m-30)
REVERT: B  417 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8975 (mm)
REVERT: B  457 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7923 (mtm)
REVERT: C    6 ASP cc_start: 0.7913 (t0) cc_final: 0.7427 (m-30)
REVERT: C   72 TRP cc_start: 0.8321 (m100) cc_final: 0.7951 (m100)
REVERT: C  140 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7833 (mt-10)
REVERT: C  460 SER cc_start: 0.8963 (m) cc_final: 0.8695 (t)
REVERT: D   14 GLU cc_start: 0.7852 (pt0) cc_final: 0.7459 (pt0)
REVERT: D   33 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7771 (mtmt)
REVERT: D  181 ASP cc_start: 0.8417 (t70) cc_final: 0.8200 (t0)
REVERT: E   33 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7846 (mtmt)
REVERT: E   72 TRP cc_start: 0.8334 (m100) cc_final: 0.7900 (m100)
REVERT: E  140 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7910 (mt-10)
REVERT: E  417 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8979 (mm)
REVERT: E  457 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7903 (mtm)
REVERT: F   72 TRP cc_start: 0.8338 (m100) cc_final: 0.7964 (m100)
REVERT: F  140 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7825 (mt-10)
REVERT: F  460 SER cc_start: 0.8969 (m) cc_final: 0.8703 (t)
  outliers start: 68
  outliers final: 56
  residues processed: 327
  average time/residue: 0.3220
  time to fit residues: 171.7525
Evaluate side-chains
  323 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 65
    poor density    : 258
  time to evaluate  : 2.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  140 GLU
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  277 ASP
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  417 LEU
Chi-restraints excluded: chain B residue  457 MET
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  140 GLU
Chi-restraints excluded: chain C residue  158 ILE
Chi-restraints excluded: chain C residue  239 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  249 VAL
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  158 ILE
Chi-restraints excluded: chain D residue  239 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  249 VAL
Chi-restraints excluded: chain D residue  272 THR
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain E residue   97 THR
Chi-restraints excluded: chain E residue  140 GLU
Chi-restraints excluded: chain E residue  158 ILE
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  272 THR
Chi-restraints excluded: chain E residue  277 ASP
Chi-restraints excluded: chain E residue  322 LEU
Chi-restraints excluded: chain E residue  339 VAL
Chi-restraints excluded: chain E residue  417 LEU
Chi-restraints excluded: chain E residue  457 MET
Chi-restraints excluded: chain F residue   90 LYS
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain F residue  239 THR
Chi-restraints excluded: chain F residue  248 VAL
Chi-restraints excluded: chain F residue  249 VAL
Chi-restraints excluded: chain F residue  272 THR
Chi-restraints excluded: chain F residue  277 ASP
Chi-restraints excluded: chain F residue  322 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 294
   random chunks:
   chunk 175 optimal weight:    7.9990
   chunk 113 optimal weight:    5.9990
   chunk 169 optimal weight:    0.2980
   chunk 85 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   chunk 54 optimal weight:    9.9990
   chunk 180 optimal weight:   20.0000
   chunk 193 optimal weight:    6.9990
   chunk 140 optimal weight:   20.0000
   chunk 26 optimal weight:   20.0000
   chunk 222 optimal weight:   20.0000
   overall best weight:    4.8588

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 254 ASN
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 ASN
** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 ASN
** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 254 ASN
** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 ASN
** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 254 ASN
** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.4183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  24612  Z= 0.281
  Angle     :  0.596   9.106  33384  Z= 0.296
  Chirality :  0.045   0.153   3618
  Planarity :  0.004   0.035   4242
  Dihedral  : 11.359 151.657   4080
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 14.19 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.76 (0.16), residues: 2970
  helix:  1.57 (0.14), residues: 1386
  sheet: -1.16 (0.25), residues: 390
  loop : -0.05 (0.20), residues: 1194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP D  72 
 HIS   0.006   0.001   HIS C 450 
 PHE   0.015   0.002   PHE B 122 
 TYR   0.013   0.002   TYR B  78 
 ARG   0.002   0.000   ARG C  86 

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

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

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 70
    poor density    : 249
  time to evaluate  : 3.070 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 GLN cc_start: 0.8385 (mm110) cc_final: 0.8165 (mp10)
REVERT: A  181 ASP cc_start: 0.8437 (t70) cc_final: 0.8229 (t0)
REVERT: B   33 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7833 (mtmt)
REVERT: B   72 TRP cc_start: 0.8352 (m100) cc_final: 0.7929 (m100)
REVERT: B   81 GLN cc_start: 0.8411 (mt0) cc_final: 0.7549 (mt0)
REVERT: B   84 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8135 (mp10)
REVERT: B  140 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7944 (mt-10)
REVERT: B  163 ASP cc_start: 0.8200 (m-30) cc_final: 0.7331 (m-30)
REVERT: B  457 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.8023 (mtm)
REVERT: C    6 ASP cc_start: 0.8001 (t0) cc_final: 0.7540 (m-30)
REVERT: C   72 TRP cc_start: 0.8336 (m100) cc_final: 0.8016 (m100)
REVERT: C  140 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7965 (mt-10)
REVERT: C  460 SER cc_start: 0.8981 (m) cc_final: 0.8699 (t)
REVERT: D   14 GLU cc_start: 0.8036 (pt0) cc_final: 0.7713 (pt0)
REVERT: D  181 ASP cc_start: 0.8437 (t70) cc_final: 0.8236 (t0)
REVERT: E   33 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7854 (mtmt)
REVERT: E   72 TRP cc_start: 0.8337 (m100) cc_final: 0.7903 (m100)
REVERT: E  140 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7946 (mt-10)
REVERT: E  457 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.8006 (mtm)
REVERT: F    6 ASP cc_start: 0.8057 (t0) cc_final: 0.7635 (m-30)
REVERT: F   72 TRP cc_start: 0.8357 (m100) cc_final: 0.8039 (m100)
REVERT: F  140 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7961 (mt-10)
REVERT: F  460 SER cc_start: 0.8977 (m) cc_final: 0.8696 (t)
  outliers start: 70
  outliers final: 56
  residues processed: 305
  average time/residue: 0.3140
  time to fit residues: 159.2747
Evaluate side-chains
  305 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 62
    poor density    : 243
  time to evaluate  : 2.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  140 GLU
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  277 ASP
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  457 MET
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  140 GLU
Chi-restraints excluded: chain C residue  158 ILE
Chi-restraints excluded: chain C residue  239 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  277 ASP
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  158 ILE
Chi-restraints excluded: chain D residue  239 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  272 THR
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain E residue   97 THR
Chi-restraints excluded: chain E residue  140 GLU
Chi-restraints excluded: chain E residue  158 ILE
Chi-restraints excluded: chain E residue  239 THR
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  272 THR
Chi-restraints excluded: chain E residue  277 ASP
Chi-restraints excluded: chain E residue  322 LEU
Chi-restraints excluded: chain E residue  457 MET
Chi-restraints excluded: chain F residue   90 LYS
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain F residue  158 ILE
Chi-restraints excluded: chain F residue  239 THR
Chi-restraints excluded: chain F residue  248 VAL
Chi-restraints excluded: chain F residue  272 THR
Chi-restraints excluded: chain F residue  277 ASP
Chi-restraints excluded: chain F residue  322 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 294
   random chunks:
   chunk 257 optimal weight:    7.9990
   chunk 271 optimal weight:    5.9990
   chunk 247 optimal weight:   10.0000
   chunk 264 optimal weight:    5.9990
   chunk 158 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   chunk 207 optimal weight:    0.6980
   chunk 81 optimal weight:    5.9990
   chunk 238 optimal weight:    0.1980
   chunk 249 optimal weight:    5.9990
   chunk 263 optimal weight:    6.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 205 GLN
** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 ASN
** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 205 GLN
** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 254 ASN
** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  24612  Z= 0.173
  Angle     :  0.550   8.955  33384  Z= 0.273
  Chirality :  0.043   0.176   3618
  Planarity :  0.004   0.040   4242
  Dihedral  : 10.915 149.394   4080
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.91 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.16), residues: 2970
  helix:  1.77 (0.14), residues: 1386
  sheet: -1.15 (0.25), residues: 402
  loop :  0.07 (0.20), residues: 1182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP D  72 
 HIS   0.005   0.001   HIS E 450 
 PHE   0.012   0.001   PHE E   9 
 TYR   0.008   0.001   TYR A  78 
 ARG   0.002   0.000   ARG F  19 

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

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

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 62
    poor density    : 261
  time to evaluate  : 2.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 GLN cc_start: 0.8337 (mm110) cc_final: 0.8121 (mp10)
REVERT: A  181 ASP cc_start: 0.8365 (t70) cc_final: 0.8157 (t0)
REVERT: A  398 THR cc_start: 0.8564 (p) cc_final: 0.8353 (p)
REVERT: B   33 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7805 (mtmt)
REVERT: B   72 TRP cc_start: 0.8265 (m100) cc_final: 0.7897 (m100)
REVERT: B   81 GLN cc_start: 0.8356 (mt0) cc_final: 0.7470 (mt0)
REVERT: B   84 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8101 (mp10)
REVERT: B  140 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7917 (mt-10)
REVERT: B  163 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7284 (m-30)
REVERT: B  457 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7922 (mtm)
REVERT: C   72 TRP cc_start: 0.8283 (m100) cc_final: 0.7933 (m100)
REVERT: C  140 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7936 (mt-10)
REVERT: C  495 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7964 (mt-10)
REVERT: D  181 ASP cc_start: 0.8373 (t70) cc_final: 0.8171 (t0)
REVERT: E   33 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7803 (mtmt)
REVERT: E   72 TRP cc_start: 0.8262 (m100) cc_final: 0.7878 (m100)
REVERT: E  140 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7920 (mt-10)
REVERT: E  457 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7916 (mtm)
REVERT: F   72 TRP cc_start: 0.8294 (m100) cc_final: 0.7944 (m100)
REVERT: F  140 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7932 (mt-10)
  outliers start: 62
  outliers final: 50
  residues processed: 307
  average time/residue: 0.2985
  time to fit residues: 152.9563
Evaluate side-chains
  308 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 251
  time to evaluate  : 2.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  140 GLU
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  277 ASP
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  457 MET
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  140 GLU
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  272 THR
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain E residue   97 THR
Chi-restraints excluded: chain E residue  140 GLU
Chi-restraints excluded: chain E residue  158 ILE
Chi-restraints excluded: chain E residue  239 THR
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  272 THR
Chi-restraints excluded: chain E residue  277 ASP
Chi-restraints excluded: chain E residue  322 LEU
Chi-restraints excluded: chain E residue  413 VAL
Chi-restraints excluded: chain E residue  457 MET
Chi-restraints excluded: chain F residue   90 LYS
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain F residue  158 ILE
Chi-restraints excluded: chain F residue  248 VAL
Chi-restraints excluded: chain F residue  272 THR
Chi-restraints excluded: chain F residue  277 ASP
Chi-restraints excluded: chain F residue  322 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 294
   random chunks:
   chunk 173 optimal weight:   20.0000
   chunk 279 optimal weight:   30.0000
   chunk 170 optimal weight:    2.9990
   chunk 132 optimal weight:    8.9990
   chunk 194 optimal weight:    5.9990
   chunk 292 optimal weight:    5.9990
   chunk 269 optimal weight:   10.0000
   chunk 233 optimal weight:    2.9990
   chunk 24 optimal weight:   20.0000
   chunk 180 optimal weight:   10.0000
   chunk 143 optimal weight:   10.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 254 ASN
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 205 GLN
** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 ASN
** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 254 ASN
** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 205 GLN
E 254 ASN
** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 254 ASN
** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.4292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  24612  Z= 0.309
  Angle     :  0.622   9.192  33384  Z= 0.308
  Chirality :  0.047   0.228   3618
  Planarity :  0.004   0.039   4242
  Dihedral  : 10.889 148.302   4080
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.79 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.86 (0.16), residues: 2970
  helix:  1.65 (0.14), residues: 1386
  sheet: -1.06 (0.25), residues: 390
  loop : -0.02 (0.20), residues: 1194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP D  72 
 HIS   0.006   0.001   HIS F 450 
 PHE   0.025   0.002   PHE F 490 
 TYR   0.016   0.002   TYR E  78 
 ARG   0.003   0.000   ARG B 261 

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

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

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5940 Ramachandran restraints generated.
    2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 63
    poor density    : 247
  time to evaluate  : 2.658 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 GLN cc_start: 0.8411 (mm110) cc_final: 0.8199 (mp10)
REVERT: B    6 ASP cc_start: 0.8059 (t0) cc_final: 0.7558 (m-30)
REVERT: B   72 TRP cc_start: 0.8310 (m100) cc_final: 0.7960 (m100)
REVERT: B   81 GLN cc_start: 0.8424 (mt0) cc_final: 0.7579 (mt0)
REVERT: B   84 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8158 (mp10)
REVERT: B  140 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7948 (mt-10)
REVERT: B  163 ASP cc_start: 0.8208 (m-30) cc_final: 0.7355 (m-30)
REVERT: B  457 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8029 (mtm)
REVERT: C   72 TRP cc_start: 0.8320 (m100) cc_final: 0.8013 (m100)
REVERT: C  140 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8006 (mt-10)
REVERT: C  460 SER cc_start: 0.8976 (m) cc_final: 0.8692 (t)
REVERT: E    6 ASP cc_start: 0.8093 (t0) cc_final: 0.7608 (m-30)
REVERT: E   72 TRP cc_start: 0.8315 (m100) cc_final: 0.7953 (m100)
REVERT: E  140 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7948 (mt-10)
REVERT: E  457 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8021 (mtm)
REVERT: F    6 ASP cc_start: 0.8072 (t0) cc_final: 0.7641 (m-30)
REVERT: F   72 TRP cc_start: 0.8339 (m100) cc_final: 0.8033 (m100)
REVERT: F  140 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7978 (mt-10)
REVERT: F  460 SER cc_start: 0.8975 (m) cc_final: 0.8693 (t)
  outliers start: 63
  outliers final: 54
  residues processed: 295
  average time/residue: 0.3300
  time to fit residues: 163.5963
Evaluate side-chains
  301 residues out of total 2502 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 241
  time to evaluate  : 2.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  140 GLU
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  277 ASP
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  457 MET
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  140 GLU
Chi-restraints excluded: chain C residue  158 ILE
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  277 ASP
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  158 ILE
Chi-restraints excluded: chain D residue  239 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  272 THR
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain E residue   97 THR
Chi-restraints excluded: chain E residue  140 GLU
Chi-restraints excluded: chain E residue  158 ILE
Chi-restraints excluded: chain E residue  239 THR
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  272 THR
Chi-restraints excluded: chain E residue  277 ASP
Chi-restraints excluded: chain E residue  322 LEU
Chi-restraints excluded: chain E residue  413 VAL
Chi-restraints excluded: chain E residue  457 MET
Chi-restraints excluded: chain F residue   90 LYS
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain F residue  158 ILE
Chi-restraints excluded: chain F residue  248 VAL
Chi-restraints excluded: chain F residue  272 THR
Chi-restraints excluded: chain F residue  277 ASP
Chi-restraints excluded: chain F residue  322 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 294
   random chunks:
   chunk 185 optimal weight:    0.9990
   chunk 248 optimal weight:    5.9990
   chunk 71 optimal weight:    9.9990
   chunk 215 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 64 optimal weight:    7.9990
   chunk 233 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 239 optimal weight:    0.9980
   chunk 29 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 297 GLN
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 ASN
** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 254 ASN
** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 254 ASN
** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.112102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.086816 restraints weight = 44859.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 2.27
r_work: 0.3039 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.4469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  24612  Z= 0.187
  Angle     :  0.565   9.324  33384  Z= 0.280
  Chirality :  0.044   0.177   3618
  Planarity :  0.004   0.040   4242
  Dihedral  : 10.578 146.415   4080
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.19 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 (0.16), residues: 2970
  helix:  1.81 (0.14), residues: 1386
  sheet: -0.80 (0.26), residues: 390
  loop :  0.01 (0.20), residues: 1194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP D  72 
 HIS   0.004   0.001   HIS F 450 
 PHE   0.019   0.001   PHE C 490 
 TYR   0.015   0.001   TYR E  78 
 ARG   0.002   0.000   ARG C  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4942.69 seconds
wall clock time: 90 minutes 7.09 seconds (5407.09 seconds total)