Starting phenix.real_space_refine
on Thu Jul 31 11:01:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vyg_21459/07_2025/6vyg_21459.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vyg_21459/07_2025/6vyg_21459.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vyg_21459/07_2025/6vyg_21459.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vyg_21459/07_2025/6vyg_21459.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vyg_21459/07_2025/6vyg_21459.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vyg_21459/07_2025/6vyg_21459.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      92      5.16       5
     C    8632      2.51       5
     N    2320      2.21       5
     O    2572      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13616
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 433, 3404
          Classifications: {'peptide': 433}
          Link IDs: {'PTRANS': 14, 'TRANS': 418}
          Chain breaks: 3
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 6.83, per 1000 atoms: 0.50
  Number of scatterers: 13616
  At special positions: 0
  Unit cell: (117.791, 96.071, 116.121, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      92     16.00
     O    2572      8.00
     N    2320      7.00
     C    8632      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 236 " - pdb=" SG  CYS A 237 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 236 " - pdb=" SG  CYS C 237 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 236 " - pdb=" SG  CYS B 237 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 236 " - pdb=" SG  CYS D 237 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.26
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3240

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 12 sheets defined
      51.3% alpha, 9.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 40
      removed outlier: 3.595A  pdb=" N   HIS A  36 " --> pdb=" O   ARG A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 68
      removed outlier: 3.876A  pdb=" N   GLU A  49 " --> pdb=" O   SER A  45 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ASP A  52 " --> pdb=" O   GLU A  48 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ARG A  67 " --> pdb=" O   GLU A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 165
      removed outlier: 3.809A  pdb=" N   GLY A 165 " --> pdb=" O   LYS A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 226
      removed outlier: 3.530A  pdb=" N   LEU A 221 " --> pdb=" O   ASP A 217 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ASN A 223 " --> pdb=" O   CYS A 219 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ASP A 224 " --> pdb=" O   LYS A 220 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ALA A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 252
      removed outlier: 3.831A  pdb=" N   ALA A 250 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 281
      removed outlier: 4.334A  pdb=" N   LYS A 280 " --> pdb=" O   PRO A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 296
      removed outlier: 3.658A  pdb=" N   PHE A 296 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 312
    Processing helix  chain 'A' and resid 321 through 326
      removed outlier: 3.850A  pdb=" N   ILE A 325 " --> pdb=" O   PHE A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 341
      removed outlier: 3.581A  pdb=" N   LEU A 330 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   GLY A 331 " --> pdb=" O   GLY A 327 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   GLU A 332 " --> pdb=" O   ALA A 328 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL A 339 " --> pdb=" O   ARG A 335 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ASN A 340 " --> pdb=" O   ARG A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 352
      removed outlier: 3.588A  pdb=" N   TRP A 351 " --> pdb=" O   GLU A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 366
      removed outlier: 3.644A  pdb=" N   GLY A 361 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 384
      removed outlier: 3.597A  pdb=" N   LYS A 377 " --> pdb=" O   GLU A 373 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL A 378 " --> pdb=" O   GLU A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 422
      removed outlier: 3.666A  pdb=" N   ARG A 420 " --> pdb=" O   ALA A 416 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ILE A 421 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LYS A 422 " --> pdb=" O   ALA A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 440
    Processing helix  chain 'A' and resid 441 through 456
      removed outlier: 3.568A  pdb=" N   CYS A 445 " --> pdb=" O   ASN A 441 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LYS A 446 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG A 447 " --> pdb=" O   TRP A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 461
      No H-bonds generated for 'chain 'A' and resid 459 through 461'
    Processing helix  chain 'A' and resid 471 through 479
      removed outlier: 4.016A  pdb=" N   GLY A 475 " --> pdb=" O   GLY A 471 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA A 477 " --> pdb=" O   GLY A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 484
      removed outlier: 3.676A  pdb=" N   VAL A 483 " --> pdb=" O   THR A 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 40
      removed outlier: 3.595A  pdb=" N   HIS B  36 " --> pdb=" O   ARG B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 68
      removed outlier: 3.877A  pdb=" N   GLU B  49 " --> pdb=" O   SER B  45 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ASP B  52 " --> pdb=" O   GLU B  48 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 165
      removed outlier: 3.808A  pdb=" N   GLY B 165 " --> pdb=" O   LYS B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 226
      removed outlier: 3.529A  pdb=" N   LEU B 221 " --> pdb=" O   ASP B 217 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ASN B 223 " --> pdb=" O   CYS B 219 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ASP B 224 " --> pdb=" O   LYS B 220 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ALA B 225 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 252
      removed outlier: 3.832A  pdb=" N   ALA B 250 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLN B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 281
      removed outlier: 4.335A  pdb=" N   LYS B 280 " --> pdb=" O   PRO B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 296
      removed outlier: 3.658A  pdb=" N   PHE B 296 " --> pdb=" O   LEU B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 312
    Processing helix  chain 'B' and resid 321 through 326
      removed outlier: 3.850A  pdb=" N   ILE B 325 " --> pdb=" O   PHE B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 341
      removed outlier: 3.581A  pdb=" N   LEU B 330 " --> pdb=" O   SER B 326 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   GLY B 331 " --> pdb=" O   GLY B 327 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   GLU B 332 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL B 339 " --> pdb=" O   ARG B 335 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ASN B 340 " --> pdb=" O   ARG B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 352
      removed outlier: 3.588A  pdb=" N   TRP B 351 " --> pdb=" O   GLU B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 366
      removed outlier: 3.643A  pdb=" N   GLY B 361 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 384
      removed outlier: 3.596A  pdb=" N   LYS B 377 " --> pdb=" O   GLU B 373 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   VAL B 378 " --> pdb=" O   GLU B 374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 422
      removed outlier: 3.665A  pdb=" N   ARG B 420 " --> pdb=" O   ALA B 416 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ILE B 421 " --> pdb=" O   ILE B 417 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LYS B 422 " --> pdb=" O   ALA B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 440
    Processing helix  chain 'B' and resid 441 through 456
      removed outlier: 3.568A  pdb=" N   CYS B 445 " --> pdb=" O   ASN B 441 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LYS B 446 " --> pdb=" O   ALA B 442 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG B 447 " --> pdb=" O   TRP B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 461
      No H-bonds generated for 'chain 'B' and resid 459 through 461'
    Processing helix  chain 'B' and resid 471 through 479
      removed outlier: 4.016A  pdb=" N   GLY B 475 " --> pdb=" O   GLY B 471 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA B 477 " --> pdb=" O   GLY B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 484
      removed outlier: 3.675A  pdb=" N   VAL B 483 " --> pdb=" O   THR B 479 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 40
      removed outlier: 3.595A  pdb=" N   HIS C  36 " --> pdb=" O   ARG C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 68
      removed outlier: 3.877A  pdb=" N   GLU C  49 " --> pdb=" O   SER C  45 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ASP C  52 " --> pdb=" O   GLU C  48 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ARG C  67 " --> pdb=" O   GLU C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 148 through 165
      removed outlier: 3.808A  pdb=" N   GLY C 165 " --> pdb=" O   LYS C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 226
      removed outlier: 3.528A  pdb=" N   LEU C 221 " --> pdb=" O   ASP C 217 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ASN C 223 " --> pdb=" O   CYS C 219 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ASP C 224 " --> pdb=" O   LYS C 220 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ALA C 225 " --> pdb=" O   LEU C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 240 through 252
      removed outlier: 3.831A  pdb=" N   ALA C 250 " --> pdb=" O   LEU C 246 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN C 252 " --> pdb=" O   SER C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 281
      removed outlier: 4.335A  pdb=" N   LYS C 280 " --> pdb=" O   PRO C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 292 through 296
      removed outlier: 3.659A  pdb=" N   PHE C 296 " --> pdb=" O   LEU C 293 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 303 through 312
    Processing helix  chain 'C' and resid 321 through 326
      removed outlier: 3.851A  pdb=" N   ILE C 325 " --> pdb=" O   PHE C 321 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 326 through 341
      removed outlier: 3.581A  pdb=" N   LEU C 330 " --> pdb=" O   SER C 326 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   GLY C 331 " --> pdb=" O   GLY C 327 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   GLU C 332 " --> pdb=" O   ALA C 328 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL C 339 " --> pdb=" O   ARG C 335 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ASN C 340 " --> pdb=" O   ARG C 336 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 348 through 352
      removed outlier: 3.589A  pdb=" N   TRP C 351 " --> pdb=" O   GLU C 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 357 through 366
      removed outlier: 3.643A  pdb=" N   GLY C 361 " --> pdb=" O   ASN C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 372 through 384
      removed outlier: 3.596A  pdb=" N   LYS C 377 " --> pdb=" O   GLU C 373 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL C 378 " --> pdb=" O   GLU C 374 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 391 through 422
      removed outlier: 3.665A  pdb=" N   ARG C 420 " --> pdb=" O   ALA C 416 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ILE C 421 " --> pdb=" O   ILE C 417 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LYS C 422 " --> pdb=" O   ALA C 418 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 435 through 440
    Processing helix  chain 'C' and resid 441 through 456
      removed outlier: 3.568A  pdb=" N   CYS C 445 " --> pdb=" O   ASN C 441 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LYS C 446 " --> pdb=" O   ALA C 442 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG C 447 " --> pdb=" O   TRP C 443 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 459 through 461
      No H-bonds generated for 'chain 'C' and resid 459 through 461'
    Processing helix  chain 'C' and resid 471 through 479
      removed outlier: 4.017A  pdb=" N   GLY C 475 " --> pdb=" O   GLY C 471 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA C 477 " --> pdb=" O   GLY C 473 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 479 through 484
      removed outlier: 3.676A  pdb=" N   VAL C 483 " --> pdb=" O   THR C 479 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 40
      removed outlier: 3.596A  pdb=" N   HIS D  36 " --> pdb=" O   ARG D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 43 through 68
      removed outlier: 3.877A  pdb=" N   GLU D  49 " --> pdb=" O   SER D  45 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ASP D  52 " --> pdb=" O   GLU D  48 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ARG D  67 " --> pdb=" O   GLU D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 148 through 165
      removed outlier: 3.808A  pdb=" N   GLY D 165 " --> pdb=" O   LYS D 161 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 217 through 226
      removed outlier: 3.528A  pdb=" N   LEU D 221 " --> pdb=" O   ASP D 217 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ASN D 223 " --> pdb=" O   CYS D 219 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ASP D 224 " --> pdb=" O   LYS D 220 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ALA D 225 " --> pdb=" O   LEU D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 240 through 252
      removed outlier: 3.831A  pdb=" N   ALA D 250 " --> pdb=" O   LEU D 246 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN D 252 " --> pdb=" O   SER D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 277 through 281
      removed outlier: 4.335A  pdb=" N   LYS D 280 " --> pdb=" O   PRO D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 292 through 296
      removed outlier: 3.659A  pdb=" N   PHE D 296 " --> pdb=" O   LEU D 293 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 312
    Processing helix  chain 'D' and resid 321 through 326
      removed outlier: 3.851A  pdb=" N   ILE D 325 " --> pdb=" O   PHE D 321 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 326 through 341
      removed outlier: 3.582A  pdb=" N   LEU D 330 " --> pdb=" O   SER D 326 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   GLY D 331 " --> pdb=" O   GLY D 327 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   GLU D 332 " --> pdb=" O   ALA D 328 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL D 339 " --> pdb=" O   ARG D 335 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ASN D 340 " --> pdb=" O   ARG D 336 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 348 through 352
      removed outlier: 3.588A  pdb=" N   TRP D 351 " --> pdb=" O   GLU D 348 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 357 through 366
      removed outlier: 3.643A  pdb=" N   GLY D 361 " --> pdb=" O   ASN D 357 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 372 through 384
      removed outlier: 3.595A  pdb=" N   LYS D 377 " --> pdb=" O   GLU D 373 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL D 378 " --> pdb=" O   GLU D 374 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 391 through 422
      removed outlier: 3.666A  pdb=" N   ARG D 420 " --> pdb=" O   ALA D 416 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ILE D 421 " --> pdb=" O   ILE D 417 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LYS D 422 " --> pdb=" O   ALA D 418 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 435 through 440
    Processing helix  chain 'D' and resid 441 through 456
      removed outlier: 3.567A  pdb=" N   CYS D 445 " --> pdb=" O   ASN D 441 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LYS D 446 " --> pdb=" O   ALA D 442 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG D 447 " --> pdb=" O   TRP D 443 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 459 through 461
      No H-bonds generated for 'chain 'D' and resid 459 through 461'
    Processing helix  chain 'D' and resid 471 through 479
      removed outlier: 4.016A  pdb=" N   GLY D 475 " --> pdb=" O   GLY D 471 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA D 477 " --> pdb=" O   GLY D 473 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 479 through 484
      removed outlier: 3.676A  pdb=" N   VAL D 483 " --> pdb=" O   THR D 479 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84
      removed outlier: 3.657A  pdb=" N   SER A  84 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   ILE A 288 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLY A 272 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   TYR A 261 " --> pdb=" O   TYR A 275 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   SER A 430 " --> pdb=" O   CYS A 260 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ILE A 262 " --> pdb=" O   SER A 430 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   PHE A 429 " --> pdb=" O   ILE A 464 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   ILE A 466 " --> pdb=" O   PHE A 429 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   CYS A 431 " --> pdb=" O   ILE A 466 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 123
      removed outlier: 9.105A  pdb=" N   GLY A 179 " --> pdb=" O   THR A  97 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   TYR A  99 " --> pdb=" O   GLY A 179 " (cutoff:3.500A)
      removed outlier: 8.811A  pdb=" N   THR A 181 " --> pdb=" O   TYR A  99 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE A 101 " --> pdb=" O   THR A 181 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   PHE A 180 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 187
    Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 84
      removed outlier: 3.657A  pdb=" N   SER B  84 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   ILE B 288 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLY B 272 " --> pdb=" O   ILE B 291 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   TYR B 261 " --> pdb=" O   TYR B 275 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   SER B 430 " --> pdb=" O   CYS B 260 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ILE B 262 " --> pdb=" O   SER B 430 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   PHE B 429 " --> pdb=" O   ILE B 464 " (cutoff:3.500A)
      removed outlier: 8.127A  pdb=" N   ILE B 466 " --> pdb=" O   PHE B 429 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   CYS B 431 " --> pdb=" O   ILE B 466 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 121 through 123
      removed outlier: 9.105A  pdb=" N   GLY B 179 " --> pdb=" O   THR B  97 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   TYR B  99 " --> pdb=" O   GLY B 179 " (cutoff:3.500A)
      removed outlier: 8.811A  pdb=" N   THR B 181 " --> pdb=" O   TYR B  99 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ILE B 101 " --> pdb=" O   THR B 181 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   PHE B 180 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 186 through 187
    Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 84
      removed outlier: 3.658A  pdb=" N   SER C  84 " --> pdb=" O   ILE C 288 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   ILE C 288 " --> pdb=" O   SER C  84 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLY C 272 " --> pdb=" O   ILE C 291 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   TYR C 261 " --> pdb=" O   TYR C 275 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   SER C 430 " --> pdb=" O   CYS C 260 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ILE C 262 " --> pdb=" O   SER C 430 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   PHE C 429 " --> pdb=" O   ILE C 464 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   ILE C 466 " --> pdb=" O   PHE C 429 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   CYS C 431 " --> pdb=" O   ILE C 466 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123
      removed outlier: 9.105A  pdb=" N   GLY C 179 " --> pdb=" O   THR C  97 " (cutoff:3.500A)
      removed outlier: 7.151A  pdb=" N   TYR C  99 " --> pdb=" O   GLY C 179 " (cutoff:3.500A)
      removed outlier: 8.812A  pdb=" N   THR C 181 " --> pdb=" O   TYR C  99 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ILE C 101 " --> pdb=" O   THR C 181 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   PHE C 180 " --> pdb=" O   VAL C 239 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 186 through 187
    Processing sheet with id=AB1, first strand: chain 'D' and resid 82 through 84
      removed outlier: 3.657A  pdb=" N   SER D  84 " --> pdb=" O   ILE D 288 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   ILE D 288 " --> pdb=" O   SER D  84 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLY D 272 " --> pdb=" O   ILE D 291 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   TYR D 261 " --> pdb=" O   TYR D 275 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   SER D 430 " --> pdb=" O   CYS D 260 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE D 262 " --> pdb=" O   SER D 430 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   PHE D 429 " --> pdb=" O   ILE D 464 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   ILE D 466 " --> pdb=" O   PHE D 429 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   CYS D 431 " --> pdb=" O   ILE D 466 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 121 through 123
      removed outlier: 9.105A  pdb=" N   GLY D 179 " --> pdb=" O   THR D  97 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   TYR D  99 " --> pdb=" O   GLY D 179 " (cutoff:3.500A)
      removed outlier: 8.812A  pdb=" N   THR D 181 " --> pdb=" O   TYR D  99 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE D 101 " --> pdb=" O   THR D 181 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   PHE D 180 " --> pdb=" O   VAL D 239 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 186 through 187

    560 hydrogen bonds defined for protein.
    1620 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.87

  Time building geometry restraints manager: 3.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 4479
        1.35 -     1.48: 3365
        1.48 -     1.61: 5920
        1.61 -     1.74: 0
        1.74 -     1.87: 128
  Bond restraints: 13892
  Sorted by residual:
  bond pdb=" CB  CYS B 237 "
       pdb=" SG  CYS B 237 "
    ideal  model  delta    sigma   weight residual
    1.808  1.866 -0.058 3.30e-02 9.18e+02 3.06e+00
  bond pdb=" CB  CYS C 237 "
       pdb=" SG  CYS C 237 "
    ideal  model  delta    sigma   weight residual
    1.808  1.866 -0.058 3.30e-02 9.18e+02 3.05e+00
  bond pdb=" CB  CYS D 237 "
       pdb=" SG  CYS D 237 "
    ideal  model  delta    sigma   weight residual
    1.808  1.865 -0.057 3.30e-02 9.18e+02 3.01e+00
  bond pdb=" CB  CYS A 237 "
       pdb=" SG  CYS A 237 "
    ideal  model  delta    sigma   weight residual
    1.808  1.865 -0.057 3.30e-02 9.18e+02 3.01e+00
  bond pdb=" CA  ASN B 315 "
       pdb=" C   ASN B 315 "
    ideal  model  delta    sigma   weight residual
    1.531  1.517  0.014 1.12e-02 7.97e+03 1.53e+00
  ... (remaining 13887 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 18561
        2.53 -     5.05: 163
        5.05 -     7.58: 16
        7.58 -    10.10: 4
       10.10 -    12.63: 4
  Bond angle restraints: 18748
  Sorted by residual:
  angle pdb=" N   CYS B 236 "
        pdb=" CA  CYS B 236 "
        pdb=" C   CYS B 236 "
      ideal   model   delta    sigma   weight residual
     111.00  123.63  -12.63 2.80e+00 1.28e-01 2.03e+01
  angle pdb=" N   CYS A 236 "
        pdb=" CA  CYS A 236 "
        pdb=" C   CYS A 236 "
      ideal   model   delta    sigma   weight residual
     111.00  123.62  -12.62 2.80e+00 1.28e-01 2.03e+01
  angle pdb=" N   CYS D 236 "
        pdb=" CA  CYS D 236 "
        pdb=" C   CYS D 236 "
      ideal   model   delta    sigma   weight residual
     111.00  123.62  -12.62 2.80e+00 1.28e-01 2.03e+01
  angle pdb=" N   CYS C 236 "
        pdb=" CA  CYS C 236 "
        pdb=" C   CYS C 236 "
      ideal   model   delta    sigma   weight residual
     111.00  123.58  -12.58 2.80e+00 1.28e-01 2.02e+01
  angle pdb=" C   CYS B 236 "
        pdb=" CA  CYS B 236 "
        pdb=" CB  CYS B 236 "
      ideal   model   delta    sigma   weight residual
     110.10  102.91    7.19 1.90e+00 2.77e-01 1.43e+01
  ... (remaining 18743 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.03: 7302
       16.03 -    32.07: 850
       32.07 -    48.10: 152
       48.10 -    64.14: 28
       64.14 -    80.17: 20
  Dihedral angle restraints: 8352
    sinusoidal: 3332
      harmonic: 5020
  Sorted by residual:
  dihedral pdb=" CA  CYS C 236 "
           pdb=" C   CYS C 236 "
           pdb=" N   CYS C 237 "
           pdb=" CA  CYS C 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  123.07   56.93     0      5.00e+00 4.00e-02 1.30e+02
  dihedral pdb=" CA  CYS D 236 "
           pdb=" C   CYS D 236 "
           pdb=" N   CYS D 237 "
           pdb=" CA  CYS D 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  123.08   56.92     0      5.00e+00 4.00e-02 1.30e+02
  dihedral pdb=" CA  CYS A 236 "
           pdb=" C   CYS A 236 "
           pdb=" N   CYS A 237 "
           pdb=" CA  CYS A 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  123.09   56.91     0      5.00e+00 4.00e-02 1.30e+02
  ... (remaining 8349 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1819
       0.064 -    0.127: 218
       0.127 -    0.191: 15
       0.191 -    0.254: 0
       0.254 -    0.318: 4
  Chirality restraints: 2056
  Sorted by residual:
  chirality pdb=" CA  CYS D 236 "
            pdb=" N   CYS D 236 "
            pdb=" C   CYS D 236 "
            pdb=" CB  CYS D 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.52e+00
  chirality pdb=" CA  CYS A 236 "
            pdb=" N   CYS A 236 "
            pdb=" C   CYS A 236 "
            pdb=" CB  CYS A 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.52e+00
  chirality pdb=" CA  CYS B 236 "
            pdb=" N   CYS B 236 "
            pdb=" C   CYS B 236 "
            pdb=" CB  CYS B 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.50e+00
  ... (remaining 2053 not shown)

  Planarity restraints: 2404
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A  68 "    0.027 5.00e-02 4.00e+02   4.10e-02 2.68e+00
        pdb=" N   PRO A  69 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A  69 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  69 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B  68 "   -0.027 5.00e-02 4.00e+02   4.07e-02 2.65e+00
        pdb=" N   PRO B  69 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B  69 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  69 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C  68 "   -0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO C  69 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO C  69 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C  69 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 2401 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.66: 152
        2.66 -     3.22: 13210
        3.22 -     3.78: 18997
        3.78 -     4.34: 26786
        4.34 -     4.90: 44694
  Nonbonded interactions: 103839
  Sorted by model distance:
  nonbonded pdb=" O   CYS A 445 "
            pdb=" NE2 GLN A 449 "
     model   vdw
     2.094 3.120
  nonbonded pdb=" O   CYS B 445 "
            pdb=" NE2 GLN B 449 "
     model   vdw
     2.094 3.120
  nonbonded pdb=" O   CYS D 445 "
            pdb=" NE2 GLN D 449 "
     model   vdw
     2.095 3.120
  nonbonded pdb=" O   CYS C 445 "
            pdb=" NE2 GLN C 449 "
     model   vdw
     2.095 3.120
  nonbonded pdb=" O   GLU B 359 "
            pdb=" OG  SER B 362 "
     model   vdw
     2.269 3.040
  ... (remaining 103834 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     30.300
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
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      :  0.004   0.058  13896  Z= 0.180
  Angle     :  0.695  12.631  18756  Z= 0.406
  Chirality :  0.044   0.318   2056
  Planarity :  0.003   0.041   2404
  Dihedral  : 14.054  80.169   5100
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  5.96 %
    Favored  : 93.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -3.60 (0.17), residues: 1700
  helix: -1.44 (0.18), residues: 688
  sheet: -1.95 (0.34), residues: 212
  loop : -3.44 (0.17), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 199 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.014   0.002   PHE B  54 
 TYR   0.016   0.001   TYR B 284 
 ARG   0.002   0.000   ARG D 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19505 (  560)
  hydrogen bonds       : angle       6.55002 ( 1620)
  SS BOND              : bond        0.01150 (    4)
  SS BOND              : angle       3.55014 (    8)
  covalent geometry    : bond        0.00383 (13892)
  covalent geometry    : angle       0.69089 (18748)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 219
  time to evaluate  : 1.391 
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: A  164 MET cc_start: 0.5303 (mtp) cc_final: 0.4797 (mmm)
REVERT: A  299 ASP cc_start: 0.7097 (p0) cc_final: 0.6838 (p0)
REVERT: B  164 MET cc_start: 0.5353 (mtp) cc_final: 0.4793 (mmm)
REVERT: B  299 ASP cc_start: 0.7147 (p0) cc_final: 0.6926 (p0)
REVERT: C  112 ARG cc_start: 0.6056 (mtp180) cc_final: 0.5078 (mtp180)
REVERT: C  164 MET cc_start: 0.5376 (mtp) cc_final: 0.4942 (mmm)
REVERT: C  203 PHE cc_start: 0.6420 (m-80) cc_final: 0.6183 (m-80)
REVERT: C  299 ASP cc_start: 0.7131 (p0) cc_final: 0.6865 (p0)
REVERT: D  164 MET cc_start: 0.5106 (mtp) cc_final: 0.4621 (mmm)
REVERT: D  299 ASP cc_start: 0.7038 (p0) cc_final: 0.6809 (p0)
  outliers start: 8
  outliers final: 4
  residues processed: 227
  average time/residue: 0.3283
  time to fit residues: 102.2375
Evaluate side-chains
  142 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 138
  time to evaluate  : 1.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain B residue  236 CYS
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain D residue  236 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 145 optimal weight:    8.9990
   chunk 130 optimal weight:    5.9990
   chunk 72 optimal weight:    8.9990
   chunk 44 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 69 optimal weight:    7.9990
   chunk 134 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 81 optimal weight:    0.4980
   chunk 100 optimal weight:    0.8980
   chunk 156 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 391 GLN
A 426 HIS
B 391 GLN
B 426 HIS
C 391 GLN
C 426 HIS
D 391 GLN
D 426 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.142960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.116876 restraints weight = 21623.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.119072 restraints weight = 13568.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.120511 restraints weight = 10254.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13896  Z= 0.119
  Angle     :  0.568   7.852  18756  Z= 0.302
  Chirality :  0.042   0.128   2056
  Planarity :  0.003   0.037   2404
  Dihedral  :  5.226  36.880   1860
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.88 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  9.55 %
    Favored  : 88.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -2.29 (0.19), residues: 1700
  helix: -0.05 (0.19), residues: 708
  sheet: -1.70 (0.34), residues: 212
  loop : -2.95 (0.18), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 383 
 HIS   0.005   0.001   HIS A  75 
 PHE   0.017   0.001   PHE A 153 
 TYR   0.011   0.001   TYR D 284 
 ARG   0.003   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05092 (  560)
  hydrogen bonds       : angle       5.01894 ( 1620)
  SS BOND              : bond        0.01102 (    4)
  SS BOND              : angle       4.51461 (    8)
  covalent geometry    : bond        0.00254 (13892)
  covalent geometry    : angle       0.56082 (18748)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 196
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.5169 (mtp) cc_final: 0.4623 (mmm)
REVERT: A  246 LEU cc_start: 0.8673 (tp) cc_final: 0.8232 (tt)
REVERT: A  299 ASP cc_start: 0.7186 (p0) cc_final: 0.6898 (p0)
REVERT: A  310 ASP cc_start: 0.8519 (t70) cc_final: 0.8316 (t0)
REVERT: B  164 MET cc_start: 0.5113 (mtp) cc_final: 0.4597 (mmm)
REVERT: B  221 LEU cc_start: 0.7138 (tt) cc_final: 0.6768 (tt)
REVERT: B  246 LEU cc_start: 0.8698 (tp) cc_final: 0.8260 (tt)
REVERT: B  299 ASP cc_start: 0.7196 (p0) cc_final: 0.6900 (p0)
REVERT: B  310 ASP cc_start: 0.8420 (t70) cc_final: 0.8204 (t0)
REVERT: C  112 ARG cc_start: 0.6054 (mtp180) cc_final: 0.5185 (mtp180)
REVERT: C  164 MET cc_start: 0.5346 (mtp) cc_final: 0.4826 (mmm)
REVERT: C  246 LEU cc_start: 0.8656 (tp) cc_final: 0.8234 (tt)
REVERT: C  299 ASP cc_start: 0.7087 (p0) cc_final: 0.6825 (p0)
REVERT: D  112 ARG cc_start: 0.6227 (mtp180) cc_final: 0.5966 (mtm180)
REVERT: D  153 PHE cc_start: 0.4653 (m-10) cc_final: 0.4400 (m-10)
REVERT: D  164 MET cc_start: 0.4674 (mtp) cc_final: 0.4430 (mmm)
REVERT: D  221 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6818 (tt)
REVERT: D  299 ASP cc_start: 0.7101 (p0) cc_final: 0.6824 (p0)
  outliers start: 24
  outliers final: 11
  residues processed: 211
  average time/residue: 0.2445
  time to fit residues: 75.8646
Evaluate side-chains
  173 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 161
  time to evaluate  : 1.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  309 MET
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain C residue  309 MET
Chi-restraints excluded: chain C residue  317 SER
Chi-restraints excluded: chain D residue  109 ARG
Chi-restraints excluded: chain D residue  209 THR
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  317 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 32 optimal weight:    7.9990
   chunk 153 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   chunk 123 optimal weight:    0.9990
   chunk 141 optimal weight:   10.0000
   chunk 69 optimal weight:   10.0000
   chunk 110 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 8 optimal weight:   20.0000
   chunk 104 optimal weight:    8.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  36 HIS
B  36 HIS
C  36 HIS
** C  65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  36 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.139000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.113085 restraints weight = 21971.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.115091 restraints weight = 14293.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.116382 restraints weight = 11080.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087  13896  Z= 0.208
  Angle     :  0.701  16.865  18756  Z= 0.354
  Chirality :  0.049   0.471   2056
  Planarity :  0.004   0.042   2404
  Dihedral  :  5.967  64.360   1856
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.18 %
    Favored  : 89.82 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.21 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -2.05 (0.19), residues: 1700
  helix:  0.15 (0.19), residues: 712
  sheet: -1.25 (0.38), residues: 192
  loop : -2.90 (0.19), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  72 
 HIS   0.004   0.001   HIS D  65 
 PHE   0.015   0.002   PHE C 108 
 TYR   0.030   0.002   TYR C 284 
 ARG   0.004   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05813 (  560)
  hydrogen bonds       : angle       5.06078 ( 1620)
  SS BOND              : bond        0.01946 (    4)
  SS BOND              : angle       5.68609 (    8)
  covalent geometry    : bond        0.00504 (13892)
  covalent geometry    : angle       0.69130 (18748)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 163
  time to evaluate  : 1.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.5334 (mtp) cc_final: 0.4747 (mmm)
REVERT: A  299 ASP cc_start: 0.7335 (p0) cc_final: 0.7011 (p0)
REVERT: B  153 PHE cc_start: 0.4833 (m-10) cc_final: 0.4616 (m-10)
REVERT: B  164 MET cc_start: 0.5365 (mtp) cc_final: 0.4732 (mmm)
REVERT: B  221 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6916 (tt)
REVERT: B  299 ASP cc_start: 0.7415 (p0) cc_final: 0.7079 (p0)
REVERT: C  112 ARG cc_start: 0.6106 (mtp180) cc_final: 0.5183 (mtp180)
REVERT: C  164 MET cc_start: 0.5275 (mtp) cc_final: 0.4723 (mmm)
REVERT: C  299 ASP cc_start: 0.7321 (p0) cc_final: 0.7020 (p0)
REVERT: D  153 PHE cc_start: 0.4476 (m-80) cc_final: 0.4245 (m-10)
REVERT: D  164 MET cc_start: 0.5156 (mtp) cc_final: 0.4575 (mmm)
REVERT: D  221 LEU cc_start: 0.7314 (tt) cc_final: 0.6885 (tt)
REVERT: D  299 ASP cc_start: 0.7317 (p0) cc_final: 0.6979 (p0)
  outliers start: 32
  outliers final: 26
  residues processed: 183
  average time/residue: 0.2341
  time to fit residues: 64.7594
Evaluate side-chains
  182 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  309 MET
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  309 MET
Chi-restraints excluded: chain C residue  317 SER
Chi-restraints excluded: chain C residue  378 VAL
Chi-restraints excluded: chain D residue  121 ILE
Chi-restraints excluded: chain D residue  209 THR
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain D residue  300 LEU
Chi-restraints excluded: chain D residue  317 SER
Chi-restraints excluded: chain D residue  378 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 141 optimal weight:    9.9990
   chunk 106 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   chunk 149 optimal weight:   10.0000
   chunk 168 optimal weight:    3.9990
   chunk 164 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 91 optimal weight:    0.0970
   chunk 160 optimal weight:   10.0000
   overall best weight:    3.1784

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

Flipped N/Q/H residues before XYZ refinement:
** C  65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.139958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.113756 restraints weight = 21968.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.115905 restraints weight = 13540.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.117315 restraints weight = 10236.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  13896  Z= 0.169
  Angle     :  0.634  12.822  18756  Z= 0.325
  Chirality :  0.046   0.281   2056
  Planarity :  0.003   0.043   2404
  Dihedral  :  5.637  51.595   1856
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 14.70 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -1.80 (0.19), residues: 1700
  helix:  0.35 (0.20), residues: 712
  sheet: -1.27 (0.38), residues: 192
  loop : -2.72 (0.19), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  72 
 HIS   0.004   0.001   HIS C  75 
 PHE   0.018   0.001   PHE C 153 
 TYR   0.023   0.001   TYR C 284 
 ARG   0.004   0.000   ARG C 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05196 (  560)
  hydrogen bonds       : angle       4.89230 ( 1620)
  SS BOND              : bond        0.02333 (    4)
  SS BOND              : angle       5.29812 (    8)
  covalent geometry    : bond        0.00398 (13892)
  covalent geometry    : angle       0.62448 (18748)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 167
  time to evaluate  : 1.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.5402 (mtp) cc_final: 0.4765 (mmm)
REVERT: A  299 ASP cc_start: 0.7467 (p0) cc_final: 0.7111 (p0)
REVERT: B  164 MET cc_start: 0.5379 (mtp) cc_final: 0.4738 (mmm)
REVERT: B  221 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6764 (tt)
REVERT: B  299 ASP cc_start: 0.7546 (p0) cc_final: 0.7220 (p0)
REVERT: C  112 ARG cc_start: 0.6073 (mtp180) cc_final: 0.5007 (mtp180)
REVERT: C  164 MET cc_start: 0.5368 (mtp) cc_final: 0.4767 (mmm)
REVERT: C  299 ASP cc_start: 0.7517 (p0) cc_final: 0.7137 (p0)
REVERT: D  164 MET cc_start: 0.5237 (mtp) cc_final: 0.4598 (mmm)
REVERT: D  236 CYS cc_start: 0.4679 (OUTLIER) cc_final: 0.4249 (t)
REVERT: D  299 ASP cc_start: 0.7459 (p0) cc_final: 0.7127 (p0)
  outliers start: 45
  outliers final: 32
  residues processed: 197
  average time/residue: 0.2492
  time to fit residues: 73.0037
Evaluate side-chains
  191 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 157
  time to evaluate  : 1.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  309 MET
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  324 MET
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  309 MET
Chi-restraints excluded: chain C residue  317 SER
Chi-restraints excluded: chain C residue  378 VAL
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain D residue  121 ILE
Chi-restraints excluded: chain D residue  209 THR
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  236 CYS
Chi-restraints excluded: chain D residue  300 LEU
Chi-restraints excluded: chain D residue  309 MET
Chi-restraints excluded: chain D residue  317 SER
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain D residue  378 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 170 optimal weight:    8.9990
   chunk 108 optimal weight:    6.9990
   chunk 128 optimal weight:    9.9990
   chunk 53 optimal weight:    8.9990
   chunk 122 optimal weight:    3.9990
   chunk 159 optimal weight:    9.9990
   chunk 100 optimal weight:    0.0770
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    0.7980
   chunk 164 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   overall best weight:    3.3744

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

Flipped N/Q/H residues before XYZ refinement:
** C  65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.139501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.112799 restraints weight = 21927.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.115188 restraints weight = 12913.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.116735 restraints weight = 9470.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.100  13896  Z= 0.183
  Angle     :  0.712  22.475  18756  Z= 0.354
  Chirality :  0.051   0.641   2056
  Planarity :  0.003   0.043   2404
  Dihedral  :  5.854  63.424   1856
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.99 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -1.76 (0.19), residues: 1700
  helix:  0.38 (0.20), residues: 712
  sheet: -1.35 (0.37), residues: 192
  loop : -2.66 (0.19), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  72 
 HIS   0.004   0.001   HIS C  75 
 PHE   0.015   0.001   PHE C 108 
 TYR   0.025   0.001   TYR C 284 
 ARG   0.007   0.000   ARG D 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05266 (  560)
  hydrogen bonds       : angle       4.91467 ( 1620)
  SS BOND              : bond        0.02264 (    4)
  SS BOND              : angle       6.68923 (    8)
  covalent geometry    : bond        0.00449 (13892)
  covalent geometry    : angle       0.69902 (18748)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 159
  time to evaluate  : 2.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.5379 (mtp) cc_final: 0.4721 (mmm)
REVERT: B  164 MET cc_start: 0.5367 (mtp) cc_final: 0.4699 (mmm)
REVERT: B  221 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6927 (tt)
REVERT: C  164 MET cc_start: 0.5378 (mtp) cc_final: 0.4770 (mmm)
REVERT: D  164 MET cc_start: 0.5232 (mtp) cc_final: 0.4621 (mmm)
REVERT: D  221 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7031 (tt)
REVERT: D  236 CYS cc_start: 0.4603 (OUTLIER) cc_final: 0.4206 (t)
  outliers start: 39
  outliers final: 31
  residues processed: 184
  average time/residue: 0.3183
  time to fit residues: 88.1632
Evaluate side-chains
  188 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 154
  time to evaluate  : 1.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  309 MET
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  309 MET
Chi-restraints excluded: chain C residue  317 SER
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  378 VAL
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain D residue  121 ILE
Chi-restraints excluded: chain D residue  209 THR
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  236 CYS
Chi-restraints excluded: chain D residue  300 LEU
Chi-restraints excluded: chain D residue  309 MET
Chi-restraints excluded: chain D residue  317 SER
Chi-restraints excluded: chain D residue  378 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 103 optimal weight:    8.9990
   chunk 141 optimal weight:   20.0000
   chunk 167 optimal weight:    9.9990
   chunk 36 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 164 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
C  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.141376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.115274 restraints weight = 22006.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.117492 restraints weight = 13555.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.118930 restraints weight = 10223.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080  13896  Z= 0.136
  Angle     :  0.614  14.718  18756  Z= 0.311
  Chirality :  0.045   0.396   2056
  Planarity :  0.003   0.040   2404
  Dihedral  :  5.609  58.997   1856
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 16.53 %
    Favored  : 80.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.20), residues: 1700
  helix:  0.59 (0.20), residues: 712
  sheet: -1.31 (0.38), residues: 192
  loop : -2.54 (0.19), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 443 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.014   0.001   PHE C 108 
 TYR   0.016   0.001   TYR C 284 
 ARG   0.008   0.000   ARG C 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04590 (  560)
  hydrogen bonds       : angle       4.72833 ( 1620)
  SS BOND              : bond        0.02242 (    4)
  SS BOND              : angle       4.22062 (    8)
  covalent geometry    : bond        0.00325 (13892)
  covalent geometry    : angle       0.60792 (18748)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 173
  time to evaluate  : 1.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.5294 (mtp) cc_final: 0.4638 (mmm)
REVERT: A  299 ASP cc_start: 0.7432 (p0) cc_final: 0.7097 (p0)
REVERT: A  449 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7412 (mp-120)
REVERT: B  164 MET cc_start: 0.5317 (mtp) cc_final: 0.4660 (mmm)
REVERT: B  221 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7089 (tt)
REVERT: B  449 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7401 (mp-120)
REVERT: C  112 ARG cc_start: 0.5947 (mtp180) cc_final: 0.4928 (mtp180)
REVERT: C  164 MET cc_start: 0.5307 (mtp) cc_final: 0.4762 (mmm)
REVERT: C  299 ASP cc_start: 0.7397 (p0) cc_final: 0.7087 (p0)
REVERT: C  449 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7378 (mp-120)
REVERT: D  164 MET cc_start: 0.5008 (mtp) cc_final: 0.4531 (mmm)
REVERT: D  221 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7080 (tt)
REVERT: D  236 CYS cc_start: 0.4657 (OUTLIER) cc_final: 0.4278 (t)
REVERT: D  299 ASP cc_start: 0.7394 (p0) cc_final: 0.7091 (p0)
REVERT: D  449 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7389 (mp-120)
  outliers start: 51
  outliers final: 32
  residues processed: 208
  average time/residue: 0.3331
  time to fit residues: 101.2785
Evaluate side-chains
  197 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 158
  time to evaluate  : 2.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  273 CYS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  449 GLN
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  449 GLN
Chi-restraints excluded: chain C residue  109 ARG
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  273 CYS
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  317 SER
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  449 GLN
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue  121 ILE
Chi-restraints excluded: chain D residue  209 THR
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  236 CYS
Chi-restraints excluded: chain D residue  273 CYS
Chi-restraints excluded: chain D residue  300 LEU
Chi-restraints excluded: chain D residue  317 SER
Chi-restraints excluded: chain D residue  324 MET
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain D residue  449 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 115 optimal weight:    9.9990
   chunk 158 optimal weight:    3.9990
   chunk 125 optimal weight:    3.9990
   chunk 102 optimal weight:   30.0000
   chunk 154 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 141 optimal weight:   20.0000
   overall best weight:    2.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.140829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.114643 restraints weight = 21902.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.116869 restraints weight = 13701.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.118289 restraints weight = 10327.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.126  13896  Z= 0.164
  Angle     :  0.726  25.320  18756  Z= 0.355
  Chirality :  0.051   0.738   2056
  Planarity :  0.003   0.039   2404
  Dihedral  :  5.705  64.556   1856
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 16.87 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -1.49 (0.20), residues: 1700
  helix:  0.65 (0.20), residues: 712
  sheet: -1.32 (0.38), residues: 192
  loop : -2.52 (0.19), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 443 
 HIS   0.004   0.001   HIS D  75 
 PHE   0.014   0.001   PHE C 108 
 TYR   0.020   0.001   TYR C 284 
 ARG   0.008   0.000   ARG A 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04731 (  560)
  hydrogen bonds       : angle       4.74661 ( 1620)
  SS BOND              : bond        0.02496 (    4)
  SS BOND              : angle       8.96182 (    8)
  covalent geometry    : bond        0.00416 (13892)
  covalent geometry    : angle       0.70242 (18748)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 167
  time to evaluate  : 2.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.5336 (mtp) cc_final: 0.4671 (mmm)
REVERT: A  299 ASP cc_start: 0.7546 (p0) cc_final: 0.7212 (p0)
REVERT: A  449 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7402 (mp-120)
REVERT: B  164 MET cc_start: 0.5163 (mtp) cc_final: 0.4685 (mmm)
REVERT: B  221 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6920 (tt)
REVERT: B  449 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7383 (mp-120)
REVERT: C  164 MET cc_start: 0.5359 (mtp) cc_final: 0.4804 (mmm)
REVERT: C  299 ASP cc_start: 0.7528 (p0) cc_final: 0.7202 (p0)
REVERT: C  449 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7372 (mp-120)
REVERT: D  164 MET cc_start: 0.5022 (mtp) cc_final: 0.4558 (mmm)
REVERT: D  221 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7042 (tt)
REVERT: D  236 CYS cc_start: 0.4571 (OUTLIER) cc_final: 0.4202 (t)
REVERT: D  299 ASP cc_start: 0.7515 (p0) cc_final: 0.7201 (p0)
REVERT: D  449 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7361 (mp-120)
  outliers start: 52
  outliers final: 38
  residues processed: 204
  average time/residue: 0.2911
  time to fit residues: 87.2756
Evaluate side-chains
  207 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 162
  time to evaluate  : 4.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  273 CYS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  449 GLN
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain B residue  449 GLN
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue  109 ARG
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  273 CYS
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  317 SER
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  378 VAL
Chi-restraints excluded: chain C residue  449 GLN
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue  121 ILE
Chi-restraints excluded: chain D residue  209 THR
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  236 CYS
Chi-restraints excluded: chain D residue  273 CYS
Chi-restraints excluded: chain D residue  300 LEU
Chi-restraints excluded: chain D residue  317 SER
Chi-restraints excluded: chain D residue  324 MET
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain D residue  378 VAL
Chi-restraints excluded: chain D residue  449 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 100 optimal weight:    0.3980
   chunk 54 optimal weight:    6.9990
   chunk 109 optimal weight:    9.9990
   chunk 87 optimal weight:    5.9990
   chunk 161 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 125 optimal weight:    5.9990
   chunk 120 optimal weight:    5.9990
   chunk 126 optimal weight:    0.9990
   chunk 43 optimal weight:   10.0000
   overall best weight:    2.0788

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

Flipped N/Q/H residues before XYZ refinement:
B  70 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.141903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.116156 restraints weight = 22010.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.118226 restraints weight = 14123.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.119509 restraints weight = 10880.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.107  13896  Z= 0.139
  Angle     :  0.656  20.769  18756  Z= 0.325
  Chirality :  0.048   0.596   2056
  Planarity :  0.003   0.038   2404
  Dihedral  :  5.587  63.670   1856
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 17.89 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -1.36 (0.20), residues: 1700
  helix:  0.75 (0.20), residues: 712
  sheet: -1.27 (0.38), residues: 192
  loop : -2.45 (0.19), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 443 
 HIS   0.004   0.001   HIS C  75 
 PHE   0.016   0.001   PHE C 153 
 TYR   0.016   0.001   TYR C 284 
 ARG   0.008   0.000   ARG C 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04396 (  560)
  hydrogen bonds       : angle       4.65711 ( 1620)
  SS BOND              : bond        0.02343 (    4)
  SS BOND              : angle       6.50130 (    8)
  covalent geometry    : bond        0.00344 (13892)
  covalent geometry    : angle       0.64239 (18748)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 172
  time to evaluate  : 3.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.5020 (mtp) cc_final: 0.4573 (mmm)
REVERT: A  299 ASP cc_start: 0.7316 (p0) cc_final: 0.7018 (p0)
REVERT: A  449 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7358 (mp-120)
REVERT: B  164 MET cc_start: 0.5063 (mtp) cc_final: 0.4582 (mmm)
REVERT: B  221 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7215 (tt)
REVERT: B  299 ASP cc_start: 0.7344 (p0) cc_final: 0.7043 (p0)
REVERT: B  449 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7354 (mp-120)
REVERT: C  164 MET cc_start: 0.5205 (mtp) cc_final: 0.4756 (mmm)
REVERT: C  299 ASP cc_start: 0.7294 (p0) cc_final: 0.7004 (p0)
REVERT: C  449 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7355 (mp-120)
REVERT: D  164 MET cc_start: 0.4918 (mtp) cc_final: 0.4557 (mmm)
REVERT: D  221 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7150 (tt)
REVERT: D  236 CYS cc_start: 0.4640 (OUTLIER) cc_final: 0.4225 (t)
REVERT: D  299 ASP cc_start: 0.7290 (p0) cc_final: 0.7008 (p0)
REVERT: D  449 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7363 (mp-120)
  outliers start: 47
  outliers final: 34
  residues processed: 207
  average time/residue: 0.3678
  time to fit residues: 114.6775
Evaluate side-chains
  203 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 162
  time to evaluate  : 2.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  273 CYS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  449 GLN
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  449 GLN
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  273 CYS
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  317 SER
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  449 GLN
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain D residue  121 ILE
Chi-restraints excluded: chain D residue  209 THR
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  236 CYS
Chi-restraints excluded: chain D residue  273 CYS
Chi-restraints excluded: chain D residue  300 LEU
Chi-restraints excluded: chain D residue  317 SER
Chi-restraints excluded: chain D residue  324 MET
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain D residue  378 VAL
Chi-restraints excluded: chain D residue  449 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 145 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 106 optimal weight:   10.0000
   chunk 115 optimal weight:    9.9990
   chunk 108 optimal weight:    3.9990
   chunk 137 optimal weight:   20.0000
   chunk 12 optimal weight:    8.9990
   chunk 136 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9980
   chunk 60 optimal weight:   10.0000
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
C  70 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.138893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.112322 restraints weight = 22027.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.114486 restraints weight = 13747.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.115761 restraints weight = 10462.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.091  13896  Z= 0.207
  Angle     :  0.698  18.888  18756  Z= 0.353
  Chirality :  0.049   0.522   2056
  Planarity :  0.004   0.040   2404
  Dihedral  :  5.775  61.060   1856
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.18 %
    Favored  : 89.82 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.16 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -1.57 (0.20), residues: 1700
  helix:  0.55 (0.20), residues: 712
  sheet: -1.35 (0.38), residues: 192
  loop : -2.55 (0.19), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 199 
 HIS   0.006   0.001   HIS C  65 
 PHE   0.015   0.002   PHE A 153 
 TYR   0.032   0.002   TYR C 284 
 ARG   0.007   0.001   ARG C 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05435 (  560)
  hydrogen bonds       : angle       4.88835 ( 1620)
  SS BOND              : bond        0.02470 (    4)
  SS BOND              : angle       5.46153 (    8)
  covalent geometry    : bond        0.00503 (13892)
  covalent geometry    : angle       0.68856 (18748)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 156
  time to evaluate  : 1.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.5341 (mtp) cc_final: 0.4717 (mmm)
REVERT: A  449 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7440 (mp-120)
REVERT: B  164 MET cc_start: 0.5333 (mtp) cc_final: 0.4696 (mmm)
REVERT: B  449 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7457 (mp-120)
REVERT: C  164 MET cc_start: 0.5354 (mtp) cc_final: 0.4775 (mmm)
REVERT: C  449 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7419 (mp-120)
REVERT: D  164 MET cc_start: 0.5135 (mtp) cc_final: 0.4586 (mmm)
REVERT: D  236 CYS cc_start: 0.4382 (OUTLIER) cc_final: 0.4038 (t)
REVERT: D  449 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7434 (mp-120)
  outliers start: 45
  outliers final: 36
  residues processed: 191
  average time/residue: 0.2528
  time to fit residues: 70.9364
Evaluate side-chains
  195 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 154
  time to evaluate  : 1.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  273 CYS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  449 GLN
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain B residue  449 GLN
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  273 CYS
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  317 SER
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  378 VAL
Chi-restraints excluded: chain C residue  449 GLN
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue  121 ILE
Chi-restraints excluded: chain D residue  209 THR
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain D residue  236 CYS
Chi-restraints excluded: chain D residue  273 CYS
Chi-restraints excluded: chain D residue  300 LEU
Chi-restraints excluded: chain D residue  317 SER
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain D residue  378 VAL
Chi-restraints excluded: chain D residue  449 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 76 optimal weight:    6.9990
   chunk 143 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9980
   chunk 119 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
D  70 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.143374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.117221 restraints weight = 21780.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.119526 restraints weight = 13550.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.120957 restraints weight = 10201.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081  13896  Z= 0.116
  Angle     :  0.619  17.459  18756  Z= 0.310
  Chirality :  0.046   0.471   2056
  Planarity :  0.003   0.038   2404
  Dihedral  :  5.515  61.513   1856
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 18.90 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -1.25 (0.20), residues: 1700
  helix:  0.86 (0.20), residues: 712
  sheet: -1.28 (0.38), residues: 192
  loop : -2.38 (0.20), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 443 
 HIS   0.005   0.001   HIS A  75 
 PHE   0.016   0.001   PHE C 153 
 TYR   0.007   0.001   TYR B 274 
 ARG   0.008   0.001   ARG C 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04051 (  560)
  hydrogen bonds       : angle       4.59477 ( 1620)
  SS BOND              : bond        0.02234 (    4)
  SS BOND              : angle       4.67682 (    8)
  covalent geometry    : bond        0.00271 (13892)
  covalent geometry    : angle       0.61193 (18748)

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

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

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3400 Ramachandran restraints generated.
    1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 173
  time to evaluate  : 2.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.5066 (mtp) cc_final: 0.4570 (mmm)
REVERT: A  299 ASP cc_start: 0.7401 (p0) cc_final: 0.7082 (p0)
REVERT: A  449 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7314 (mp-120)
REVERT: B  164 MET cc_start: 0.5210 (mtp) cc_final: 0.4685 (mmm)
REVERT: B  299 ASP cc_start: 0.7432 (p0) cc_final: 0.7108 (p0)
REVERT: B  449 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7337 (mp-120)
REVERT: C  164 MET cc_start: 0.5269 (mtp) cc_final: 0.4787 (mmm)
REVERT: C  299 ASP cc_start: 0.7419 (p0) cc_final: 0.7067 (p0)
REVERT: D  164 MET cc_start: 0.5078 (mtp) cc_final: 0.4691 (mmm)
REVERT: D  236 CYS cc_start: 0.4226 (OUTLIER) cc_final: 0.3833 (t)
REVERT: D  299 ASP cc_start: 0.7422 (p0) cc_final: 0.7070 (p0)
REVERT: D  449 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7317 (mp-120)
  outliers start: 37
  outliers final: 29
  residues processed: 200
  average time/residue: 0.3757
  time to fit residues: 109.9841
Evaluate side-chains
  199 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 166
  time to evaluate  : 2.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  449 GLN
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  449 GLN
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  317 SER
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  378 VAL
Chi-restraints excluded: chain C residue  449 GLN
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain D residue  121 ILE
Chi-restraints excluded: chain D residue  209 THR
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain D residue  236 CYS
Chi-restraints excluded: chain D residue  300 LEU
Chi-restraints excluded: chain D residue  317 SER
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain D residue  378 VAL
Chi-restraints excluded: chain D residue  449 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 83 optimal weight:    0.0020
   chunk 116 optimal weight:    9.9990
   chunk 146 optimal weight:   10.0000
   chunk 91 optimal weight:    0.0270
   chunk 27 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 126 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    2.4052

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.141953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.114983 restraints weight = 22121.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.117433 restraints weight = 13389.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.118945 restraints weight = 9948.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079  13896  Z= 0.144
  Angle     :  0.640  16.943  18756  Z= 0.319
  Chirality :  0.046   0.460   2056
  Planarity :  0.003   0.038   2404
  Dihedral  :  5.520  60.123   1856
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 18.70 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -1.27 (0.20), residues: 1700
  helix:  0.83 (0.20), residues: 712
  sheet: -1.27 (0.39), residues: 192
  loop : -2.38 (0.20), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 199 
 HIS   0.010   0.001   HIS A  65 
 PHE   0.017   0.001   PHE D 153 
 TYR   0.021   0.001   TYR C 284 
 ARG   0.007   0.000   ARG C 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04458 (  560)
  hydrogen bonds       : angle       4.65443 ( 1620)
  SS BOND              : bond        0.02172 (    4)
  SS BOND              : angle       4.60106 (    8)
  covalent geometry    : bond        0.00345 (13892)
  covalent geometry    : angle       0.63292 (18748)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 4359.28 seconds
wall clock time: 80 minutes 18.24 seconds (4818.24 seconds total)